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Journal articles on the topic 'Insect genomes'

Author: Grafiati

Published: 4 June 2021

Last updated: 17 February 2022

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1

Hotaling, Scott, Joanna L. Kelley, and Paul B. Frandsen. "Aquatic Insects Are Dramatically Underrepresented in Genomic Research." Insects 11, no. 9 (2020): 601. http://dx.doi.org/10.3390/insects11090601.

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Aquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. However, aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ~9 terrestrial insect genomes. Instead, ~24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if the quality of genomic resources is considered; for instance, while no aquatic insect genome ha

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2

Feyereisen, R. "Evolution of insect P450." Biochemical Society Transactions 34, no. 6 (2006): 1252–55. http://dx.doi.org/10.1042/bst0341252.

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The first fully sequenced insect genomes were those of the fruitfly and the mosquito, both from the order Diptera. Now, with an increasing number and diversity of insect genomes becoming available, the diversity of insect P450 genes can be better appreciated and tentative ideas about the evolution of the CYP (cytochrome P450) superfamily in insects can be proposed. There are four large clades of insect P450 genes that existed before the divergence of the class Insecta and that are also represented by CYP families in vertebrates: the CYP2 clade, the CYP3 clade, the CYP4 clade and the mitochondr

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3

Robertson, Hugh M. "Insect Genomes." American Entomologist 51, no. 3 (2005): 166–73. http://dx.doi.org/10.1093/ae/51.3.166.

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4

Karpe, Snehal Dilip, Vikas Tiwari, and Sowdhamini Ramanathan. "InsectOR—Webserver for sensitive identification of insect olfactory receptor genes from non-model genomes." PLOS ONE 16, no. 1 (2021): e0245324. http://dx.doi.org/10.1371/journal.pone.0245324.

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Insect Olfactory Receptors (ORs) are diverse family of membrane protein receptors responsible for most of the insect olfactory perception and communication, and hence they are of utmost importance for developing repellents or pesticides. Accurate gene prediction of insect ORs from newly sequenced genomes is an important but challenging task. We have developed a dedicated webserver, ‘insectOR’, to predict and validate insect OR genes using multiple gene prediction algorithms, accompanied by relevant validations. It is possible to employ this server nearly automatically and perform rapid predict

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5

Peccoud, Jean, Vincent Loiseau, Richard Cordaux, and Clément Gilbert. "Massive horizontal transfer of transposable elements in insects." Proceedings of the National Academy of Sciences 114, no. 18 (2017): 4721–26. http://dx.doi.org/10.1073/pnas.1621178114.

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Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 2

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6

Rosenfeld, Jeffrey A., Jonathan Foox, and Rob DeSalle. "Insect genome content phylogeny and functional annotation of core insect genomes." Molecular Phylogenetics and Evolution 97 (April 2016): 224–32. http://dx.doi.org/10.1016/j.ympev.2015.10.014.

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7

Van Dam, Matthew H., Analyn Anzano Cabras, James B. Henderson, et al. "The Easter Egg Weevil (Pachyrhynchus) genome reveals syntenic patterns in Coleoptera across 200 million years of evolution." PLOS Genetics 17, no. 8 (2021): e1009745. http://dx.doi.org/10.1371/journal.pgen.1009745.

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Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders. We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open-source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currentl

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8

Gregory, T. Ryan. "Genome size of the northern walkingstick, Diapheromera femorata (Phasmida: Heteronemiidae)." Canadian Journal of Zoology 80, no. 7 (2002): 1303–5. http://dx.doi.org/10.1139/z02-106.

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The haploid genome size (C value) of the northern walkingstick, Diapheromera femorata (Say), was estimated to be 1C = 2.55 pg using Feulgen image-analysis densitometry of haemocyte and sperm nuclei. This relatively large genome is similar in size to the genomes of the few other phasmids studied so far, and is consistent with hypotheses regarding an upper limit to the size of many insect genomes imposed by the process of metamorphosis, which is relaxed among hemimetabolous orders. Comments on sperm morphology in D. femorata are also provided, and another possible relationship between genome siz

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9

Li, F., X. Zhao, M. Li, et al. "Insect genomes: progress and challenges." Insect Molecular Biology 28, no. 6 (2019): 739–58. http://dx.doi.org/10.1111/imb.12599.

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10

Saha, Surya, Amanda M. Cooksey, Anna K. Childers, Monica F. Poelchau, and Fiona M. McCarthy. "Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes." Insects 12, no. 8 (2021): 748. http://dx.doi.org/10.3390/insects12080748.

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Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and provide the foundational information required to apply ‘omics technologies to a more diverse set of species. However, biologists require genome annotation to use these genomes and derive a better understanding of complex biological systems. Genome annotation incorporates two related, but distinct, processes: Demarcating genes and other elements present in ge

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11

López-Fernández, C., E. Pradillo, M. Zabal-Aguirre, J. L. Fernández, C. García de la Vega, and J. Gosálvez. "Telomeric and interstitial telomeric-like DNA sequences in Orthoptera genomes." Genome 47, no. 4 (2004): 757–63. http://dx.doi.org/10.1139/g03-143.

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A (TTAGG)n-specific telomeric DNA probe was hybridized to 11 orthopteroid insect genomes by fluorescence in situ hybridization. Nine different genera, mainly distributed within two evolutionary branches with male chromosome numbers 2n = 23 and 2n = 17 were included in the analysis. Telomere sequences yielded positive signals in every telomere and there was a considerable number of interstitial telomeric-like sequences, mainly located at the distal end of some, but not all, subterminal chromosome regions. One of the species, Pyrgomorpha conica, showed massive hybridization signals associated wi

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12

Douglas, Angela E., and John A. Raven. "Genomes at the interface between bacteria and organelles." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1429 (2003): 5–18. http://dx.doi.org/10.1098/rstb.2002.1188.

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The topic of the transition of the genome of a free–living bacterial organism to that of an organelle is addressed by considering three cases. Two of these are relatively clear–cut as involving respectively organisms (cyanobacteria) and organelles (plastids). Cyanobacteria are usually free–living but some are involved in symbioses with a range of eukaryotes in which the cyanobacterial partner contributes photosynthesis, nitrogen fixation, or both of these. In several of these symbioses the cyanobacterium is vertically transmitted, and in a few instances, sufficient unsuccessful attempts have b

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13

Kulathinal, R. J. "Compensated Deleterious Mutations in Insect Genomes." Science 306, no. 5701 (2004): 1553–54. http://dx.doi.org/10.1126/science.1100522.

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14

Robinson, G. E., K. J. Hackett, M. Purcell-Miramontes, et al. "Creating a Buzz About Insect Genomes." Science 331, no. 6023 (2011): 1386. http://dx.doi.org/10.1126/science.331.6023.1386.

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15

Majid, Muhammad, and Huang Yuan. "Comparative Analysis of Transposable Elements in Genus Calliptamus Grasshoppers Revealed That Satellite DNA Contributes to Genome Size Variation." Insects 12, no. 9 (2021): 837. http://dx.doi.org/10.3390/insects12090837.

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Transposable elements (TEs) play a significant role in both eukaryotes and prokaryotes genome size evolution, structural changes, duplication, and functional variabilities. However, the large number of different repetitive DNA has hindered the process of assembling reference genomes, and the genus level TEs diversification of the grasshopper massive genomes is still under investigation. The genus Calliptamus diverged from Peripolus around 17 mya and its species divergence dated back about 8.5 mya, but their genome size shows rather large differences. Here, we used low-coverage Illumina unassem

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16

Wilson, Alex C. C., and Rebecca P. Duncan. "Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10255–61. http://dx.doi.org/10.1073/pnas.1423305112.

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The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboratio

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17

Shen, Sam H., Charles B. Stauft, Oleksandr Gorbatsevych, et al. "Large-scale recoding of an arbovirus genome to rebalance its insect versus mammalian preference." Proceedings of the National Academy of Sciences 112, no. 15 (2015): 4749–54. http://dx.doi.org/10.1073/pnas.1502864112.

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The protein synthesis machineries of two distinct phyla of the Animal kingdom, insects of Arthropoda and mammals of Chordata, have different preferences for how to best encode proteins. Nevertheless, arboviruses (arthropod-borne viruses) are capable of infecting both mammals and insects just like arboviruses that use insect vectors to infect plants. These organisms have evolved carefully balanced genomes that can efficiently use the translational machineries of different phyla, even if the phyla belong to different kingdoms. Using dengue virus as an example, we have undone the genome encoding

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18

Sun, Ling V., Jeremy M. Foster, George Tzertzinis, et al. "Determination of Wolbachia Genome Size by Pulsed-Field Gel Electrophoresis." Journal of Bacteriology 183, no. 7 (2001): 2219–25. http://dx.doi.org/10.1128/jb.183.7.2219-2225.2001.

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ABSTRACT Genome sizes of six different Wolbachia strains from insect and nematode hosts have been determined by pulsed-field gel electrophoresis of purified DNA both before and after digestion with rare-cutting restriction endonucleases. Enzymes SmaI,ApaI, AscI, and FseI cleaved the studied Wolbachia strains at a small number of sites and were used for the determination of the genome sizes ofwMelPop, wMel, and wMelCS (each 1.36 Mb), wRi (1.66 Mb), wBma (1.1 Mb), and wDim (0.95 Mb). The Wolbachia genomes studied were all much smaller than the genomes of free-living bacteria such as Escherichia

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19

Dayaram, Anisha, Kristen A. Potter, Angela B. Moline, et al. "High global diversity of cycloviruses amongst dragonflies." Journal of General Virology 94, no. 8 (2013): 1827–40. http://dx.doi.org/10.1099/vir.0.052654-0.

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Members of the family Circoviridae, specifically the genus Circovirus, were thought to infect only vertebrates; however, members of a sister group under the same family, the proposed genus Cyclovirus, have been detected recently in insects. In an effort to explore the diversity of cycloviruses and better understand the evolution of these novel ssDNA viruses, here we present five cycloviruses isolated from three dragonfly species (Orthetrum sabina, Xanthocnemis zealandica and Rhionaeschna multicolor) collected in Australia, New Zealand and the USA, respectively. The genomes of these five viruse

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20

Brown, Susan J., and Denis Tagu. "Editorial overview: Insect genomics: How to sequence five thousand insect genomes?" Current Opinion in Insect Science 7 (February 2015): iv—v. http://dx.doi.org/10.1016/j.cois.2015.02.006.

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21

Perry, Caitlyn, Jack Scanlan, and Charles Robin. "Mining insect genomes for functionally affiliated genes." Current Opinion in Insect Science 31 (February 2019): 114–22. http://dx.doi.org/10.1016/j.cois.2018.12.006.

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22

Sattelle, David B., Andrew K. Jones, and Steven D. Buckingham. "Insect genomes: challenges and opportunities for Neuroscience." Invertebrate Neuroscience 7, no. 3 (2007): 133–36. http://dx.doi.org/10.1007/s10158-007-0054-2.

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23

Jones, Julia C., Andreas Wallberg, Matthew J. Christmas, Karen M. Kapheim, and Matthew T. Webster. "Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee." Molecular Biology and Evolution 36, no. 10 (2019): 2277–91. http://dx.doi.org/10.1093/molbev/msz130.

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Abstract Social insect genomes exhibit the highest rates of crossing over observed in plants and animals. The evolutionary causes of these extreme rates are unknown. Insight can be gained by comparing recombination rate variation across the genomes of related social and solitary insects. Here, we compare the genomic recombination landscape of the highly social honey bee, Apis mellifera, with the solitary alfalfa leafcutter bee, Megachile rotundata, by analyzing patterns of linkage disequilibrium in population-scale genome sequencing data. We infer that average recombination rates are extremely

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24

Lindeberg, Magdalen, Christopher R. Myers, Alan Collmer, and David J. Schneider. "Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization." Molecular Plant-Microbe Interactions® 21, no. 6 (2008): 685–700. http://dx.doi.org/10.1094/mpmi-21-6-0685.

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Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syr

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25

Stewart, James Bruce, and Andrew T. Beckenbach. "Insect mitochondrial genomics 2: the complete mitochondrial genome sequence of a giant stonefly, Pteronarcys princeps, asymmetric directional mutation bias, and conserved plecopteran A+T-region elements." Genome 49, no. 7 (2006): 815–24. http://dx.doi.org/10.1139/g06-037.

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Mitochondrial (mt) genome sequences of insects are receiving renewed attention in molecular phylogentic studies, studies of mt-genome rearrangement, and other unusual molecular phenomena, such as translational frameshifting. At present, the basal neopteran lineages are poorly represented by mt-genome sequences. Complete mt-genome sequences are available in the databases for only the Orthoptera and Blatteria; 9 orders are unrepresented. Here, we present the complete mt-genome sequence of a giant stonefly, Pteronarcys princeps (Plecoptera; Pteronarcyidae). The 16 004 bp genome is typical in its

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26

Gilbert, Clément, Jean Peccoud, and Richard Cordaux. "Transposable Elements and the Evolution of Insects." Annual Review of Entomology 66, no. 1 (2021): 355–72. http://dx.doi.org/10.1146/annurev-ento-070720-074650.

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Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between clos

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Walkowiak, Sean, Liangliang Gao, Cecile Monat, et al. "Multiple wheat genomes reveal global variation in modern breeding." Nature 588, no. 7837 (2020): 277–83. http://dx.doi.org/10.1038/s41586-020-2961-x.

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AbstractAdvances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and diff

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Rosario, Karyna, Anisha Dayaram, Milen Marinov, et al. "Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta)." Journal of General Virology 93, no. 12 (2012): 2668–81. http://dx.doi.org/10.1099/vir.0.045948-0.

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Viruses with circular ssDNA genomes that encode a replication initiator protein (Rep) are among the smallest viruses known to infect both eukaryotic and prokaryotic organisms. In the past few years an overwhelming diversity of novel circular Rep-encoding ssDNA (CRESS-DNA) viruses has been unearthed from various hosts and environmental sources. Since there is limited information regarding CRESS-DNA viruses in invertebrates, this study explored the diversity of CRESS-DNA viruses circulating among insect populations by targeting dragonflies (Epiprocta), top insect predators that accumulate viruse

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Wang, Xiaozhu, Xiao Xiong, Wenqi Cao, Chao Zhang, John H. Werren, and Xu Wang. "Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology." Genome Biology and Evolution 11, no. 10 (2019): 3008–13. http://dx.doi.org/10.1093/gbe/evz223.

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Abstract Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intrace

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Asma, Hasiba, and Marc S. Halfon. "Annotating the Insect Regulatory Genome." Insects 12, no. 7 (2021): 591. http://dx.doi.org/10.3390/insects12070591.

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An ever-growing number of insect genomes is being sequenced across the evolutionary spectrum. Comprehensive annotation of not only genes but also regulatory regions is critical for reaping the full benefits of this sequencing. Driven by developments in sequencing technologies and in both empirical and computational discovery strategies, the past few decades have witnessed dramatic progress in our ability to identify cis-regulatory modules (CRMs), sequences such as enhancers that play a major role in regulating transcription. Nevertheless, providing a timely and comprehensive regulatory annotat

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31

Hill, Kathleen A., and Shiva M. Singh. "The evolution of species-type specificity in the global DNA sequence organization of mitochondrial genomes." Genome 40, no. 3 (1997): 342–56. http://dx.doi.org/10.1139/g97-047.

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Prokaryote genomes and nuclear genomes of eukaryotes have a global DNA sequence organization that is species type specific, determined primarily by nearest-neighbor nucleotide associations, and independent of gene function and sequence length. The determinants of such a global structure have remained largely uncharacterized. The monophyletic and endosymbiotic origin of mitochondria permit examination of the influence of evolutionary time and host species type. Different global structures were seen among (i) protozoan and plant, (ii) fungal, (iii) algal (iv) nematode, (v) echinoderm, (vi) insec

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Takeshita, Kazutaka, and Yoshitomo Kikuchi. "Genomic Comparison of Insect Gut Symbionts from Divergent Burkholderia Subclades." Genes 11, no. 7 (2020): 744. http://dx.doi.org/10.3390/genes11070744.

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Stink bugs of the superfamilies Coreoidea and Lygaeoidea establish gut symbioses with environmentally acquired bacteria of the genus Burkholderia sensu lato. In the genus Burkholderia, the stink bug-associated strains form a monophyletic clade, named stink bug-associated beneficial and environmental (SBE) clade (or Caballeronia). Recently, we revealed that members of the family Largidae of the superfamily Pyrrhocoroidea are associated with Burkholderia but not specifically with the SBE Burkholderia; largid bugs harbor symbionts that belong to a clade of plant-associated group of Burkholderia,

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Cui, Jie, and Edward C. Holmes. "Endogenous RNA viruses of plants in insect genomes." Virology 427, no. 2 (2012): 77–79. http://dx.doi.org/10.1016/j.virol.2012.02.014.

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34

Yin, Chuanlin, Gengyu Shen, Dianhao Guo, et al. "InsectBase: a resource for insect genomes and transcriptomes." Nucleic Acids Research 44, no. D1 (2015): D801—D807. http://dx.doi.org/10.1093/nar/gkv1204.

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35

Blanchetot, Alain. "Detection of highly polymorphic regions in insect genomes." Nucleic Acids Research 17, no. 8 (1989): 3313. http://dx.doi.org/10.1093/nar/17.8.3313.

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36

Gorrochotegui-Escalante, N., and W. C. Black IV. "Amplifying whole insect genomes with multiple displacement amplification." Insect Molecular Biology 12, no. 2 (2003): 195–200. http://dx.doi.org/10.1046/j.1365-2583.2003.00401.x.

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DUNKOV, B., and T. GEORGIEVA. "Insect iron binding proteins: Insights from the genomes." Insect Biochemistry and Molecular Biology 36, no. 4 (2006): 300–309. http://dx.doi.org/10.1016/j.ibmb.2006.01.007.

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Gloss, Andrew D., Patrick Abbot, and Noah K. Whiteman. "How interactions with plant chemicals shape insect genomes." Current Opinion in Insect Science 36 (December 2019): 149–56. http://dx.doi.org/10.1016/j.cois.2019.09.005.

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Schmidt, Hanno, Sören Lukas Hellmann, Ann-Marie Waldvogel, Barbara Feldmeyer, Thomas Hankeln, and Markus Pfenninger. "A High-Quality Genome Assembly from Short and Long Reads for the Non-biting Midge Chironomus riparius (Diptera)." G3: Genes|Genomes|Genetics 10, no. 4 (2020): 1151–57. http://dx.doi.org/10.1534/g3.119.400710.

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Chironomus riparius is of great importance as a study species in various fields like ecotoxicology, molecular genetics, developmental biology and ecology. However, only a fragmented draft genome exists to date, hindering the recent rush of population genomic studies in this species. Making use of 50 NGS datasets, we present a hybrid genome assembly from short and long sequence reads that make C. riparius’ genome one of the most contiguous Dipteran genomes published, the first complete mitochondrial genome of the species, and the respective recombination rate among the first insect recombinatio

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Matsuura, Yu, Minoru Moriyama, Piotr Łukasik, et al. "Recurrent symbiont recruitment from fungal parasites in cicadas." Proceedings of the National Academy of Sciences 115, no. 26 (2018): E5970—E5979. http://dx.doi.org/10.1073/pnas.1803245115.

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Diverse insects are associated with ancient bacterial symbionts, whose genomes have often suffered drastic reduction and degeneration. In extreme cases, such symbiont genomes seem almost unable to sustain the basic cellular functioning, which comprises an open question in the evolution of symbiosis. Here, we report an insect group wherein an ancient symbiont lineage suffering massive genome erosion has experienced recurrent extinction and replacement by host-associated pathogenic microbes. Cicadas are associated with the ancient bacterial co-obligate symbiontsSulciaandHodgkinia, whose streamli

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Rafael, Míriam Silva, Leticia Cegatti Bridi, Igor V. Sharakhov, et al. "Physical Mapping of the Anopheles (Nyssorhynchus) darlingi Genomic Scaffolds." Insects 12, no. 2 (2021): 164. http://dx.doi.org/10.3390/insects12020164.

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The genome assembly of Anopheles darlingi consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among Anopheles species. Anopheles darlingi genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the An. darlingi scaffolds with homologous sequences of the Anopheles albimanus and Anopheles gambiae genomes identifie

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Jing, Xiangfeng, Thomas A. White, Xiaowei Yang, and Angela E. Douglas. "The molecular correlates of organ loss: the case of insect Malpighian tubules." Biology Letters 11, no. 5 (2015): 20150154. http://dx.doi.org/10.1098/rsbl.2015.0154.

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Malpighian tubules play an essential role in excretion, osmoregulation and immunity of most insects. Exceptionally, aphids lack Malpighian tubules, providing the opportunity to investigate the fate of genes expressed in an organ that has undergone evolutionary reduction and loss. Making use of the sequenced genomes of Drosophila melanogaster and the pea aphid Acyrthosiphon pisum , we demonstrated that more than 50% of Drosophila genes expressed specifically in the Malpighian tubules had orthologues in the pea aphid genome and that most of the pea aphid orthologues with detectable expression we

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Deutsch, Manuel J., Elisabeth Ott, Peer Papior, and Aloys Schepers. "The Latent Origin of Replication of Epstein-Barr Virus Directs Viral Genomes to Active Regions of the Nucleus." Journal of Virology 84, no. 5 (2009): 2533–46. http://dx.doi.org/10.1128/jvi.01909-09.

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ABSTRACT The Epstein-Barr virus efficiently infects human B cells. The EBV genome is maintained extrachromosomally and replicates synchronously with the host's chromosomes. The latent origin of replication (oriP) guarantees plasmid stability by mediating two basic functions: replication and segregation of the viral genome. While the segregation process of EBV genomes is well understood, little is known about its chromatin association and nuclear distribution during interphase. Here, we analyzed the nuclear localization of EBV genomes and the role of functional oriP domains FR and DS for basic

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Wu, Yi, Yangming Lan, Liyuan Xia, et al. "The First Complete Mitochondrial Genomes of Two Sibling Species from Nitidulid Beetles Pests." Insects 11, no. 1 (2019): 24. http://dx.doi.org/10.3390/insects11010024.

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Carpophilus dimidiatus (Fabricius, 1792) and Carpophilus pilosellus Motschulsky are two sibling species and economically important storage pests worldwide. The first complete mitochondrial (mt) genomes of both were sequenced using next-generation sequencing. The mt genomes of C. dimidiatus and C. pilosellus are circular, with total lengths of 15,717 bp and 15,686 bp, respectively. Gene order and content for both species are similar to what has been observed in ancestral insects and consist of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and a control region. Compari

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Miele, Solange Ana Belen, Matías Javier Garavaglia, Mariano Nicolás Belaich, and Pablo Daniel Ghiringhelli. "Baculovirus: Molecular Insights on Their Diversity and Conservation." International Journal of Evolutionary Biology 2011 (April 11, 2011): 1–15. http://dx.doi.org/10.4061/2011/379424.

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The Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp. In this study, genome sequences from 57 baculoviruses were analyzed to reevaluate the number and identity of core genes and to understand the distribution of the remaining coding sequences. Thirty one core genes with orthologs in all genomes were identified along with other 895 genes differing in their degrees of representation among reported genomes. Many of these latter genes are common to well-defined lineages, whereas others are unique to one or a few of the viruses. Phylo

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Clark, Alvin J., Mauricio Pontes, Tait Jones, and Colin Dale. "A Possible Heterodimeric Prophage-Like Element in the Genome of the Insect Endosymbiont Sodalis glossinidius." Journal of Bacteriology 189, no. 7 (2007): 2949–51. http://dx.doi.org/10.1128/jb.00913-06.

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ABSTRACT Extrachromosomal element pSOG3 (52,162 nucleotides) in the genome of Sodalis glossinidius contains redundant phage-related gene pairs, indicating that it may have been formed by the fusion of two ancestral phage genomes followed by gene degradation. We suggest that pSOG3 is a prophage that has undergone genome degeneration accompanying host adaptation to symbiosis.

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Masri, Reem A., Dmitriy A. Karagodin, Atashi Sharma, and Maria V. Sharakhova. "A Gene-Based Method for Cytogenetic Mapping of Repeat-Rich Mosquito Genomes." Insects 12, no. 2 (2021): 138. http://dx.doi.org/10.3390/insects12020138.

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Long-read sequencing technologies have opened up new avenues of research on the mosquito genome biology, enabling scientists to better understand the remarkable abilities of vectors for transmitting pathogens. Although new genome mapping technologies such as Hi-C scaffolding and optical mapping may significantly improve the quality of genomes, only cytogenetic mapping, with the help of fluorescence in situ hybridization (FISH), connects genomic scaffolds to a particular chromosome and chromosome band. This mapping approach is important for creating and validating chromosome-scale genome assemb

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Steinwaerder, Dirk S., Cheryl A. Carlson, and André Lieber. "Generation of Adenovirus Vectors Devoid of All Viral Genes by Recombination between Inverted Repeats." Journal of Virology 73, no. 11 (1999): 9303–13. http://dx.doi.org/10.1128/jvi.73.11.9303-9313.1999.

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ABSTRACT Direct or inverse repeated sequences are important functional features of prokaryotic and eukaryotic genomes. Considering the unique mechanism, involving single-stranded genomic intermediates, by which adenovirus (Ad) replicates its genome, we investigated whether repetitive homologous sequences inserted into E1-deleted adenoviral vectors would affect replication of viral DNA. In these studies we found that inverted repeats (IRs) inserted into the E1 region could mediate predictable genomic rearrangements, resulting in vector genomes devoid of all viral genes. These genomes (termed ΔA

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McDonagh, Laura M., Helen West, James W. Harrison, and Jamie R. Stevens. "Which mitochondrial gene (if any) is best for insect phylogenetics?" Insect Systematics & Evolution 47, no. 3 (2016): 245–66. http://dx.doi.org/10.1163/1876312x-47032142.

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Despite the benefits of whole-genome analysis, in many instances — particularly in applied entomology — mitochondrial genes continue to offer a reliable, rapid and cheap alternative. To date, most studies using insect mitochondrial DNA have analysed single genes and none have rigorously attempted to assess which genes are best suited for studying particular insect orders; here, we address this issue and use the ability of individual genes to recover ordinal monophyly of various insect orders as a metric. Phylogenies were constructed for nine insect orders and three outgroups, using 12 protein-

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Borst, Eva-Maria, and Martin Messerle. "Analysis of Human Cytomegalovirus oriLyt Sequence Requirements in the Context of the Viral Genome." Journal of Virology 79, no. 6 (2005): 3615–26. http://dx.doi.org/10.1128/jvi.79.6.3615-3626.2005.

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ABSTRACT During the lytic phase of infection, replication of herpesvirus genomes initiates at the lytic origin of replication, oriLyt. Many herpesviruses harbor more than one lytic origin, but so far, only one oriLyt has been identified for human cytomegalovirus (HCMV). Evidence for the existence of additional lytic origins of HCMV has remained elusive. On the basis of transient replication assays with cloned viral fragments, HCMV oriLyt was described as a core region of 1.5 kbp (minimal oriLyt) flanked by auxiliary sequences required for maximal replication activity (complete oriLyt). It rema

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