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Journal articles on the topic 'Genomic phylostratigraphy'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Moyers, Bryan A., and Jianzhi Zhang. "Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution." Molecular Biology and Evolution 32, no. 1 (2014): 258–67. http://dx.doi.org/10.1093/molbev/msu286.

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Phylostratigraphy is a method for dating the evolutionary emergence of a gene or gene family by identifying its homologs across the tree of life, typically by using BLAST searches. Applying this method to all genes in a species, or genomic phylostratigraphy, allows investigation of genome-wide patterns in new gene origination at different evolutionary times and thus has been extensively used. However, gene age estimation depends on the challenging task of detecting distant homologs via sequence similarity, which is expected to have differential accuracies for different genes. Here, we evaluate

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2

Domazet-Lošo, Tomislav, Josip Brajković, and Diethard Tautz. "A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages." Trends in Genetics 23, no. 11 (2007): 533–39. http://dx.doi.org/10.1016/j.tig.2007.08.014.

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3

Shi, Lei, Abderahmane Derouiche, Santosh Pandit, et al. "Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation." Molecular Biology and Evolution 37, no. 6 (2020): 1667–78. http://dx.doi.org/10.1093/molbev/msaa035.

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Abstract Bacilli can form dormant, highly resistant, and metabolically inactive spores to cope with extreme environmental challenges. In this study, we examined the evolutionary age of Bacillus subtilis sporulation genes using the approach known as genomic phylostratigraphy. We found that B. subtilis sporulation genes cluster in several groups that emerged at distant evolutionary time-points, suggesting that the sporulation process underwent several stages of expansion. Next, we asked whether such evolutionary stratification of the genome could be used to predict involvement in sporulation of

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4

Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (May 27, 2022): 583. http://dx.doi.org/10.12688/f1000research.110492.1.

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Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, the system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there is no genomic and transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephala

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Nesterenko, Maksim, and Aleksei Miroliubov. "From head to rootlet: comparative transcriptomic analysis of a rhizocephalan barnacle Peltogaster reticulata (Crustacea: Rhizocephala)." F1000Research 11 (January 9, 2023): 583. http://dx.doi.org/10.12688/f1000research.110492.2.

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Background: Rhizocephalan barnacles stand out in the diverse world of metazoan parasites. The body of a rhizocephalan female is modified beyond revealing any recognizable morphological features, consisting of the interna, a system of rootlets, and the externa, a sac-like reproductive body. Moreover, rhizocephalans have an outstanding ability to control their hosts, literally turning them into “zombies”. Despite all these amazing traits, there are no genomic or transcriptomic data about any Rhizocephala. Methods: We collected transcriptomes from four body parts of an adult female rhizocephalan

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6

Ivanov, R. A., A. M. Mukhin, F. V. Kazantsev, et al. "Orthoweb: a software package for evolutionary analysis of gene networks." Vavilov Journal of Genetics and Breeding 28, no. 8 (2025): 874–81. https://doi.org/10.18699/vjgb-24-95.

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This article introduces Orthoweb (https://orthoweb.sysbio.cytogen.ru/), a software package developed for the calculation of evolutionary indices, including phylostratigraphic indices and divergence indices (Ka/Ks) for individual genes as well as for gene networks. The phylostratigraphic age index (PAI) allows the evolutionary stage of a gene’s emergence (and thus indirectly the approximate time of its origin, known as “evolutionary age”) to be assessed based on the analysis of orthologous genes across closely and distantly related taxa. Additionally, Orthoweb supports the calculation of the tr

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7

Glover, Natasha, Christophe Dessimoz, Ingo Ebersberger, et al. "Advances and Applications in the Quest for Orthologs." Molecular Biology and Evolution 36, no. 10 (2019): 2157–64. http://dx.doi.org/10.1093/molbev/msz150.

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Abstract Gene families evolve by the processes of speciation (creating orthologs), gene duplication (paralogs), and horizontal gene transfer (xenologs), in addition to sequence divergence and gene loss. Orthologs in particular play an essential role in comparative genomics and phylogenomic analyses. With the continued sequencing of organisms across the tree of life, the data are available to reconstruct the unique evolutionary histories of tens of thousands of gene families. Accurate reconstruction of these histories, however, is a challenging computational problem, and the focus of the Quest

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8

Jers, Carsten, Hrvoje Mišetić, Vaishnavi Ravikumar, et al. "Gene age and genome organization in Escherichia coli and Bacillus subtilis." Frontiers in Microbiology 16 (June 18, 2025). https://doi.org/10.3389/fmicb.2025.1512923.

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Using genomic phylostratigraphy, we examined the organization of Escherichia coli and Bacillus subtilis genomes from the perspective of evolutionary age of their genes. Phylostratigraphy analysis classifies individual genes into age-related bins, called phylostrata. Based on this analysis, several common features emerged in the genomes of the two model bacteria. More recent genes tend to be shorter and are expressed less frequently, or only in specific conditions. In terms of genomic location, new genes are enriched in areas containing prophages, suggesting a link with horizontal gene transfer

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9

Sestak, Martin Sebastijan, Vedran Bozicevic, Robert Bakaric, Vedran Dunjko, and Tomislav Domazet-Loso. "Phylostratigraphic profiles reveal a deep evolutionary history of the vertebrate head sensory systems." April 12, 2013. https://doi.org/10.1186/1742-9994-10-18.

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Background The vertebrate head is a highly derived trait with a heavy concentration of sophisticated sensory organs that allow complex behaviour in this lineage. The head sensory structures arise during vertebrate development from cranial placodes and the neural crest. It is generally thought that derivatives of these ectodermal embryonic tissues played a central role in the evolutionary transition at the onset of vertebrates. Despite the obvious importance of head sensory organs for vertebrate biology, their evolutionary history is still uncertain. Results To give a fresh perspective on the a

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10

Barrera-Redondo, Josué, Jaruwatana Sodai Lotharukpong, Hajk-Georg Drost, and Susana M. Coelho. "Uncovering gene-family founder events during major evolutionary transitions in animals, plants and fungi using GenEra." Genome Biology 24, no. 1 (2023). http://dx.doi.org/10.1186/s13059-023-02895-z.

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AbstractWe present GenEra (https://github.com/josuebarrera/GenEra), a DIAMOND-fueled gene-family founder inference framework that addresses previously raised limitations and biases in genomic phylostratigraphy, such as homology detection failure. GenEra also reduces computational time from several months to a few days for any genome of interest. We analyze the emergence of taxonomically restricted gene families during major evolutionary transitions in plants, animals, and fungi. Our results indicate that the impact of homology detection failure on inferred patterns of gene emergence is lineage

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11

Nesterenko, Maksim, Sergei Shchenkov, Sofia Denisova, and Viktor Starunov. "The digenean complex life cycle: phylostratigraphy analysis of the molecular signatures." Biological Communications 67, no. 2 (2022). http://dx.doi.org/10.21638/spbu03.2022.201.

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The parasitic flatworms from Digenea group have been the object of numerous in-depth studies for several centuries. The question of the evolutionary origin and transformation of the digenean complex life cycle remains relevant and open due to the biodiversity of these parasites and the absence of fossil records. However, modern technologies and analysis methods allow to get closer to understanding the molecular basis of both the realization of the cycle and its complication. In the present study, we have applied phylostratigraphy and evolutionary transcriptomics approaches to the available dig

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12

Pai, Vaibhav P., Léo Pio-Lopez, Megan M. Sperry, Patrick Erickson, Parande Tayyebi, and Michael Levin. "Basal Xenobot transcriptomics reveals changes and novel control modality in cells freed from organismal influence." Communications Biology 8, no. 1 (2025). https://doi.org/10.1038/s42003-025-08086-9.

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Abstract Would transcriptomes change if cell collectives acquired a novel morphogenetic and behavioral phenotype in the absence of genomic editing, transgenes, heterologous materials, or drugs? We investigate the effects of morphology and nascent emergent life history on gene expression in the basal (no engineering, no sculpting) form of Xenobots —autonomously motile constructs derived from Xenopus embryo ectodermal cell explants. To investigate gene expression differences between cells in the context of an embryo with those that have been freed from instructive signals and acquired novel live

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13

Damatac, Amor, Sara Koska, Kristian K. Ullrich, Tomislav Domazet-Lošo, Alexander Klimovich, and Markéta Kaucká. "Evolutionary trends in the emergence of skeletal cell types." Evolution Letters, May 18, 2025. https://doi.org/10.1093/evlett/qraf012.

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Abstract Cell types are fundamental functional units of multicellular organisms. The evolutionary emergence of new cell types is underpinned by genetic changes, such as gene co-option and cis-regulatory evolution, that propel the assembly or rewiring of molecular networks and give rise to new cell types with specialized functions. Here, we integrate genomic phylostratigraphy with single-cell transcriptomics to explore the evolutionary trends in the assembly of the skeletal cell type-specific gene expression programs. In particular, we investigate how the emergence of lineage-specific genes con

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14

Petroll, Romy, Ranjith K. Papareddy, Rafal Krela, et al. "The expansion and diversification of epigenetic regulatory networks underpins major transitions in the evolution of land plants." Molecular Biology and Evolution, March 25, 2025. https://doi.org/10.1093/molbev/msaf064.

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Abstract Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While DNA and H3K9 methylation silence transposable elements (TEs), H3K27me3 marks deposited by the Polycomb repressive complex 2 (PRC2) silence varying proportions of TEs and genes across different lineages. Despite the major development role epigenetic silencing plays in multicellular eukaryotes, little is known about how epigenetic regulatory networks were shaped over evolutionary time. Here, we analyse epigenomes from diverse species across the green lineage to infer the chronolo

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15

Remmel, Andreas, Karl K. Käther, Peter F. Stadler, and Steffen Lemke. "Recently Evolved, Stage‐Specific Genes Are Enriched at Life‐Stage Transitions in Flies." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, July 15, 2025. https://doi.org/10.1002/jez.b.23317.

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ABSTRACTUnderstanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal, and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster (D. melanogaster) has been extensively studied, less is known about the evolutionary dynamics that could govern stage‐specific gene expression. To address this question, we compared the

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16

Blank-Landeshammer, B., I. Teichert, R. Märker, M. Nowrousian, U. Kück, and A. Sickmann. "Combination of Proteogenomics with PeptideDe NovoSequencing Identifies New Genes and Hidden Posttranscriptional Modifications." mBio 10, no. 5 (2019). http://dx.doi.org/10.1128/mbio.02367-19.

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ABSTRACTProteogenomics combines proteomics, genomics, and transcriptomics and has considerably improved genome annotation in poorly investigated phylogenetic groups for which homology information is lacking. Furthermore, it can be advantageous when reinvestigating well-annotated genomes. Here, we applied an advanced proteogenomics approach, combining standard proteogenomics with peptidede novosequencing, to refine annotation of the well-studied model fungusSordaria macrospora. We investigated samples from different developmental and physiological conditions, resulting in the detection of 104 s

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17

Manley, Bethan F., Jaruwatana S. Lotharukpong, Josué Barrera-Redondo, et al. "A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis." G3 Genes|Genomes|Genetics, March 31, 2023. http://dx.doi.org/10.1093/g3journal/jkad077.

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Abstract The root systems of most plant species are aided by the soil foraging capacities of symbiotic Arbuscular Mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent advances in our knowledge of the ecology and molecular biology of this mutualistic symbiosis, our understanding of the AM fungi genome biology is just emerging. Presented here is a close to T2T genome assembly of the model AM fungus Rhizophagus irregularis DAOM197198, achieved through Nanopore long-read DNA sequencing and Hi-C data. This haploid genome assembly of Rhizophagus irregularis, alongside short- and l

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18

Zheng, Eric B., and Li Zhao. "Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins." eLife 11 (September 30, 2022). http://dx.doi.org/10.7554/elife.78772.

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De novo gene origination, where a previously non-genic genomic sequence becomes genic through evolution, has been increasingly recognized as an important source of evolutionary novelty across diverse taxa. Many de novo genes have been proposed to be protein-coding, and in several cases have been experimentally shown to yield protein products. However, the systematic study of de novo proteins has been hampered by doubts regarding the translation of their transcripts without the experimental observation of protein products. Using a systematic, ORF-focused mass-spectrometry-first computational ap

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19

Hayford, Rita K., Olivia C. Haley, Ethalinda K. Cannon, et al. "Functional annotation and meta-analysis of maize transcriptomes reveal genes involved in biotic and abiotic stress." BMC Genomics 25, no. 1 (2024). http://dx.doi.org/10.1186/s12864-024-10443-7.

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Abstract Background Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress. Results We mapped high-quality RNA-Seq expression read

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