Journal articles: 'Genomic comparisons'

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Flanagan, Keith, Robert Stevens, Matthew Pocock, Pete Lee, and Anil Wipat. "Ontology for Genome Comparison and Genomic Rearrangements." Comparative and Functional Genomics 5, no. 6-7 (2004): 537–44. http://dx.doi.org/10.1002/cfg.436.

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We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

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Mrázek, Jan, Alfred M. Spormann, and Samuel Karlin. "Genomic comparisons among ?-proteobacteria." Environmental Microbiology 8, no. 2 (February 2006): 273–88. http://dx.doi.org/10.1111/j.1462-2920.2005.00894.x.

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Karlin, S., and I. Ladunga. "Comparisons of eukaryotic genomic sequences." Proceedings of the National Academy of Sciences 91, no. 26 (December 20, 1994): 12832–36. http://dx.doi.org/10.1073/pnas.91.26.12832.

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Tekaia, Fredj, Antonio Lazcano, and Bernard Dujon. "The Genomic Tree as Revealed from Whole Proteome Comparisons." Genome Research 9, no. 6 (June 1, 1999): 550–57. http://dx.doi.org/10.1101/gr.9.6.550.

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The availability of a number of complete cellular genome sequences allows the development of organisms’ classification, taking into account their genome content, the loss or acquisition of genes, and overall gene similarities as signatures of common ancestry. On the basis of correspondence analysis and hierarchical classification methods, a methodological framework is introduced here for the classification of the available 20 completely sequenced genomes and partial information for Schizosaccharomyces pombe, Homo sapiens, and Mus musculus. The outcome of such an analysis leads to a classification of genomes that we call a genomic tree. Although these trees are phenograms, they carry with them strong phylogenetic signatures and are remarkably similar to 16S-like rRNA-based phylogenies. Our results suggest that duplication and deletion events that took place through evolutionary time were globally similar in related organisms. The genomic trees presented here place the Archaea in the proximity of the Bacteria when the whole gene content of each organism is considered, and when ancestral gene duplications are eliminated. Genomic trees represent an additional approach for the understanding of evolution at the genomic level and may contribute to the proper assessment of the evolutionary relationships between extant species.

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Varki, Ajit, and David L. Nelson. "Genomic Comparisons of Humans and Chimpanzees." Annual Review of Anthropology 36, no. 1 (September 2007): 191–209. http://dx.doi.org/10.1146/annurev.anthro.36.081406.094339.

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Diaz-del-Pino, Sergio, Esteban Perez-Wohlfeil, and Oswaldo Trelles. "Unraveling Genome Evolution Throughout Visual Analysis: The XCout Portal." Bioinformatics and Biology Insights 15 (January 2021): 117793222110214. http://dx.doi.org/10.1177/11779322211021422.

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Due to major breakthroughs in sequencing technologies throughout the last decades, the time and cost per sequencing experiment have reduced drastically, overcoming the data generation barrier during the early genomic era. Such a shift has encouraged the scientific community to develop new computational methods that are able to compare large genomic sequences, thus enabling large-scale studies of genome evolution. The field of comparative genomics has proven itself invaluable for studying the evolutionary mechanisms and the forces driving genome evolution. In this line, a full genome comparison study between 2 species requires a quadratic number of comparisons in terms of the number of sequences (around 400 chromosome comparisons in the case of mammalian genomes); however, when studying conserved syntenies or evolutionary rearrangements, many sequence comparisons can be skipped for not all will contain significant signals. Subsequently, the scientific community has developed fast heuristics to perform multiple pairwise comparisons between large sequences to determine whether significant sets of conserved similarities exist. The data generation problem is no longer an issue, yet the limitations have shifted toward the analysis of such massive data. Therefore, we present XCout, a Web-based visual analytics application for multiple genome comparisons designed to improve the analysis of large-scale evolutionary studies using novel techniques in Web visualization. XCout enables to work on hundreds of comparisons at once, thus reducing the time of the analysis by identifying significant signals between chromosomes across multiple species. Among others, XCout introduces several techniques to aid in the analysis of large-scale genome rearrangements, particularly (1) an interactive heatmap interface to display comparisons using automatic color scales based on similarity thresholds to ease detection at first sight, (2) an overlay system to detect individual signal contributions between chromosomes, (3) a tracking tool to trace conserved blocks across different species to perform evolutionary studies, and (4) a search engine to search annotations throughout different species.

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Karlin, S., L. Brocchieri, A. Campbell, M. Cyert, and J. Mrazek. "Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes." Proceedings of the National Academy of Sciences 102, no. 20 (May 9, 2005): 7309–14. http://dx.doi.org/10.1073/pnas.0502314102.

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Welsh, Rory M., Elizabeth Misas, Kaitlin Forsberg, Meghan Lyman, and Nancy A. Chow. "Candida auris Whole-Genome Sequence Benchmark Dataset for Phylogenomic Pipelines." Journal of Fungi 7, no. 3 (March 16, 2021): 214. http://dx.doi.org/10.3390/jof7030214.

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Candida auris is a multidrug-resistant pathogen that represents a serious public health threat due to its rapid global emergence, increasing incidence of healthcare-associated outbreaks, and high rates of antifungal resistance. Whole-genome sequencing and genomic surveillance have the potential to bolster C. auris surveillance networks moving forward. Laboratories conducting genomic surveillance need to be able to compare analyses from various national and international surveillance partners to ensure that results are mutually trusted and understood. Therefore, we established an empirical outbreak benchmark dataset consisting of 23 C. auris genomes to help validate comparisons of genomic analyses and facilitate communication among surveillance networks. Our outbreak benchmark dataset represents a polyclonal phylogeny with three subclades. The genomes in this dataset are from well-vetted studies that are supported by multiple lines of evidence, which demonstrate that the whole-genome sequencing data, phylogenetic tree, and epidemiological data are all in agreement. This C. auris benchmark set allows for standardized comparisons of phylogenomic pipelines, ultimately promoting effective C. auris collaborations.

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Cork, Douglas J., Steven Lembark, Sodsai Tovanabutra, Merlin L. Robb, and Jerome H. Kim. "W-Curve Alignments for HIV-1 Genomic Comparisons." PLoS ONE 5, no. 6 (June 1, 2010): e10829. http://dx.doi.org/10.1371/journal.pone.0010829.

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Sahl, Jason W., Hans Steinsland, Julia C. Redman, Samuel V. Angiuoli, James P. Nataro, Halvor Sommerfelt, and David A. Rasko. "A Comparative Genomic Analysis of Diverse Clonal Types of EnterotoxigenicEscherichia coliReveals Pathovar-Specific Conservation." Infection and Immunity 79, no. 2 (November 15, 2010): 950–60. http://dx.doi.org/10.1128/iai.00932-10.

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ABSTRACTEnterotoxigenicEscherichia coli(ETEC) is a major cause of diarrheal illness in children less than 5 years of age in low- and middle-income nations, whereas it is an emerging enteric pathogen in industrialized nations. Despite being an important cause of diarrhea, little is known about the genomic composition of ETEC. To address this, we sequenced the genomes of five ETEC isolates obtained from children in Guinea-Bissau with diarrhea. These five isolates represent distinct and globally dominant ETEC clonal groups. Comparative genomic analyses utilizing a gene-independent whole-genome alignment method demonstrated that sequenced ETEC strains share approximately 2.7 million bases of genomic sequence. Phylogenetic analysis of this “core genome” confirmed the diverse history of the ETEC pathovar and provides a finer resolution of theE. colirelationships than multilocus sequence typing. No identified genomic regions were conserved exclusively in all ETEC genomes; however, we identified more genomic content conserved among ETEC genomes than among non-ETECE. coligenomes, suggesting that ETEC isolates share a genomic core. Comparisons of known virulence and of surface-exposed and colonization factor genes across all sequenced ETEC genomes not only identified variability but also indicated that some antigens are restricted to the ETEC pathovar. Overall, the generation of these five genome sequences, in addition to the two previously generated ETEC genomes, highlights the genomic diversity of ETEC. These studies increase our understanding of ETEC evolution, as well as provide insight into virulence factors and conserved proteins, which may be targets for vaccine development.

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Nguyen, Nga Thi Thuy, Pierre Vincens, Jean François Dufayard, Hugues Roest Crollius, and Alexandra Louis. "Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors." Nucleic Acids Research 50, no. D1 (November 18, 2021): D1025—D1031. http://dx.doi.org/10.1093/nar/gkab1091.

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Abstract Genomicus is a database and web-server dedicated to comparative genomics in eukaryotes. Its main functionality is to graphically represent the conservation of genomic blocks between multiple genomes, locally around a specific gene of interest or genome-wide through karyotype comparisons. Since 2010 and its first release, Genomicus has synchronized with 60 Ensembl releases and seen the addition of functions that have expanded the type of analyses that users can perform. Today, five public instances of Genomicus are supporting a total number of 1029 extant genomes and 621 ancestral reconstructions from all eukaryotes kingdoms available in Ensembl and Ensembl Genomes databases complemented with four additional instances specific to taxonomic groups of interest. New visualization and query tools are described in this manuscript. Genomicus is freely available at http://www.genomicus.bio.ens.psl.eu/genomicus.

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Xiong, Zhi Yong, Guang Xuan Tan, Guang Yuan He, Guang Cun He, and Yun Chun Song. "Cytogenetic comparisons between A and G genomes in Oryza using genomic in situ hybridization." Cell Research 16, no. 3 (March 2006): 260–66. http://dx.doi.org/10.1038/sj.cr.7310033.

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Li, Ning, Gui-Lin Hu, and Bao-Zhen Hua. "Complete mitochondrial genomes of Bittacus strigosus and Panorpa debilis and genomic comparisons of Mecoptera." International Journal of Biological Macromolecules 140 (November 2019): 672–81. http://dx.doi.org/10.1016/j.ijbiomac.2019.08.152.

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Lo, Van Thi, Sun Woo Yoon, Yong Gun Choi, Dae Gwin Jeong, and Hye Kwon Kim. "Genomic Comparisons of Alphacoronaviruses and Betacoronaviruses from Korean Bats." Viruses 14, no. 7 (June 25, 2022): 1389. http://dx.doi.org/10.3390/v14071389.

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Coronaviruses are well known as a diverse family of viruses that affect a wide range of hosts. Since the outbreak of severe acute respiratory syndrome, a variety of bat-associated coronaviruses have been identified in many countries. However, they do not represent all the specific geographic locations of their hosts. In this study, full-length genomes representing newly identified bat coronaviruses in South Korea were obtained using an RNA sequencing approach. The analysis, based on genome structure, conserved replicase domains, spike gene, and nucleocapsid genes revealed that bat Alphacoronaviruses are from three different viral species. Among them, the newly identified B20-97 strain may represent a new putative species, closely related to PEDV. In addition, the newly-identified MERS-related coronavirus exhibited shared genomic nucleotide identities of less than 76.4% with other Merbecoviruses. Recombination analysis and multiple alignments of spike and RBD amino acid sequences suggested that this strain underwent recombination events and could possibly use hDPP4 molecules as its receptor. The bat SARS-related CoV B20-50 is unlikely to be able to use hACE2 as its receptor and lack of an open reading frame in ORF8 gene region. Our results illustrate the diversity of coronaviruses in Korean bats and their evolutionary relationships. The evolution of the bat coronaviruses related ORF8 accessory gene is also discussed.

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Mardis, Elaine R., Peter Humphrey, Sean McGrath, Ryan Demeter, Vincent Magrini, Nathan Dees, Krishna Kanthi, Christopher Maher, Li Ding, and Adam Kibel. "Abstract IA2: Genomic comparisons of coincident prostate cancer foci." Cancer Research 72, no. 4 Supplement (February 6, 2012): IA2. http://dx.doi.org/10.1158/1538-7445.prca2012-ia2.

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Karlin, S., E. S. Mocarski, and G. A. Schachtel. "Molecular evolution of herpesviruses: genomic and protein sequence comparisons." Journal of Virology 68, no. 3 (1994): 1886–902. http://dx.doi.org/10.1128/jvi.68.3.1886-1902.1994.

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Achtman, Mark. "Insights from genomic comparisons of genetically monomorphic bacterial pathogens." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1590 (March 19, 2012): 860–67. http://dx.doi.org/10.1098/rstb.2011.0303.

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Some of the most deadly bacterial diseases, including leprosy, anthrax and plague, are caused by bacterial lineages with extremely low levels of genetic diversity, the so-called ‘genetically monomorphic bacteria’. It has only become possible to analyse the population genetics of such bacteria since the recent advent of high-throughput comparative genomics. The genomes of genetically monomorphic lineages contain very few polymorphic sites, which often reflect unambiguous clonal genealogies. Some genetically monomorphic lineages have evolved in the last decades, e.g. antibiotic-resistant Staphylococcus aureus , whereas others have evolved over several millennia, e.g. the cause of plague, Yersinia pestis . Based on recent results, it is now possible to reconstruct the sources and the history of pandemic waves of plague by a combined analysis of phylogeographic signals in Y. pestis plus polymorphisms found in ancient DNA. Different from historical accounts based exclusively on human disease, Y. pestis evolved in China, or the vicinity, and has spread globally on multiple occasions. These routes of transmission can be reconstructed from the genealogy, most precisely for the most recent pandemic that was spread from Hong Kong in multiple independent waves in 1894.

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HESLOP-HARRISON, J. S. "Molecular cytogenetics, cytology and genomic comparisons in the Triticeae." Hereditas 116, no. 1-2 (February 14, 2008): 93–99. http://dx.doi.org/10.1111/j.1601-5223.1992.tb00210.x.

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HESLOP-HARRISON, J. S. "Molecular cytogenetics, cytology and genomic comparisons in the Triticeae." Hereditas 116 (February 14, 2008): 93–99. http://dx.doi.org/10.1111/j.1601-5223.1992.tb00805.x.

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Sendell-Price, Ashley T., Kristen C. Ruegg, Eric C. Anderson, Claudio S. Quilodrán, Benjamin M. Van Doren, Vinh L. Underwood, Tim Coulson, and Sonya M. Clegg. "The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes (Zosterops lateralis)." G3 Genes|Genomes|Genetics 10, no. 9 (September 1, 2020): 3147–63. http://dx.doi.org/10.1534/g3.120.401352.

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Abstract Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.

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Zhou, Shiguo, Andrew Kile, Michael Bechner, Michael Place, Erika Kvikstad, Wen Deng, Jun Wei, et al. "Single-Molecule Approach to Bacterial Genomic Comparisons via Optical Mapping." Journal of Bacteriology 186, no. 22 (November 15, 2004): 7773–82. http://dx.doi.org/10.1128/jb.186.22.7773-7782.2004.

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ABSTRACT Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.

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Boore, Jeffrey L., and Susan I. Fuerstenberg. "Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1496 (January 11, 2008): 1445–51. http://dx.doi.org/10.1098/rstb.2007.2234.

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The first whole genomes to be compared for phylogenetic inference were those of mitochondria, which provided the first sets of genome-level characters for phylogenetic reconstruction. Most powerful among these characters has been the comparisons of the relative arrangements of genes, which has convincingly resolved numerous branch points, including those that had remained recalcitrant even to very large molecular sequence comparisons. Now the world faces a tsunami of complete nuclear genome sequences. In addition to the tremendous amount of DNA sequence that is becoming available for comparison, there is also a potential for many more genome-level characters to be developed, including the relative positions of introns, the domain structures of proteins, gene family membership, the presence of particular biochemical pathways, aspects of DNA replication or transcription, and many others. These characters can be especially convincing owing to their low likelihood of reverting to a primitive condition or occurring independently in separate lineages, thereby reducing the occurrence of homoplasy. The comparisons of organelle genomes pioneered the way for using such features for phylogenetic reconstructions, and it is almost certainly true, as ever more genomic sequence becomes available, that further use of genome-level characters will play a big role in outlining the relationships among major animal groups.

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Dunn, Casey W., Felipe Zapata, Catriona Munro, Stefan Siebert, and Andreas Hejnol. "Pairwise comparisons across species are problematic when analyzing functional genomic data." Proceedings of the National Academy of Sciences 115, no. 3 (January 4, 2018): E409—E417. http://dx.doi.org/10.1073/pnas.1707515115.

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There is considerable interest in comparing functional genomic data across species. One goal of such work is to provide an integrated understanding of genome and phenotype evolution. Most comparative functional genomic studies have relied on multiple pairwise comparisons between species, an approach that does not incorporate information about the evolutionary relationships among species. The statistical problems that arise from not considering these relationships can lead pairwise approaches to the wrong conclusions and are a missed opportunity to learn about biology that can only be understood in an explicit phylogenetic context. Here, we examine two recently published studies that compare gene expression across species with pairwise methods, and find reason to question the original conclusions of both. One study interpreted pairwise comparisons of gene expression as support for the ortholog conjecture, the hypothesis that orthologs tend to have more similar attributes (expression in this case) than paralogs. The other study interpreted pairwise comparisons of embryonic gene expression across distantly related animals as evidence for a distinct evolutionary process that gave rise to phyla. In each study, distinct patterns of pairwise similarity among species were originally interpreted as evidence of particular evolutionary processes, but instead, we find that they reflect species relationships. These reanalyses concretely show the inadequacy of pairwise comparisons for analyzing functional genomic data across species. It will be critical to adopt phylogenetic comparative methods in future functional genomic work. Fortunately, phylogenetic comparative biology is also a rapidly advancing field with many methods that can be directly applied to functional genomic data.

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Dadvar, Ehsan. "Genomic and Phenotypic Variability of Mycobaterium avium Subspecies." McGill Science Undergraduate Research Journal 5, no. 1 (March 31, 2010): 11–17. http://dx.doi.org/10.26443/msurj.v5i1.67.

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Introduction: Mycobacterium avium complex consists of M. intracellulare and the subspecies of M. avium subsp. avium, M. avium subsp. paratuberculosis and M. avium subsp. hominissuis. Despite their taxonomic relationship, these subspecies are organisms with distinct phenotypes, ranging from environmental bacteria that cause infections in immunocompromised hosts to pathogens targeting birds and ruminants. The reasons for the variable pathogenicity and host range of M. avium subspecies are not known. We hypothesize that genotypic differences between M. avium subsp. avium and M. avium subsp. paraturberculosis can explain different pathogenic outcomes. Methods: We used tri-genomic comparisons to look for DNA fragments unique to each subspecies. We also used an acute model of mouse infection to determine different phenotypic outcomes in response to infection with different Mycobacterium subspecies. results: Through tri-genomic comparisons we identified genetic regions of interest that may contain genes to explain phenotypic or pathogenic differences among subspecies. In an 8 week course infection, mice infected with M. avium subspecies avium had the highest bacterial burden in their spleens and livers. at the same time, mice infected with M. avium subspecies paraturberculosis had the lowest bacterial burden. discussion: Differences in the genomic sequences of the M. avium subspecies suggests that these sequences encode pathogenic factors. Consequently, this study shows that the sequencing of M. avium subspecies genomes can be useful for predicting and explaining variation in pathogenesis.

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Cormier, Danielle Taylor, Autumn Brooke Berry, Matthew Rhodes, and Jeffrey Copeland. "What makes humans human? a review of important genetic differences between chimpanzees and humans." Journal of Student Research 6, no. 2 (December 31, 2017): 1–6. http://dx.doi.org/10.47611/jsr.v6i2.291.

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What makes humans human? Genomic comparisons of humans and chimpanzees provide a new tool for addressing this interesting question. Genetic comparisons show remarkable similarity between chimpanzees and humans; indeed, the human and chimp genome are 96% similar, with only a 1% difference in nucleotide substitutions and a 3% difference in chromosomal insertions and deletions. But even modest differences in genomes can have profound biological effects. In this review, we tackle this formidable topic by summarizing the effects of transposon mobility, uniquely human genes and small nucleotide changes in conferring important phenotypic changes from chimpanzee to human.

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Acs-Szabo, Lajos, Laszlo Attila Papp, Matthias Sipiczki, and Ida Miklos. "Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection." Journal of Fungi 7, no. 10 (October 14, 2021): 864. http://dx.doi.org/10.3390/jof7100864.

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Fission yeasts have a unique life history and exhibit distinct evolutionary patterns from other yeasts. Besides, the species demonstrate stable genome structures despite the relatively fast evolution of their genomic sequences. To reveal what could be the reason for that, comparative genomic analyses were carried out. Our results provided evidence that the structural and sequence evolution of the fission yeasts were correlated. Moreover, we revealed ancestral locally collinear blocks (aLCBs), which could have been inherited from their last common ancestor. These aLCBs proved to be the most conserved regions of the genomes as the aLCBs contain almost eight genes/blocks on average in the same orientation and order across the species. Gene order of the aLCBs is mainly fission-yeast-specific but supports the idea of filamentous ancestors. Nevertheless, the sequences and gene structures within the aLCBs are as mutable as any sequences in other parts of the genomes. Although genes of certain Gene Ontology (GO) categories tend to cluster at the aLCBs, those GO enrichments are not related to biological functions or high co-expression rates, they are, rather, determined by the density of essential genes and Rec12 cleavage sites. These data and our simulations indicated that aLCBs might not only be remnants of ancestral gene order but are also maintained by natural selection.

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Louis, Alexandra, Emmanuelle Ollivier, Jean-Christophe Aude, and Jean-Loup Risler. "Massive Sequence Comparisons as a Help in Annotating Genomic Sequences." Genome Research 11, no. 7 (June 12, 2001): 1296–303. http://dx.doi.org/10.1101/gr.177601.

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An all-by-all comparison of all the publicly available protein sequences from plants has been performed, followed by a clusterization process. Within each of the 1064 resulting clusters—containing sequences that are orthologous as well as paralogous—the sequences have been submitted to a pyramidal classification and their domains delineated by an automated procedure à la PRODOM. This process provides a means for easily checking for any apparent inconsistency in a cluster, for example, whether one sequence is shorter or longer than the others, one domain is missing, etc. In such cases, the alignment of the DNA sequence of the gene with that of a close homologous protein often reveals (in 10% of the clusters) probable sequencing errors (leading to frameshifts) or probable wrong intron/exon predictions. The composition of the clusters, their pyramidal classifications, and domain decomposition, as well as our comments when appropriate, are available fromhttp://chlora.infobiogen.fr:1234/PHYTOPROT.

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Louis, A. "Massive Sequence Comparisons as a Help in Annotating Genomic Sequences." Genome Research 11, no. 7 (June 12, 2001): 1296–303. http://dx.doi.org/10.1101/gr.gr-1776r.

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Leinonen, Tuomas, R. J. Scott McCairns, Robert B. O'Hara, and Juha Merilä. "QST–FST comparisons: evolutionary and ecological insights from genomic heterogeneity." Nature Reviews Genetics 14, no. 3 (February 5, 2013): 179–90. http://dx.doi.org/10.1038/nrg3395.

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Mochizuki, M., H. Kawabata, and Wang Jin Sheng. "Antigenic and Genomic Comparisons of Some Feline Parvovirus Subspecies Strains." Journal of Veterinary Medicine, Series B 38, no. 1-10 (January 12, 1991): 99–105. http://dx.doi.org/10.1111/j.1439-0450.1991.tb00852.x.

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Rosso, Fernando, and olga Lucia agudelo Rojas. "1296. Genomic Analysis of Human-Associated Outbreak Caused by Salmonella enterica serovar Infantis in Cali, Colombia." Open Forum Infectious Diseases 8, Supplement_1 (November 1, 2021): S736—S737. http://dx.doi.org/10.1093/ofid/ofab466.1488.

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Abstract Background Salmonella enterica serovar Infantis is emerging as a leading cause of foodborne infections. The Colombian National Health Institute reported 263 Infantis among all received Salmonella(n=12,966) from 1997 to 2018 being the 5th most frequent serovar in human clinical samples during this period. In this study, Infantis outbreak-associated isolates were sequenced and collectively analysed with global strains from different sources to compare their genomic content and phylogeny Figure 1. Genomic Comparisons Methods Between September 15-20 of 2019, 160 patients with gastroenteric symptoms resulting from the ingestion of a common food, arrived at Fundación Valle del Lilí. Salmonella spp were cultured from stool specimens of patients and 15 isolates were sent to the Genomic Unit of Agrosavia for whole-genome sequencing. Genomic DNA was sequenced using an Illumina®MiSeqX10 platform. Genome assembly was performed with standardized bioinformatics pipelines and in-silico serotyping with SISTR. Genomic comparisons included newly-sequenced isolates of Infantis(n=6) from a Colombian poultry farms as well as datasets from Patric(n=441) and EnteroBase(n=54). Results The 15 outbreak isolates were identified by in silico serotyping as S. Infantis, these isolates showed phenotypic sensitivity to all tested antibiotics except by tetracycline. Antimicrobial resistance plasmids IncFIBKpn3, IncX4 and the host-environment persistence plasmid pSL483 were only detected in 2 outbreak-related and 1 in poultry isolates. Out of a total of 511 high-quality sequences, ST32 was the most prevalent and were phylogenetically grouped into a single non-host specific clade. Outbreak-isolates were included in a monophyletic group with some genomes from the US and Chile, suggesting that the parent strain could have originated in those countries. Conclusion The magnitude of the outbreak(288 informed-cases) evidenced a high-virulent potential of outbreak-isolates. Routine sequencing of S.enterica and availability of genomes in Colombia can improve outbreak detection and resolution in the future. The presence of plasmids, although with low frequency, suggests a risk of the appearance of resistant clones. Disclosures All Authors: No reported disclosures

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Wallace, Lalena, Sean C. Daugherty, Sushma Nagaraj, J. Kristie Johnson, Anthony D. Harris, and David A. Rasko. "Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution." Antimicrobial Agents and Chemotherapy 60, no. 10 (July 25, 2016): 5933–41. http://dx.doi.org/10.1128/aac.00477-16.

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ABSTRACTDespite the increasing prevalence of the nosocomial pathogenAcinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons ofA. baumanniihave focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates ofAcinetobacterspecies, 203 of which wereA. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, theA. baumanniiisolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups ofA. baumanniiwas comprised solely of strains from the international clonal lineage 2. The genomic content of theA. baumanniiisolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison ofAcinetobacterisolates from a surveillance study to date and provides important information that will contribute to our understanding of the success ofA. baumanniias a human pathogen.

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Maphosa, Mkhululi N., Emma T. Steenkamp, Aquillah M. Kanzi, Stephanie van Wyk, Lieschen De Vos, Quentin C. Santana, Tuan A. Duong, and Brenda D. Wingfield. "Intra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum." Journal of Fungi 8, no. 7 (June 23, 2022): 657. http://dx.doi.org/10.3390/jof8070657.

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Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.

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Yang, Chu-Wen, and Mei-Fang Chen. "Low compositions of human toll-like receptor 7/8-stimulating RNA motifs in the MERS-CoV, SARS-CoV and SARS-CoV-2 genomes imply a substantial ability to evade human innate immunity." PeerJ 9 (February 24, 2021): e11008. http://dx.doi.org/10.7717/peerj.11008.

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Background The innate immune system especially Toll-like receptor (TLR) 7/8 and the interferon pathway, constitutes an important first line of defense against single-stranded RNA viruses. However, large-scale, systematic comparisons of the TLR 7/8-stimulating potential of genomic RNAs of single-stranded RNA viruses are rare. In this study, a computational method to evaluate the human TLR 7/8-stimulating ability of single-stranded RNA virus genomes based on their human TLR 7/8-stimulating trimer compositions was used to analyze 1,002 human coronavirus genomes. Results The human TLR 7/8-stimulating potential of coronavirus genomic (positive strand) RNAs followed the order of NL63-CoV > HKU1-CoV >229E-CoV ≅ OC63-CoV > SARS-CoV-2 > MERS-CoV > SARS-CoV. These results suggest that among these coronaviruses, MERS-CoV, SARS-CoV and SARS-CoV-2 may have a higher ability to evade the human TLR 7/8-mediated innate immune response. Analysis with a logistic regression equation derived from human coronavirus data revealed that most of the 1,762 coronavirus genomic (positive strand) RNAs isolated from bats, camels, cats, civets, dogs and birds exhibited weak human TLR 7/8-stimulating potential equivalent to that of the MERS-CoV, SARS-CoV and SARS-CoV-2 genomic RNAs. Conclusions Prediction of the human TLR 7/8-stimulating potential of viral genomic RNAs may be useful for surveillance of emerging coronaviruses from nonhuman mammalian hosts.

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Ebmeyer, Stefan, Roelof Dirk Coertze, Fanny Berglund, Erik Kristiansson, and D. G. Joakim Larsson. "GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids." Bioinformatics 38, no. 6 (December 24, 2021): 1727–28. http://dx.doi.org/10.1093/bioinformatics/btab855.

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Abstract Summary Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene–loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the >800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView. Availability and implementation GEnView is implemented in Python 3. Instructions for download and usage can be found at https://github.com/EbmeyerSt/GEnView under GLP3. Supplementary information Supplementary data are available at Bioinformatics online.

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Xu, Jie, Michele Frick, André Laroche, Zhong-Fu Ni, Bao-Yun Li, and Zhen-Xiang Lu. "Isolation and characterization of the rye Waxy gene." Genome 52, no. 7 (July 2009): 658–64. http://dx.doi.org/10.1139/g09-036.

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Complete genomic and cDNA sequences of the Waxy gene encoding granule-bound starch synthase I (GBSSI) were isolated from the rye genome and characterized. The full-length rye Waxy genomic DNA and cDNA are 2767 bp and 1815 bp, respectively. The genomic sequence has 11 exons interrupted by 10 introns. The rye Waxy gene is GC-rich, with a higher GC frequency in the coding region, especially in the third position of the codons. Exon regions of the rye Waxy gene are more conserved than intron regions when compared with the homologous sequences of other cereals. The mature rye GBSSI proteins share more than 95% sequence identity with their homologs in wheat and barley. A phylogenetic tree based on sequence comparisons of available plant GBSSI proteins shows the evolutionary relationship among Waxy genes from rye and other plant genomes. The identification of the rye Waxy gene will enable the manipulation of starch metabolism in rye and triticale.

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Beare, Paul A., James E. Samuel, Dale Howe, Kimmo Virtaneva, Stephen F. Porcella, and Robert A. Heinzen. "Genetic Diversity of the Q Fever Agent, Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons." Journal of Bacteriology 188, no. 7 (April 1, 2006): 2309–24. http://dx.doi.org/10.1128/jb.188.7.2309-2324.2006.

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ABSTRACT Coxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups of C. burnetii are revealed by restriction fragment-length polymorphisms (RFLP). Here we comprehensively define the genetic diversity of C. burnetii by hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among all C. burnetii isolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential of Coxiella species.

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Cuevas, Angélica, Fabrice Eroukhmanoff, Mark Ravinet, Glenn-Peter Sætre, and Anna Runemark. "Predictors of genomic differentiation within a hybrid taxon." PLOS Genetics 18, no. 2 (February 11, 2022): e1010027. http://dx.doi.org/10.1371/journal.pgen.1010027.

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Hybridization is increasingly recognized as an important evolutionary force. Novel genetic methods now enable us to address how the genomes of parental species are combined in hybrid lineages. However, we still do not know the relative importance of admixed proportions, genome architecture and local selection in shaping hybrid genomes. Here, we take advantage of the genetically divergent island populations of Italian sparrow on Crete, Corsica and Sicily to investigate the predictors of genomic variation within a hybrid taxon. We test if differentiation is affected by recombination rate, selection, or variation in ancestry proportions. We find that the relationship between recombination rate and differentiation is less pronounced within hybrid lineages than between the parent species, as expected if purging of minor parent ancestry in low recombination regions reduces the variation available for differentiation. In addition, we find that differentiation between islands is correlated with differences in signatures of selection in two out of three comparisons. Signatures of selection within islands are correlated across all islands, suggesting that shared selection may mould genomic differentiation. The best predictor of strong differentiation within islands is the degree of differentiation from house sparrow, and hence loci with Spanish sparrow ancestry may vary more freely. Jointly, this suggests that constraints and selection interact in shaping the genomic landscape of differentiation in this hybrid species.

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Schulz-Streeck, Torben, Joseph O. Ogutu, and Hans-Peter Piepho. "Comparisons of single-stage and two-stage approaches to genomic selection." Theoretical and Applied Genetics 126, no. 1 (August 19, 2012): 69–82. http://dx.doi.org/10.1007/s00122-012-1960-1.

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Cassat, James E., Paul M. Dunman, Fionnuala McAleese, Ellen Murphy, Steven J. Projan, and Mark S. Smeltzer. "Comparative Genomics of Staphylococcus aureus Musculoskeletal Isolates." Journal of Bacteriology 187, no. 2 (January 15, 2005): 576–92. http://dx.doi.org/10.1128/jb.187.2.576-592.2005.

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ABSTRACT Much of the research aimed at defining the pathogenesis of Staphylococcus aureus has been done with a limited number of strains, most notably the 8325-4 derivative RN6390. Several lines of evidence indicate that this strain is unique by comparison to clinical isolates of S. aureus. Based on this, we have focused our efforts on two clinical isolates (UAMS-1 and UAMS-601), both of which are hypervirulent in our animal models of musculoskeletal infection. In this study, we used comparative genomic hybridization to assess the genome content of these two isolates relative to RN6390 and each of seven sequenced S. aureus isolates. Our comparisons were done by using an amplicon-based microarray from the Pathogen Functional Genomics Resource Center and an Affymetrix GeneChip that collectively represent the genomes of all seven sequenced strains. Our results confirmed that UAMS-1 and UAMS-601 share specific attributes that distinguish them from RN6390. Potentially important differences included the presence of cna and the absence of isaB, sarT, sarU, and sasG in the UAMS isolates. Among the sequenced strains, the UAMS isolates were most closely related to the dominant European clone EMRSA-16. In contrast, RN6390, NCTC 8325, and COL formed a distinct cluster that, by comparison to the other four sequenced strains (Mu50, N315, MW2, and SANGER-476), was the most distantly related to the UAMS isolates and EMRSA-16.

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Walker, Conor R., Aylwyn Scally, Nicola De Maio, and Nick Goldman. "Short-range template switching in great ape genomes explored using pair hidden Markov models." PLOS Genetics 17, no. 3 (March 2, 2021): e1009221. http://dx.doi.org/10.1371/journal.pgen.1009221.

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Many complex genomic rearrangements arise through template switch errors, which occur in DNA replication when there is a transient polymerase switch to an alternate template nearby in three-dimensional space. While typically investigated at kilobase-to-megabase scales, the genomic and evolutionary consequences of this mutational process are not well characterised at smaller scales, where they are often interpreted as clusters of independent substitutions, insertions and deletions. Here we present an improved statistical approach using pair hidden Markov models, and use it to detect and describe short-range template switches underlying clusters of mutations in the multi-way alignment of hominid genomes. Using robust statistics derived from evolutionary genomic simulations, we show that template switch events have been widespread in the evolution of the great apes’ genomes and provide a parsimonious explanation for the presence of many complex mutation clusters in their phylogenetic context. Larger-scale mechanisms of genome rearrangement are typically associated with structural features around breakpoints, and accordingly we show that atypical patterns of secondary structure formation and DNA bending are present at the initial template switch loci. Our methods improve on previous non-probabilistic approaches for computational detection of template switch mutations, allowing the statistical significance of events to be assessed. By specifying realistic evolutionary parameters based on the genomes and taxa involved, our methods can be readily adapted to other intra- or inter-species comparisons.

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Scanlan, D. J., M. Ostrowski, S. Mazard, A. Dufresne, L. Garczarek, W. R. Hess, A. F. Post, M. Hagemann, I. Paulsen, and F. Partensky. "Ecological Genomics of Marine Picocyanobacteria." Microbiology and Molecular Biology Reviews 73, no. 2 (June 2009): 249–99. http://dx.doi.org/10.1128/mmbr.00035-08.

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SUMMARY Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus numerically dominate the picophytoplankton of the world ocean, making a key contribution to global primary production. Prochlorococcus was isolated around 20 years ago and is probably the most abundant photosynthetic organism on Earth. The genus comprises specific ecotypes which are phylogenetically distinct and differ markedly in their photophysiology, allowing growth over a broad range of light and nutrient conditions within the 45°N to 40°S latitudinal belt that they occupy. Synechococcus and Prochlorococcus are closely related, together forming a discrete picophytoplankton clade, but are distinguishable by their possession of dissimilar light-harvesting apparatuses and differences in cell size and elemental composition. Synechococcus strains have a ubiquitous oceanic distribution compared to that of Prochlorococcus strains and are characterized by phylogenetically discrete lineages with a wide range of pigmentation. In this review, we put our current knowledge of marine picocyanobacterial genomics into an environmental context and present previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

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Meuwissen, Theo, Ben Hayes, Iona MacLeod, and Michael Goddard. "Identification of Genomic Variants Causing Variation in Quantitative Traits: A Review." Agriculture 12, no. 10 (October 17, 2022): 1713. http://dx.doi.org/10.3390/agriculture12101713.

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Many of the important traits of livestock are complex or quantitative traits controlled by thousands of variants in the DNA sequence of individual animals and environmental factors. Identification of these causal variants would be advantageous for genomic prediction, to understand the physiology and evolution of important traits and for genome editing. However, it is difficult to identify these causal variants because their effects are small and they are in linkage disequilibrium with other DNA variants. Nevertheless, it should be possible to identify probable causal variants for complex traits just as we do for simple traits provided we compensate for the small effect size with larger sample size. In this review we consider eight types of evidence needed to identify causal variants. Large and diverse samples of animals, accurate genotypes, multiple phenotypes, annotation of genomic sites, comparisons across species, comparisons across the genome, the physiological role of candidate genes and experimental mutation of the candidate genomic site.

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Minutillo, S. A., A. Marais, T. Mascia, C. Faure, L. Svanella-Dumas, S. Theil, A. Payet, et al. "Complete Nucleotide Sequence of Artichoke latent virus Shows it to be a Member of the Genus Macluravirus in the Family Potyviridae." Phytopathology® 105, no. 8 (August 2015): 1155–60. http://dx.doi.org/10.1094/phyto-01-15-0010-r.

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Complete genomic sequences of Artichoke latent virus (ArLV) have been obtained by classical or high-throughput sequencing for an ArLV isolate from Italy (ITBr05) and for two isolates from France (FR37 and FR50). The genome is 8,278 to 8,291 nucleotides long and has a genomic organization comparable with that of Chinese yam necrotic mosaic virus (CYNMV), the only macluravirus fully sequenced to date. The cleavage sites of the viral polyprotein have been tentatively identified by comparison with CYNMV, confirming that macluraviruses are characterized by the absence of a P1 protein, a shorter and N-terminally truncated coat protein (CP). Sequence comparisons firmly place ArLV within the genus Macluravirus, and confirm previous results suggesting that Ranunculus latent virus (RALV), a previously described Macluravirus sp., is very closely related to ArLV. Serological relationships and comparisons of the CP gene and of the partial RaLV sequence available all indicate that RaLV should not be considered as a distinct species but as a strain of ArLV. The results obtained also suggest that the spectrum of currently used ArLV-specific molecular hybridization or polymerase chain reaction detection assays should be improved to cover all isolates and strains in the ArLV species.

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Leonard, Guy, Aurélie Labarre, David S. Milner, Adam Monier, Darren Soanes, Jeremy G. Wideman, Finlay Maguire, et al. "Comparative genomic analysis of the ‘pseudofungus’ Hyphochytrium catenoides." Open Biology 8, no. 1 (January 2018): 170184. http://dx.doi.org/10.1098/rsob.170184.

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Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives. Here we report the first draft genome sequence of a hyphochytriomycete ‘pseudofungus’; Hyphochytrium catenoides . Using phylogenomic approaches, we identify genes of recent viral ancestry, with related viral derived genes also present on the genomes of oomycetes, suggesting a complex history of viral coevolution and integration across the Pseudofungi. H. catenoides has a complex life cycle involving diverse filamentous structures and a flagellated zoospore with a single anterior tinselate flagellum. We use genome comparisons, drug sensitivity analysis and high-throughput culture arrays to investigate the ancestry of oomycete/pseudofungal characteristics, demonstrating that many of the genetic features associated with parasitic traits evolved specifically within the oomycete radiation. Comparative genomics also identified differences in the repertoire of genes associated with filamentous growth between the Fungi and the Pseudofungi, including differences in vesicle trafficking systems, cell-wall synthesis pathways and motor protein repertoire, demonstrating that unique cellular systems underpinned the convergent evolution of filamentous osmotrophic growth in these two eukaryotic groups.

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Smith, Theresa J., Gary Xie, Charles H. D. Williamson, Karen K. Hill, Rafael A. Fernández, Jason W. Sahl, Paul Keim, and Shannon L. Johnson. "Genomic Characterization of Newly Completed Genomes of Botulinum Neurotoxin-Producing Species from Argentina, Australia, and Africa." Genome Biology and Evolution 12, no. 3 (March 1, 2020): 229–42. http://dx.doi.org/10.1093/gbe/evaa043.

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Abstract Botulinum neurotoxin-producing clostridia are diverse in the types of toxins they produce as well as in their overall genomic composition. They are globally distributed, with prevalent species and toxin types found within distinct geographic regions, but related strains containing the same toxin types may also be located on distinct continents. The mechanisms behind the spread of these bacteria and the independent movements of their bont genes may be understood through examination of their genetic backgrounds. The generation of 15 complete genomic sequences from bacteria isolated in Argentina, Australia, and Africa allows for a thorough examination of genome features, including overall relationships, bont gene cluster locations and arrangements, and plasmid comparisons, in bacteria isolated from various areas in the southern hemisphere. Insights gained from these examinations provide an understanding of the mechanisms behind the independent movements of these elements among distinct species.

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Morozova, Olena, Sofie R. Salama, Isabel Bjork, Theodore C. Goldstein, Sabine Mueller, Leonard S. Sender, Alejandro Sweet-Cordero, and David Haussler. "Comparative genomic analysis for pediatric cancer patients evaluated in a California Initiative to Advance Precision Medicine Demonstration Project." Journal of Clinical Oncology 35, no. 15_suppl (May 20, 2017): TPS10578. http://dx.doi.org/10.1200/jco.2017.35.15_suppl.tps10578.

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TPS10578 Background: California Kids Cancer Comparison (CKCC), a demonstration project for the California Initiative to Advance Precision Medicine, evaluates the utility of incorporating gene expression information into the genomic analysis of difficult-to-treat pediatric cancers. CKCC is a partnership between UC Santa Cruz and clinical genomic trials conducted by Children’s Hospital of Orange County, UC San Francisco (Pacific Pediatric Neuro Oncology Consortium), and Stanford University. Methods: CKCC compares each prospective tumor’s RNA sequencing profile to over 11,000 uniformly analyzed tumor profiles from pediatric and adult cancer patients. These comparisons are used to identify genes and pathways that are significantly over expressed in each patient’s tumor. The pathways are reviewed by data analysis for the potential for clinical impact and presented to the treating oncologist in a molecular tumor board setting.

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Copley, Richard R. "The animal in the genome: comparative genomics and evolution." Philosophical Transactions of the Royal Society B: Biological Sciences 363, no. 1496 (January 11, 2008): 1453–61. http://dx.doi.org/10.1098/rstb.2007.2235.

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Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis -regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.

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Pflug, James M., Valerie Renee Holmes, Crystal Burrus, J. Spencer Johnston, and David R. Maddison. "Measuring Genome Sizes Using Read-Depth, k-mers, and Flow Cytometry: Methodological Comparisons in Beetles (Coleoptera)." G3: Genes|Genomes|Genetics 10, no. 9 (June 29, 2020): 3047–60. http://dx.doi.org/10.1534/g3.120.401028.

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Measuring genome size across different species can yield important insights into evolution of the genome and allow for more informed decisions when designing next-generation genomic sequencing projects. New techniques for estimating genome size using shallow genomic sequence data have emerged which have the potential to augment our knowledge of genome sizes, yet these methods have only been used in a limited number of empirical studies. In this project, we compare estimation methods using next-generation sequencing (k-mer methods and average read depth of single-copy genes) to measurements from flow cytometry, a standard method for genome size measures, using ground beetles (Carabidae) and other members of the beetle suborder Adephaga as our test system. We also present a new protocol for using read-depth of single-copy genes to estimate genome size. Additionally, we report flow cytometry measurements for five previously unmeasured carabid species, as well as 21 new draft genomes and six new draft transcriptomes across eight species of adephagan beetles. No single sequence-based method performed well on all species, and all tended to underestimate the genome sizes, although only slightly in most samples. For one species, Bembidion sp. nr. transversale, most sequence-based methods yielded estimates half the size suggested by flow cytometry.

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Dye, Charlotte, and Stuart G. Siddell. "Genomic RNA sequence of feline coronavirus strain FCoV C1Je." Journal of Feline Medicine and Surgery 9, no. 3 (June 2007): 202–13. http://dx.doi.org/10.1016/j.jfms.2006.12.002.

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This paper reports the first genomic RNA sequence of a field strain feline coronavirus (FCoV). Viral RNA was isolated at post mortem from the jejunum and liver of a cat with feline infectious peritonitis (FIP). A consensus sequence of the jejunum-derived genomic RNA (FCoV C1Je) was determined from overlapping cDNA fragments produced by reverse transcriptase polymerase chain reaction (RT-PCR) amplification. RT-PCR products were sequenced by a reiterative sequencing strategy and the genomic RNA termini were determined using a rapid amplification of cDNA ends PCR strategy. The FCoV C1Je genome was found to be 29,255 nucleotides in length, excluding the poly(A) tail. Comparison of the FCoV C1Je genomic RNA sequence with that of the laboratory strain FCoV FIP virus (FIPV) 79-1146 showed that both viruses have a similar genome organisation and predictions made for the open reading frames and cis-acting elements of the FIPV 79-1146 genome hold true for FCoV C1Je. In addition, the sequence of the 3′-proximal third of the liver derived genomic RNA (FCoV C1Li), which encompasses the structural and accessory protein genes of the virus, was also determined. Comparisons of the enteric (jejunum) and non-enteric (liver) derived viral RNA sequences revealed 100% nucleotide identity, a finding that questions the well accepted ‘internal mutation theory’ of FIPV pathogenicity.

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Journal articles on the topic 'Genomic comparisons'

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