Journal articles: 'Phylogenetic footprints'

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Witt, Ulrich, and Georg Schwesinger. "Phylogenetic footprints in organizational behavior." Journal of Economic Behavior & Organization 90 (June 2013): S33—S44. http://dx.doi.org/10.1016/j.jebo.2012.12.011.

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Matthews, Philippa C., Alasdair J. Leslie, Aris Katzourakis, Hayley Crawford, Rebecca Payne, Andrew Prendergast, Karen Power, et al. "HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering." Journal of Virology 83, no. 9 (February 25, 2009): 4605–15. http://dx.doi.org/10.1128/jvi.02017-08.

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ABSTRACT The selection of escape mutations has a major impact on immune control of infections with viruses such as human immunodeficiency virus (HIV). Viral evasion of CD8+ T-cell responses leaves predictable combinations of escape mutations, termed HLA “footprints.” The most clearly defined footprints are those associated with HLA alleles that are linked with successful control of HIV, such as HLA-B*57. Here we investigated the extent to which HLA footprint sites in HIV type 1 (HIV-1) are associated with viral evolution among and within clades. First, we examined the extent to which amino acid differences between HIV-1 clades share identity with sites of HLA-mediated selection pressure and observed a strong association, in particular with respect to sites of HLA-B selection (P < 10−6). Similarly, the sites of amino acid variability within a clade were found to overlap with sites of HLA-selected mutation. Second, we studied the impact of HLA selection on interclade phylogeny. Removing the sites of amino acid variability did not significantly affect clade-specific clustering, reflecting the central role of founder effects in establishing distinct clades. However, HLA footprints may underpin founder strains, and we show that amino acid substitutions between clades alter phylogeny, underlining a potentially substantial role for HLA in driving ongoing viral evolution. Finally, we investigated the impact of HLA selection on within-clade phylogeny and demonstrate that even a single HLA allele footprint can result in significant phylogenetic clustering of sequences. In conclusion, these data highlight the fact that HLA can be a strong selection force for both intra- and interclade HIV evolution at a population level.

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Lautrédou, A. C., D. D. Hinsinger, C. Gallut, C. H. C. Cheng, M. Berkani, C. Ozouf-Costaz, C. Cruaud, G. Lecointre, and A. Dettai. "Phylogenetic footprints of an Antarctic radiation: The Trematominae (Notothenioidei, Teleostei)." Molecular Phylogenetics and Evolution 65, no. 1 (October 2012): 87–101. http://dx.doi.org/10.1016/j.ympev.2012.05.032.

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Schallau, Anna, Irina Kakhovskaya, Anne Tewes, Andreas Czihal, Jens Tiedemann, Michaela Mohr, Ivo Grosse, Renate Manteuffel, and Helmut Bäumlein. "Phylogenetic footprints in fern spore- and seed-specific gene promoters." Plant Journal 53, no. 3 (October 30, 2007): 414–24. http://dx.doi.org/10.1111/j.1365-313x.2007.03354.x.

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Leung, J. Y., F. E. McKenzie, A. M. Uglialoro, P. O. Flores-Villanueva, B. C. Sorkin, E. J. Yunis, D. L. Hartl, and A. E. Goldfeld. "Identification of phylogenetic footprints in primate tumor necrosis factor-alpha promoters." Proceedings of the National Academy of Sciences 97, no. 12 (June 6, 2000): 6614–18. http://dx.doi.org/10.1073/pnas.97.12.6614.

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Sevillya, Gur, and Sagi Snir. "Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification." Molecular Phylogenetics and Evolution 136 (July 2019): 128–37. http://dx.doi.org/10.1016/j.ympev.2019.03.010.

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Prohaska, Sonja J., Claudia Fried, Christoph Flamm, Günter P. Wagner, and Peter F. Stadler. "Surveying phylogenetic footprints in large gene clusters: applications to Hox cluster duplications." Molecular Phylogenetics and Evolution 31, no. 2 (May 2004): 581–604. http://dx.doi.org/10.1016/j.ympev.2003.08.009.

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Shelton, David A., Lauren Stegman, Ross Hardison, Webb Miller, Jeffery H. Bock, Jerry L. Slightom, Morris Goodman, and Deborah L. Gumucio. "Phylogenetic Footprinting of Hypersensitive Site 3 of the β-Globin Locus Control Region." Blood 89, no. 9 (May 1, 1997): 3457–69. http://dx.doi.org/10.1182/blood.v89.9.3457.

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Abstract Hypersensitive site 3 (HS3) of the β-like globin locus control region has been implicated as an important regulator of the β-like globin genes, but the trans factors that bind HS3 have only been partially characterized. Using a five-species alignment (human, galago, rabbit, goat, and mouse) that represents 370 million years of evolution, we have identified 24 phylogenetic footprints in the HS3 core and surrounding regions. Probes corresponding to the human sequence at each footprint have been used in binding studies to identify the nuclear factors that bind within and near these conserved sequence elements. Among the high-affinity interactions observed were several binding sites for proteins with repressor activity, including YY1, CCAAT displacement protein, and G1/G2 complexes (uncharacterized putative repressors) and several binding sites for the stage selector protein. To complement this analysis, orthologous galago sequences were also used to derive probes and the pattern of proteins binding to human and galago probes was compared. Binding interactions differing between these two species could be responsible for the different expression patterns shown by the two γ genes (galago γ is embryonic; human γ is fetal). Alternatively, binding interactions that are conserved in the two species may be important in the regulation of common expression patterns (eg, repression of γ in adult life).

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Kim, Jung-whan, Karen I. Zeller, Yunyue Wang, Anil G. Jegga, Bruce J. Aronow, Kathryn A. O'Donnell, and Chi V. Dang. "Evaluation of Myc E-Box Phylogenetic Footprints in Glycolytic Genes by Chromatin Immunoprecipitation Assays." Molecular and Cellular Biology 24, no. 13 (July 1, 2004): 5923–36. http://dx.doi.org/10.1128/mcb.24.13.5923-5936.2004.

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ABSTRACT Prediction of gene regulatory sequences using phylogenetic footprinting has advanced considerably but lacks experimental validation. Here, we report whether transcription factor binding sites predicted by dot plotting or web-based Trafac analysis could be validated by chromatin immunoprecipitation assays. MYC overexpression enhances glycolysis without hypoxia and hence may contribute to altered tumor metabolism. Because the full spectrum of glycolytic genes directly regulated by Myc is not known, we chose Myc as a model transcription factor to determine whether it binds target glycolytic genes that have conserved canonical Myc binding sites or E boxes (5′-CACGTG-3′). Conserved canonical E boxes in ENO1, HK2, and LDHA occur in 31- to 111-bp islands with high interspecies sequence identity (>65%). Trafac analysis revealed another region in ENO1 that corresponds to a murine region with a noncanonical E box. Myc bound all these conserved regions well in the human P493-6 B lymphocytes. We also determined whether Myc could bind nonconserved canonical E boxes found in the remaining human glycolytic genes. Myc bound PFKM, but it did not significantly bind GPI, PGK1, and PKM2. Binding to BPGM, PGAM2, and PKLR was not detected. Both GAPD and TPI1 do not have conserved E boxes but are induced and bound by Myc through regions with noncanonical E boxes. Our results indicate that Myc binds well to conserved canonical E boxes, but not nonconserved E boxes. However, the binding of Myc to unpredicted genomic regions with noncanonical E boxes reveals a limitation of phylogenetic footprinting. In aggregate, these observations indicate that Myc is an important regulator of glycolytic genes, suggesting that MYC plays a key role in a switch to glycolytic metabolism during cell proliferation or tumorigenesis.

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Oleksyk, Taras K., Michael W. Smith, and Stephen J. O'Brien. "Genome-wide scans for footprints of natural selection." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1537 (January 12, 2010): 185–205. http://dx.doi.org/10.1098/rstb.2009.0219.

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Detecting recent selected ‘genomic footprints’ applies directly to the discovery of disease genes and in the imputation of the formative events that molded modern population genetic structure. The imprints of historic selection/adaptation episodes left in human and animal genomes allow one to interpret modern and ancestral gene origins and modifications. Current approaches to reveal selected regions applied in genome-wide selection scans (GWSSs) fall into eight principal categories: (I) phylogenetic footprinting, (II) detecting increased rates of functional mutations, (III) evaluating divergence versus polymorphism, (IV) detecting extended segments of linkage disequilibrium, (V) evaluating local reduction in genetic variation, (VI) detecting changes in the shape of the frequency distribution (spectrum) of genetic variation, (VII) assessing differentiating between populations ( F ST ), and (VIII) detecting excess or decrease in admixture contribution from one population. Here, we review and compare these approaches using available human genome-wide datasets to provide independent verification (or not) of regions found by different methods and using different populations. The lessons learned from GWSSs will be applied to identify genome signatures of historic selective pressures on genes and gene regions in other species with emerging genome sequences. This would offer considerable potential for genome annotation in functional, developmental and evolutionary contexts.

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Gumucio, D. L., H. Heilstedt-Williamson, T. A. Gray, S. A. Tarlé, D. A. Shelton, D. A. Tagle, J. L. Slightom, M. Goodman, and F. S. Collins. "Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes." Molecular and Cellular Biology 12, no. 11 (November 1992): 4919–29. http://dx.doi.org/10.1128/mcb.12.11.4919.

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Tissue- and developmental stage-specific expression of the human beta-like globin genes is regulated by a combination of ubiquitous and erythroid-restricted trans factors that bind to cis elements near each of the five active genes. Additional interactions of these cis and trans factors with sequences located in the far 5' end of the cluster occur by as yet obscure mechanisms. Because of the complexity of this regulatory puzzle, precise identification of the determinants that control hemoglobin switching has proven difficult. Phylogenetic footprinting is an evolutionary approach to this problem which is based on the supposition that the basic mechanisms of switching are conserved throughout mammalian phylogeny. Alignment of the 5' flanking regions of the gamma genes of several species allows the identification of footprints of 100% conserved sequence. We have now tested oligomers spanning 13 such phylogenetic footprints and find that 12 are bound by nuclear proteins. One conserved element located at -1086 from the gamma genes exhibits repressor activity in transient transfection studies. The protein that binds this element, CSBP-1 (conserved sequence-binding protein 1), also binds at three sites within a silencer element upstream from the epsilon globin gene. Further analysis reveals that the CSBP-1 binding activity is identical to that of a recently cloned zinc finger protein that has been shown to act as a repressor in other systems. The binding of CSPB-1 to silencer sequences in the epsilon and gamma globin genes may be important in the stage-specific silencing of these genes.

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Gumucio, D. L., H. Heilstedt-Williamson, T. A. Gray, S. A. Tarlé, D. A. Shelton, D. A. Tagle, J. L. Slightom, M. Goodman, and F. S. Collins. "Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes." Molecular and Cellular Biology 12, no. 11 (November 1992): 4919–29. http://dx.doi.org/10.1128/mcb.12.11.4919-4929.1992.

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Tissue- and developmental stage-specific expression of the human beta-like globin genes is regulated by a combination of ubiquitous and erythroid-restricted trans factors that bind to cis elements near each of the five active genes. Additional interactions of these cis and trans factors with sequences located in the far 5' end of the cluster occur by as yet obscure mechanisms. Because of the complexity of this regulatory puzzle, precise identification of the determinants that control hemoglobin switching has proven difficult. Phylogenetic footprinting is an evolutionary approach to this problem which is based on the supposition that the basic mechanisms of switching are conserved throughout mammalian phylogeny. Alignment of the 5' flanking regions of the gamma genes of several species allows the identification of footprints of 100% conserved sequence. We have now tested oligomers spanning 13 such phylogenetic footprints and find that 12 are bound by nuclear proteins. One conserved element located at -1086 from the gamma genes exhibits repressor activity in transient transfection studies. The protein that binds this element, CSBP-1 (conserved sequence-binding protein 1), also binds at three sites within a silencer element upstream from the epsilon globin gene. Further analysis reveals that the CSBP-1 binding activity is identical to that of a recently cloned zinc finger protein that has been shown to act as a repressor in other systems. The binding of CSPB-1 to silencer sequences in the epsilon and gamma globin genes may be important in the stage-specific silencing of these genes.

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13

Matthews, P. C., A. J. Leslie, A. Katzourakis, H. Crawford, R. Payne, A. Prendergast, K. Power, et al. "HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering." Journal of Virology 85, no. 9 (April 15, 2011): 4635. http://dx.doi.org/10.1128/jvi.00375-11.

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Demirci, Sevgin, Roven Rommel Fuentes, Willem van Dooijeweert, Saulo Aflitos, Elio Schijlen, Thamara Hesselink, Dick de Ridder, Aalt D. J. van Dijk, and Sander Peters. "Chasing breeding footprints through structural variations in Cucumis melo and wild relatives." G3 Genes|Genomes|Genetics 11, no. 1 (December 22, 2020): 1–12. http://dx.doi.org/10.1093/g3journal/jkaa038.

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Abstract Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melonbreeding history, analyzing structural variations ranging from 50 bp up to 100 kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found six mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance, and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives, and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development.

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Shifman, Anton, Noga Ninyo, Uri Gophna, and Sagi Snir. "Phylo SI: a new genome-wide approach for prokaryotic phylogeny." Nucleic Acids Research 42, no. 4 (November 15, 2013): 2391–404. http://dx.doi.org/10.1093/nar/gkt1138.

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Abstract The evolutionary history of all life forms is usually represented as a vertical tree-like process. In prokaryotes, however, the vertical signal is partly obscured by the massive influence of horizontal gene transfer (HGT). The HGT creates widespread discordance between evolutionary histories of different genes as genomes become mosaics of gene histories. Thus, the Tree of Life (TOL) has been questioned as an appropriate representation of the evolution of prokaryotes. Nevertheless a common hypothesis is that prokaryotic evolution is primarily tree-like, and a routine effort is made to place new isolates in their appropriate location in the TOL. Moreover, it appears desirable to exploit non–tree-like evolutionary processes for the task of microbial classification. In this work, we present a novel technique that builds on the straightforward observation that gene order conservation (‘synteny’) decreases in time as a result of gene mobility. This is particularly true in prokaryotes, mainly due to HGT. Using a ‘synteny index’ (SI) that measures the average synteny between a pair of genomes, we developed the phylogenetic reconstruction tool ‘Phylo SI’. Phylo SI offers several attractive properties such as easy bootstrapping, high sensitivity in cases where phylogenetic signal is weak and computational efficiency. Phylo SI was tested both on simulated data and on two bacterial data sets and compared with two well-established phylogenetic methods. Phylo SI is particularly efficient on short evolutionary distances where synteny footprints remain detectable, whereas the nucleotide substitution signal is too weak for reliable sequence-based phylogenetic reconstruction. The method is publicly available at http://research.haifa.ac.il/ssagi/software/PhyloSI.zip.

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Xu, Fuyu, Myoung-Ryoul Park, Ai Kitazumi, Venura Herath, Bijayalaxmi Mohanty, Song Yun, and Benildo G. de los Reyes. "Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints." BMC Genomics 13, no. 1 (2012): 497. http://dx.doi.org/10.1186/1471-2164-13-497.

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Zhang, Shulin, Yaling Cai, Jinggong Guo, Kun Li, Renhai Peng, Fang Liu, Jeremy A. Roberts, Yuchen Miao, and Xuebin Zhang. "Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints." Evolutionary Bioinformatics 15 (January 2019): 117693431988994. http://dx.doi.org/10.1177/1176934319889948.

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Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

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Trovant, Berenice, J. M. (Lobo) Orensanz, Daniel E. Ruzzante, Wolfgang Stotz, and Néstor G. Basso. "Scorched mussels (BIVALVIA: MYTILIDAE: BRACHIDONTINAE) from the temperate coasts of South America: Phylogenetic relationships, trans-Pacific connections and the footprints of Quaternary glaciations." Molecular Phylogenetics and Evolution 82 (January 2015): 60–74. http://dx.doi.org/10.1016/j.ympev.2014.10.002.

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Langham, Richard J., Justine Walsh, Molly Dunn, Cynthia Ko, Stephen A. Goff, and Michael Freeling. "Genomic Duplication, Fractionation and the Origin of Regulatory Novelty." Genetics 166, no. 2 (February 1, 2004): 935–45. http://dx.doi.org/10.1093/genetics/166.2.935.

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Abstract Having diverged 50 MYA, rice remained diploid while the maize lineage became tetraploid and then fractionated by losing genes from one or the other duplicate region. We sequenced and annotated 13 maize genes (counting the duplicate gene as one gene) on one or the other of the pair of homeologous maize regions; 12 genes were present in one cluster in rice. Excellent maize-rice synteny was evident, but only after the fractionated maize regions were condensed onto a finished rice map. Excluding the gene we used to define homeologs, we found zero retention. Once retained, fractionation (loss of functioning DNA sequence) could occur within cis-acting gene space. We chose a retained duplicate basic leucine zipper transcription factor gene because it was well marked with big, exact phylogenetic footprints (CNSs). Detailed alignments of lg2 and retained duplicate lrs1 to their rice ortholog found that fractionation of conserved noncoding sequences (CNSs) was rare, as expected. Of 30 CNSs, 27 were conserved. The 3 unexpected, missing CNSs and a large insertion support subfunctionalization as a reflection of fractionation of cis-acting gene space and the recent evolution of lg2’s novel maize leaf and shoot developmental functions. In general, the principles of fractionation and consolidation work well in making sense of maize gene and genomic sequence data.

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Emera, Deena, Jun Yin, Steven K. Reilly, Jake Gockley, and James P. Noonan. "Origin and evolution of developmental enhancers in the mammalian neocortex." Proceedings of the National Academy of Sciences 113, no. 19 (April 25, 2016): E2617—E2626. http://dx.doi.org/10.1073/pnas.1603718113.

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Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained “proto-enhancers.” Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve.

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VUILLAUMIER, Sandrine, Isabelle DIXMERAS, Habib MESSAÏ, Claudine LAPOUMÉROULIE, Dominique LALLEMAND, Jean GEKAS, F. Farid CHEHAB, Christine PERRET, Jacques ELION, and Erick DENAMUR. "Cross-species characterization of the promoter region of the cystic fibrosis transmembrane conductance regulator gene reveals multiple levels of regulation." Biochemical Journal 327, no. 3 (November 1, 1997): 651–62. http://dx.doi.org/10.1042/bj3270651.

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The cystic fibrosis transmembrane conductance regulator (CFTR) gene is highly conserved within vertebrate species. Its pattern of expression in vivo seems to be tightly regulated both developmentally and in a tissue-specific manner, but shows differences with species. To identify transcriptional regulatory elements in the CFTR promoter region, we have used a combined approach based both on the analysis of the chromatin structure in vivo in rat tissues and on evolutionary clues (i.e. phylogenetic footprinting). In CFTR-expressing tissues, 15 DNase I-hypersensitive sites were identified within a 36 kb region encompassing exon 1. Eleven of them are clustered in a 3.5 kb region that exhibits eleven phylogenetic footprints observed when comparing sequences from eight mammalian species representing four orders (Primates, Artiodactylia, Lagomorpha and Rodentia). Comparison of the two sets of data allows the identification of two types of regulatory elements. Some are conserved between species, such as a non-consensus cAMP response element (CRE) and a PMA-responsive element (TRE) located respectively at positions -0.1 and -1.3 kb relative to ATG. Some are species-specific elements such as a 300 bp purine·pyrimidine (Pu·Py) stretch that is present only in rodents. Analysis of protein/DNA interactions in vitro with rat tissue protein extracts on the conserved elements revealed that the TRE site binds a specific heterodimeric complex composed of Fra-2, Jun D and a protein immunologically related to Jun/CRE-binding protein in the duodenum, whereas the CRE-like site binds ATF-1 ubiquitously. Functional analysis in Caco-2 cells showed that the CRE-like site supports a high basal transcriptional activity but is not able by itself to induce a response to cAMP, whereas the TRE site acts as a weak transactivator stimulated by PMA. Lastly, we found that the rodent-specific Pu·Py stretch confers nuclease S1 hypersensitivity under conditions of acidic pH and supercoiling. This indicates a non-B DNA conformation and thus reinforces the biological significance of non-random Pu·Py strand asymmetry in the regulation of transcription. Thus the tight transcriptional regulation of CFTR expression involves the combination of multiple regulatory elements that act in the chromatin environment in vivo. Some of them are conserved throughout evolution, such as the CRE-like element, which is clearly involved in the basal level of transcription; others are species-specific.

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Dorit, Robert L., and Francisco Jos� Ayala. "ADH evolution and the phylogenetic footprint." Journal of Molecular Evolution 40, no. 6 (June 1995): 658–62. http://dx.doi.org/10.1007/bf00160514.

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Islam, Ariful, Md Abu Sayeed, Md Abul Kalam, Jinnat Ferdous, Md Kaisar Rahman, Josefina Abedin, Shariful Islam, et al. "Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally." Microorganisms 9, no. 8 (August 10, 2021): 1696. http://dx.doi.org/10.3390/microorganisms9081696.

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations—N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.

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Weidman, J. R. "Phylogenetic Footprint Analysis of IGF2 in Extant Mammals." Genome Research 14, no. 9 (September 1, 2004): 1726–32. http://dx.doi.org/10.1101/gr.2774804.

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Blanchette, M. "FootPrinter: a program designed for phylogenetic footprinting." Nucleic Acids Research 31, no. 13 (July 1, 2003): 3840–42. http://dx.doi.org/10.1093/nar/gkg606.

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Lemey, Philippe, Inge Derdelinckx, Andrew Rambaut, Kristel Van Laethem, Stephanie Dumont, Steve Vermeulen, Eric Van Wijngaerden, and Anne-Mieke Vandamme. "Molecular Footprint of Drug-Selective Pressure in a Human Immunodeficiency Virus Transmission Chain." Journal of Virology 79, no. 18 (September 15, 2005): 11981–89. http://dx.doi.org/10.1128/jvi.79.18.11981-11989.2005.

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ABSTRACT Known human immunodeficiency virus (HIV) transmission histories are invaluable models for investigating the evolutionary and transmission dynamics of the virus and to assess the accuracy of phylogenetic reconstructions. Here we have characterized an HIV-1 transmission chain consisting of nine infected patients, almost all of whom were treated with antiviral drugs at later stages of infection. Partial pol and env gp41 regions of the HIV genome were directly sequenced from plasma viral RNA for at least one sample from each patient. Phylogenetic analyses in pol using likelihood methods inferred an evolutionary history not fully compatible with the known transmission history. This could be attributed to parallel evolution of drug resistance mutations resulting in the incorrect clustering of multidrug-resistant virus. On the other hand, a fully compatible phylogenetic tree was reconstructed from the env sequences. We were able to identify and quantify the molecular footprint of drug-selective pressure in pol using maximum likelihood inference under different codon substitution models. An increased fixation rate of mutations in the HIV population of the multidrug-resistant patient was demonstrated using molecular clock modeling. We show that molecular evolutionary analyses, guided by a known transmission history, can reveal the presence of confounding factors like natural selection and caution should be taken when accurate descriptions of HIV evolution are required.

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Cavender-Bares, Jeannine, David D. Ackerly, and Kenneth H. Kozak. "Integrating ecology and phylogenetics: the footprint of history in modern-day communities1." Ecology 93, sp8 (August 2012): S1—S3. http://dx.doi.org/10.1890/12-0092.1.

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Xu, Dong-dong, De-pei Liu, Xin-jun Ji, Xiang Lv, and Chih-chuan Liang. "In vivo DNA-protein interactions at hypersensitive site 3.5 of the human β-globin locus control region." Biochemistry and Cell Biology 79, no. 6 (December 1, 2001): 747–54. http://dx.doi.org/10.1139/o01-151.

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Using ligation-mediated polymerase chain reaction and in vivo footprinting methods to study the status of DNAprotein interactions at hypersensitive site 3.5 (HS3.5) of the locus control region in K562 and HEL cells, we found that there was protein occupancy in vivo at HS3.5 in both cell lines and the status of DNAprotein interaction was different between K562 and HEL. These data provide direct evidence that specific nuclear factor DNA complexes form in vivo at functionally important sequence motifs of the HS3.5 in erythroid cells. This indicates that HS3.5 may play an important role in the regulation of the β-globin gene cluster. K562 is a human erythroleukemia cell line in which the embryonic ε-globin gene is predominantly expressed, while the HEL cell line expresses predominantly the fetal β-globin genes. Thus, HS3.5 might also be involved in the regulation of developmental stage-specific expression of β-globin genes. Our results are also consistent with the model that each hypersensitive site acts as a functional unit and HS3.5 may facilitate the formation of the HS3 functional unit.Key words: β-globin gene, hypersensitive site, phylogenetic footprint, differential phylogenetic footprint, in vivo footprinting, developmental regulation.

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LaGrandeur, T. E., A. Hüttenhofer, H. F. Noller, and N. R. Pace. "Phylogenetic comparative chemical footprint analysis of the interaction between ribonuclease P RNA and tRNA." EMBO Journal 13, no. 17 (September 1994): 3945–52. http://dx.doi.org/10.1002/j.1460-2075.1994.tb06710.x.

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Takata, Naoki, Shigeru Saito, Claire Saito, and Matsuo Uemura. "Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators." BMC Evolutionary Biology 10, no. 1 (2010): 126. http://dx.doi.org/10.1186/1471-2148-10-126.

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Gosai, Haren B., Bhumi K. Sachaniya, Haresh Z. Panseriya, and Bharti P. Dave. "Functional and phylogenetic diversity assessment of microbial communities at Gulf of Kachchh, India: An ecological footprint." Ecological Indicators 93 (October 2018): 65–75. http://dx.doi.org/10.1016/j.ecolind.2018.04.072.

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Blomqvist, Soile, Carita Savolainen-Kopra, Anja Paananen, Tapani Hovi, and Merja Roivainen. "Molecular characterization of human rhinovirus field strains isolated during surveillance of enteroviruses." Journal of General Virology 90, no. 6 (June 1, 2009): 1371–81. http://dx.doi.org/10.1099/vir.0.008508-0.

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Human rhinoviruses (HRVs), which are the most frequent causative agents of acute upper respiratory tract infections, are abundant worldwide. We have identified HRV strains in environmental specimens collected in Finland, Latvia and Slovakia during the surveillance of polio- and other enteroviruses. These acid-sensitive HRV strains were isolated under conditions optimized for growth of most of the enteroviruses, i.e. in stationary human rhabdomyosarcoma cells incubated at 36 °C. Phylogenetic analysis of the sequences derived from the partial 5′ non-coding region and the capsid region coding for proteins VP4/VP2 and VP1 showed that the HRV field strains clustered together with prototype strains of the HRV minor receptor group. Partial sequences of the 3D polymerase coding region generally followed this pattern, with the exception of a set of three HRV field strains that formed a subcluster not close to any of the established HRV-A types, suggesting that recombination may have occurred during evolution of these HRV strains. Phylogenetic analysis of the VP4/VP2 capsid protein coding region showed that the ‘environmental’ HRV field strains were practically identical to HRV strains recently sequenced by others in Australia, the United States and Japan. Analysis of amino acids corresponding to the intercellular adhesion molecule-1 receptor footprint in major receptor group HRVs and also in the low-density lipoprotein receptor footprint of minor receptor group HRVs showed conservation of the ‘minor receptor group-like’ amino acids, indicating that the field strains may have maintained their minor receptor group specificity.

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R. Marcelino, Vanessa, Ma Chiela M. Cremen, Chistopher J. Jackson, Anthony A. W. Larkum, and Heroen Verbruggen. "Evolutionary Dynamics of Chloroplast Genomes in Low Light: A Case Study of the Endolithic Green Alga Ostreobium quekettii." Genome Biology and Evolution 8, no. 9 (August 25, 2016): 2939–51. http://dx.doi.org/10.1093/gbe/evw206.

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Abstract Some photosynthetic organisms live in extremely low light environments. Light limitation is associated with selective forces as well as reduced exposure to mutagens, and over evolutionary timescales it can leave a footprint on species’ genomes. Here, we present the chloroplast genomes of four green algae (Bryopsidales, Ulvophyceae), including the endolithic (limestone-boring) alga Ostreobium quekettii, which is a low light specialist. We use phylogenetic models and comparative genomic tools to investigate whether the chloroplast genome of Ostreobium corresponds to our expectations of how low light would affect genome evolution. Ostreobium has the smallest and most gene-dense chloroplast genome among Ulvophyceae reported to date, matching our expectation that light limitation would impose resource constraints reflected in the chloroplast genome architecture. Rates of molecular evolution are significantly slower along the phylogenetic branch leading to Ostreobium, in agreement with the expected effects of low light and energy levels on molecular evolution. We expected the ability of Ostreobium to perform photosynthesis in very low light to be associated with positive selection in genes related to the photosynthetic machinery, but instead, we observed that these genes may be under stronger purifying selection. Besides shedding light on the genome dynamics associated with a low light lifestyle, this study helps to resolve the role of environmental factors in shaping the diversity of genome architectures observed in nature.

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Vlasak, Marketa, Soile Blomqvist, Tapani Hovi, Elizabeth Hewat, and Dieter Blaas. "Sequence and Structure of Human Rhinoviruses Reveal the Basis of Receptor Discrimination." Journal of Virology 77, no. 12 (June 15, 2003): 6923–30. http://dx.doi.org/10.1128/jvi.77.12.6923-6930.2003.

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ABSTRACT The sequences of the capsid protein VP1 of all minor receptor group human rhinoviruses were determined. A phylogenetic analysis revealed that minor group HRVs were not more related to each other than to the nine major group HRVs whose sequences are known. Examination of the surface exposed amino acid residues of HRV1A and HRV2, whose X-ray structures are available, and that of three-dimensional models computed for the remaining eight minor group HRVs indicated a pattern of positively charged residues within the region, which, in HRV2, was shown to be the binding site of the very-low-density lipoprotein (VLDL) receptor. A lysine in the HI loop of VP1 (K224 in HRV2) is strictly conserved within the minor group. It lies in the middle of the footprint of a single repeat of the VLDL receptor on HRV2. Major group virus serotypes exhibit mostly negative charges at the corresponding positions and do not bind the negatively charged VLDL receptor, presumably because of charge repulsion.

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Faria, Nuno R., Ioannis Hodges-Mameletzis, Joana C. Silva, Berta Rodés, Smit Erasmus, Stefania Paolucci, Jean Ruelle, et al. "Phylogeographical footprint of colonial history in the global dispersal of human immunodeficiency virus type 2 group A." Journal of General Virology 93, no. 4 (April 1, 2012): 889–99. http://dx.doi.org/10.1099/vir.0.038638-0.

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Human immunodeficiency virus type 2 (HIV-2) emerged in West Africa and has spread further to countries that share socio-historical ties with this region. However, viral origins and dispersal patterns at a global scale remain poorly understood. Here, we adopt a Bayesian phylogeographic approach to investigate the spatial dynamics of HIV-2 group A (HIV-2A) using a collection of 320 partial pol and 248 partial env sequences sampled throughout 19 countries worldwide. We extend phylogenetic diffusion models that simultaneously draw information from multiple loci to estimate location states throughout distinct phylogenies and explicitly attempt to incorporate human migratory fluxes. Our study highlights that Guinea-Bissau, together with Côte d’Ivoire and Senegal, have acted as the main viral sources in the early stages of the epidemic. We show that convenience sampling can obfuscate the estimation of the spatial root of HIV-2A. We explicitly attempt to circumvent this by incorporating rate priors that reflect the ratio of human flow from and to West Africa. We recover four main routes of HIV-2A dispersal that are laid out along colonial ties: Guinea-Bissau and Cape Verde to Portugal, Côte d’Ivoire and Senegal to France. Within Europe, we find strong support for epidemiological linkage from Portugal to Luxembourg and to the UK. We demonstrate that probabilistic models can uncover global patterns of HIV-2A dispersal providing sampling bias is taken into account and we provide a scenario for the international spread of this virus.

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Yuan, Yao-Wu, and Richard G. Olmstead. "Evolution and phylogenetic utility of the PHOT gene duplicates in the Verbena complex (Verbenaceae): dramatic intron size variation and footprint of ancestral recombination." American Journal of Botany 95, no. 9 (September 2008): 1166–76. http://dx.doi.org/10.3732/ajb.0800133.

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Zang, Mingyue, Qian Su, Yuhao Weng, Lu Lu, Xueyan Zheng, Daiquan Ye, Renhua Zheng, Tielong Cheng, Jisen Shi, and Jinhui Chen. "Complete Chloroplast Genome of Fokienia hodginsii (Dunn) Henry et Thomas: Insights into Repeat Regions Variation and Phylogenetic Relationships in Cupressophyta." Forests 10, no. 7 (June 26, 2019): 528. http://dx.doi.org/10.3390/f10070528.

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Fokienia hodginsii (Dunn) Henry et Thomas is a relic gymnosperm with broad application value. It is a fit candidate when choosing species for the construction of artificial forests. We determined the complete chloroplast genome sequence of F. hodginsii, which is 129,534 bp in length and encodes 83 protein genes, 33 transfer RNA (tRNA) genes, as well as four ribosomal RNA genes. The GC content of the complete sequence and protein coding regions is 34.8% and 36.2%, respectively. We identified 11 tandem repeats, 11 forward repeats, and three palindromic repeats and classified them by size. Following our microsatellite analysis, a total number of 73 simple sequence repeats were detected, preferentially within the intergenic space. Being a member of Cupressophyta, F. hodginsii owns several common characters; the trnR-CCG gene has been deleted, while the trnI-CAU and trnQ-UUG genes have been duplicated. Moreover, the accD gene, which encodes acetyl-CoA carboxylase, contains 771 codons in F. hodginsii, similar to Cryptomeria japonica (L. F.) D. Don, further supporting the diversity of accD and its size expansion in Cupressophyta. Concerning the loss of inverted repeat (IR) regions, the 86-bp sequence with the duplicated trnI-CAU gene is inferred to be the footprint of IR contraction. Phylogenetically, F. hodginsii is placed as a sister taxon to Chamaecyparis hodginsii (Dunn) Rushforth. This work offers meaningful guidance as well as reference value to the breeding research and improvement of F. hodginsii. Moreover, it gives us a better understanding of the genomic structure and evolutionary history of gymnosperms, especially coniferales.

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ROBERTS, Stefan G. E., Roy LAYFIELD, Andrew J. BANNISTER, and Charles J. McDONALD. "Gene sequence of mouse B-type proline-rich protein MP4. Transcriptional start point and an upstream phylogenetic footprint with ets-like and rel/NFkB-like elements." European Journal of Biochemistry 202, no. 3 (December 1991): 969–74. http://dx.doi.org/10.1111/j.1432-1033.1991.tb16457.x.

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How, S. W., S. Y. Lim, P. B. Lim, A. M. Aris, G. C. Ngoh, T. P. Curtis, and A. S. M. Chua. "Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community." Water Science and Technology 77, no. 9 (March 28, 2018): 2274–83. http://dx.doi.org/10.2166/wst.2018.143.

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Abstract Intensive aeration for nitrification is a major energy consumer in sewage treatment plants (STPs). Low-dissolved-oxygen (low-DO) nitrification has the potential to lower the aeration demand. However, the applicability of low-DO nitrification in the tropical climate is not well-understood. In this study, the potential of low-DO nitrification in tropical setting was first examined using batch kinetic experiments. Subsequently, the performance of low-DO nitrification was investigated in a laboratory-scale sequential batch reactor (SBR) for 42 days using real tropical sewage. The batch kinetic experiments showed that the seed sludge has a relatively high oxygen affinity. Thus, the rate of nitrification was not significantly reduced at low DO concentrations (0.5 mg/L). During the operation of the low-DO nitrification SBR, 90% of NH4-N was removed. The active low-DO nitrification was mainly attributed to the limited biodegradable organics in the sewage. Fluorescence in-situ hybridisation and 16S rRNA amplicon sequencing revealed the nitrifiers were related to Nitrospira genus and Nitrosomonadaceae family. Phylogenetic analysis suggests 47% of the operational taxonomic units in Nitrospira genus are closely related to a comammox bacteria. This study has demonstrated active low-DO nitrification in tropical setting, which is a more sustainable process that could significantly reduce the energy footprint of STPs.

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Boxall, Naomi J., Peter D. Franzmann, Amanda L. Tilbury, Hugh J. Nyeboer, Anthony J. McKinnon, David C. Sutton, and Anna H. Kaksonen. "Characterisation of a Novel Genus of Oxalate-Degrading Beta-Proteobacteria Isolated from a Full-Scale Bioreactor Treating Bayer Liquor Organic Wastes." Advanced Materials Research 825 (October 2013): 79–83. http://dx.doi.org/10.4028/www.scientific.net/amr.825.79.

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A novel industrial-scale bioreactor was implemented by Alcoa of Australia (Alcoa) at its Kwinana alumina refinery (Western Australia) for the degradation of oxalate, an organic byproduct of the Bayer alumina refining process. At the Kwinana refinery oxalate is removed from the Bayer Liquor via a separate side-stream as it increases the operating costs associated with the process and, at sufficiently high levels, may adversely affect the quality and yield of the final alumina product. The bioreactor process provides a more economic and environmentally friendly method for the treatment of removed oxalate compared with chemical conversion or storage of the solid by-product. In previous studies, the microbial community composition of the bioreactor was investigated and was found to be largely dominated by microorganisms of the α-, β- and γ-Proteobacteriasubgroups. During the present study, two bacteria that had the ability to use oxalate as a sole source of carbon and energy were isolated from samples obtained from the bioreactor. Phylogenetic and physiological analyses indicated that the two isolates were probably strains of a novel species of a novel genus within the β-Proteobacteriasubgroup. Isolation and characterisation of the microbial communities within the bioreactor system has the potential to improve process operation, which may have a positive impact on the biological oxalate destruction process and the footprint of alumina production.

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Rutley, Nicholas, Laetitia Poidevin, Tirza Doniger, Richard L. Tillett, Abhishek Rath, Javier Forment, Gilad Luria, et al. "Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana." Plant Reproduction 34, no. 1 (January 18, 2021): 61–78. http://dx.doi.org/10.1007/s00497-020-00400-1.

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Abstract Key message Arabidopsis pollen transcriptome analysis revealed new intergenic transcripts of unknown function, many of which are long non-coding RNAs, that may function in pollen-specific processes, including the heat stress response. Abstract The male gametophyte is the most heat sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison with HS in cauline leaves and other RNAseq experiments indicated that 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed that 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional and play a significant role in pollen biology, including the HS response.

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Wei, Yanping, Dong Xiao, Changwei Zhang, and Xilin Hou. "The Expanded SWEET Gene Family Following Whole Genome Triplication in Brassica rapa." Genes 10, no. 9 (September 18, 2019): 722. http://dx.doi.org/10.3390/genes10090722.

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The SWEET family, which includes transcripts of a cohort of plant hexose and sucrose transporters, is considered key to improving crop stress tolerance and yield through its role in manipulating the carbohydrate partitioning process. The functions and regulatory roles of this gene family are variable among different species; thus, to determine these roles, more species-specific information is needed. Brassica rapa displays complicated regulation after a whole-genome triplication (WGT) event, which provides enormous advantages for use in genetic studies, thus it is an ideal model for exploring the functional and regulatory roles of SWEETs from a genetic perspective. In this study, the results of a homology search and phylogenetic relationship analysis revealed the evolutionary footprint of SWEETs among different plant taxa, which showed that plant SWEETs may have originated from Clade II and then expanded from vascular plants. The amino acid sequence characteristics and an analysis of the exon-intron structure of BrSWEETs duplicates clarified that SWEETs retention occurred after a WGT event in B. rapa. An analysis of the transcriptional levels of BrSWEETs in different tissues identified the expression differences among duplicated co-orthologs. In addition, qRT-PCR indicated that the BrSWEETs’ co-orthologs were varied in their stress responses. This study greatly enriches our knowledge of SWEETs in the B. rapa species, which will contribute to future studies on the Brassica-specific regulatory pathways and to creating genetic innovations.

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Nakamura, Haruna, Mitsuto Aibara, Rei Kajitani, Hillary D. J. Mrosso, Semvua I. Mzighani, Atsushi Toyoda, Takehiko Itoh, Norihiro Okada, and Masato Nikaido. "Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation." Molecular Biology and Evolution 38, no. 8 (March 21, 2021): 3111–25. http://dx.doi.org/10.1093/molbev/msab084.

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Abstract The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.

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Ševčíková, Tereza, Tatiana Yurchenko, Karen P. Fawley, Raquel Amaral, Hynek Strnad, Lilia M. A. Santos, Marvin W. Fawley, and Marek Eliáš. "Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts." Genome Biology and Evolution 11, no. 2 (January 10, 2019): 362–79. http://dx.doi.org/10.1093/gbe/evz004.

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Abstract Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte–Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.

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Stansell, Zachary, Katie Hyma, Jonathan Fresnedo-Ramírez, Qi Sun, Sharon Mitchell, Thomas Björkman, and Jian Hua. "Genotyping-by-sequencing of Brassica oleracea vegetables reveals unique phylogenetic patterns, population structure and domestication footprints." Horticulture Research 5, no. 1 (July 1, 2018). http://dx.doi.org/10.1038/s41438-018-0040-3.

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Matsuno, Keita, Masahiro Kajihara, Ryo Nakao, Naganori Nao, Akina Mori-Kajihara, Mieko Muramatsu, Yongjin Qiu, et al. "The Unique Phylogenetic Position of a Novel Tick-Borne Phlebovirus Ensures an Ixodid Origin of the GenusPhlebovirus." mSphere 3, no. 3 (June 13, 2018). http://dx.doi.org/10.1128/msphere.00239-18.

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ABSTRACTThe recent emergence of novel tick-borne RNA viruses has complicated the epidemiological landscape of tick-borne infectious diseases, posing a significant challenge to public health systems that seek to counteract tick-borne diseases. The identification of two novel tick-borne phleboviruses (TBPVs), severe fever with thrombocytopenia syndrome virus (SFTSV) and Heartland virus (HRTV), as causative agents of severe illness in humans has accelerated the investigation and discoveries of novel TBPVs. In the present study, we isolated a novel TBPV designated Mukawa virus (MKWV) from host-questingIxodes persulcatusfemales captured in Japan. Genetic characterization revealed that MKWV is a member of the genusPhlebovirusin the familyPhenuiviridae. Interestingly, MKWV is genetically distinct from other known TBPVs and shares a most recent common ancestor with mosquito/sandfly-borne (insect-borne) phleboviruses. Despite its genetic similarity to insect-borne phleboviruses, the molecular footprints of its viral proteins and its biological characteristics define MKWV as a tick-borne virus that can be transmitted to mammals. A phylogenetic ancestral-state reconstruction for arthropod vectors of phleboviruses including MKWV based on viral L segment sequences indicated that ticks likely harbored ancestral phleboviruses that evolved into both the tick-borne and MKWV/insect-borne phlebovirus lineages. Overall, our findings suggest that most of the phlebovirus evolution has occurred in hard ticks to generate divergent viruses, which may provide a seminal foundation for understanding the mechanisms underlying the evolution and emergence of pathogenic phleboviruses, such as Rift Valley fever virus and SFTSV/HRTV.IMPORTANCEThe emergence of novel tick-borne RNA viruses causing severe illness in humans has complicated the epidemiological landscape of tick-borne diseases, requiring further investigation to safeguard public health. In the present study, we discovered a novel tick-borne phlebovirus fromIxodes persulcatusticks in Japan. While its viral RNA genome sequences were similar to those of mosquito/sandfly-borne viruses, molecular and biological footprints confirmed that this is a tick-borne virus. The unique evolutionary position of the virus allowed us to estimate the ancestral phlebovirus vector, which was likely a hard tick. Our findings may provide a better understanding of the evolution and emergence of phleboviruses associated with emerging infectious diseases, such as severe fever with thrombocytopenia syndrome (SFTS) and Heartland virus disease.

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Qvarnström, Martin, Per E. Ahlberg, and Grzegorz Niedźwiedzki. "Tyrannosaurid-like osteophagy by a Triassic archosaur." Scientific Reports 9, no. 1 (January 30, 2019). http://dx.doi.org/10.1038/s41598-018-37540-4.

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Abstract Here we present evidence for osteophagy in the Late Triassic archosaur Smok wawelski Niedźwiedzki, Sulej and Dzik, 2012, a large theropod-like predator from Poland. Ten medium to large-sized coprolites are matched, by their dimensions and by association with body fossils and footprints, to S. wawelski. The coprolites contain fragments of large serrated teeth as well as up to 50 percent by volume of bone fragments, with distinct fragmentation and angularity, from several prey taxa. This suggests pronounced osteophagy. Further evidence for bone-crushing behaviour is provided by isolated worn teeth, bone-rich regurgitalites (fossil regurgitates) and numerous examples of crushed or bite-marked dicynodont bones, all collected from the same bone-bearing beds in the Lipie Śląskie clay-pit. Several of the anatomical characters related to osteophagy, such as a massive head and robust body, seem to be shared by S. wawelski and the tyrannosaurids, despite their wide phylogenetic separation. These large predators thus provide evidence of convergence driven by similar feeding ecology at the beginning and end of the age of dinosaurs.

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Sorkheh, Karim, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, and Júlia Halász. "RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species." Scientific Reports 7, no. 1 (July 20, 2017). http://dx.doi.org/10.1038/s41598-017-06084-4.

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Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.

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De Panis, D., S. A. Lambertucci, G. Wiemeyer, H. Dopazo, F. C. Almeida, C. J. Mazzoni, M. Gut, I. Gut, and J. Padró. "Mitogenomic analysis of extant condor species provides insight into the molecular evolution of vultures." Scientific Reports 11, no. 1 (August 24, 2021). http://dx.doi.org/10.1038/s41598-021-96080-6.

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AbstractThe evolution of large vultures linked to mountainous habitats was accompanied by extreme physiological and behavioral specializations for energetically efficient flights. However, little is known on the genetic traits associated with the evolution of these obligate soaring scavengers. Mitochondrial DNA plays a vital role in regulating oxidative stress and energy production, and hence may be an important target of selection for flight performance. Herein, we characterized the first mitogenomes of the Andean and California condors, the world’s heaviest flying birds and the only living representatives of the Vultur and Gymnogyps genus. We reconstructed the phylogenetic relationships and evaluated possible footprints of convergent evolution associated to the life-history traits and distributional range of vultures. Our phylogenomic analyses supported the independent evolution of vultures, with the origin of Cathartidae in the early Paleogene (~ 61 Mya), and estimated the radiation of extant condors during the late Miocene (~ 11 Mya). Selection analyses indicated that vultures exhibit signals of relaxation of purifying selection relative to other accipitrimorph raptors, possibly indicating the degeneration of flapping flight ability. Overall, our results suggest that the extreme specialization of vultures for efficient soaring flight has compensated the evolution of large body sizes mitigating the selection pressure on mtDNA.

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Ramos, Elisa Karen da Silva, Lucas Freitas, and Mariana F. Nery. "The role of selection in the evolution of marine turtles mitogenomes." Scientific Reports 10, no. 1 (October 12, 2020). http://dx.doi.org/10.1038/s41598-020-73874-8.

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Abstract Sea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.

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Journal articles on the topic 'Phylogenetic footprints'

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