Journal articles: 'Comparative Genomics Analysis'

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Alam, Intikhab, Mike Cornell, Darren M. Soanes, Cornelia Hedeler, Han Min Wong, Magnus Rattray, Simon J. Hubbard, Nicholas J. Talbot, Stephen G. Oliver, and Norman W. Paton. "A Methodology for Comparative Functional Genomics." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 2007): 112–22. http://dx.doi.org/10.1515/jib-2007-69.

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Abstract The continuing and rapid increase in the number of fully sequenced genomes is creating new opportunities for comparative studies. However, although many genomic databases store data from multiple organisms, for the most part they provide limited support for comparative genomics. We argue that refocusing genomic data management to provide more direct support for comparative studies enables systematic identification of important relationships between species, thereby increasing the value that can be obtained from sequenced genomes. The principal result of the paper is a methodology, in which comparative analyses are constructed over a foundation based on sequence clusters and evolutionary relationships. This methodology has been applied in a systematic study of the fungi, and we describe how comparative analyses have been implemented as an analysis library over the e-Fungi data warehouse.

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LAKE, J. "Phylogenetic analysis and comparative genomics." Trends in Biotechnology 16 (November 1998): 22–23. http://dx.doi.org/10.1016/s0167-7799(98)00132-2.

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Holmer, Rens, Robin van Velzen, Rene Geurts, Ton Bisseling, Dick de Ridder, and Sandra Smit. "GeneNoteBook, a collaborative notebook for comparative genomics." Bioinformatics 35, no. 22 (June 14, 2019): 4779–81. http://dx.doi.org/10.1093/bioinformatics/btz491.

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Abstract Summary Analysis and comparison of genomic and transcriptomic datasets have become standard procedures in biological research. However, for non-model organisms no efficient tools exist to visually work with multiple genomes and their metadata, and to annotate such data in a collaborative way. Here we present GeneNoteBook: a web based collaborative notebook for comparative genomics. GeneNoteBook allows experimental and computational researchers to query, browse, visualize and curate bioinformatic analysis results for multiple genomes. GeneNoteBook is particularly suitable for the analysis of non-model organisms, as it allows for comparing newly sequenced genomes to those of model organisms. Availability and implementation GeneNoteBook is implemented as a node.js web application and depends on MongoDB and NCBI BLAST. Source code is available at https://github.com/genenotebook/genenotebook. Additionally, GeneNoteBook can be installed through Bioconda and as a Docker image. Full installation instructions and online documentation are available at https://genenotebook.github.io. Supplementary information Supplementary data are available at Bioinformatics online.

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Valentin, Guignon, Toure Abdel, Droc Gaëtan, Dufayard Jean-François, Conte Matthieu, and Rouard Mathieu. "GreenPhylDB v5: a comparative pangenomic database for plant genomes." Nucleic Acids Research 49, no. D1 (November 25, 2020): D1464—D1471. http://dx.doi.org/10.1093/nar/gkaa1068.

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Abstract Comparative genomics is the analysis of genomic relationships among different species and serves as a significant base for evolutionary and functional genomic studies. GreenPhylDB (https://www.greenphyl.org) is a database designed to facilitate the exploration of gene families and homologous relationships among plant genomes, including staple crops critically important for global food security. GreenPhylDB is available since 2007, after the release of the Arabidopsis thaliana and Oryza sativa genomes and has undergone multiple releases. With the number of plant genomes currently available, it becomes challenging to select a single reference for comparative genomics studies but there is still a lack of databases taking advantage several genomes by species for orthology detection. GreenPhylDBv5 introduces the concept of comparative pangenomics by harnessing multiple genome sequences by species. We created 19 pangenes and processed them with other species still relying on one genome. In total, 46 plant species were considered to build gene families and predict their homologous relationships through phylogenetic-based analyses. In addition, since the previous publication, we rejuvenated the website and included a new set of original tools including protein-domain combination, tree topologies searches and a section for users to store their own results in order to support community curation efforts.

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Blanca, Léo, Eugène Christo-Foroux, Sofia Rigou, and Matthieu Legendre. "Comparative Analysis of the Circular and Highly Asymmetrical Marseilleviridae Genomes." Viruses 12, no. 11 (November 7, 2020): 1270. http://dx.doi.org/10.3390/v12111270.

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Marseilleviridae members are large dsDNA viruses with icosahedral particles 250 nm in diameter infecting Acanthamoeba. Their 340 to 390 kb genomes encode 450 to 550 protein-coding genes. Since the discovery of marseillevirus (the prototype of the family) in 2009, several strains were isolated from various locations, among which 13 are now fully sequenced. This allows the organization of their genomes to be deciphered through comparative genomics. Here, we first experimentally demonstrate that the Marseilleviridae genomes are circular. We then acknowledge a strong bias in sequence conservation, revealing two distinct genomic regions. One gathers most Marseilleviridae paralogs and has undergone genomic rearrangements, while the other, enriched in core genes, exhibits the opposite pattern. Most of the genes whose protein products compose the viral particles are located in the conserved region. They are also strongly biased toward a late gene expression pattern. We finally discuss the potential advantages of Marseilleviridae having a circular genome, and the possible link between the biased distribution of their genes and the transcription as well as DNA replication mechanisms that remain to be characterized.

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Dodeweerd, Anne-Marie van, Caroline R. Hall, Elisabeth G. Bent, Samantha J. Johnson, Michael W. Bevan, and Ian Bancroft. "Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana." Genome 42, no. 5 (October 1, 1999): 887–92. http://dx.doi.org/10.1139/g99-033.

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Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.Key words: plant genomics, comparative mapping.

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Peng, Qin, Yihui Yuan, Meiying Gao, Xupeng Chen, Biao Liu, Pengming Liu, Yan Wu, and Dandan Wu. "Genomic characteristics and comparative genomics analysis of Penicillium chrysogenum KF-25." BMC Genomics 15, no. 1 (2014): 144. http://dx.doi.org/10.1186/1471-2164-15-144.

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Liu, J. "Genomic resources and their informatic analysis for comparative genomics in catfish." Aquaculture 272 (2007): S286. http://dx.doi.org/10.1016/j.aquaculture.2007.07.128.

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Koike, Hideaki, Andrea Aerts, Kurt LaButti, Igor V. Grigoriev, and Scott E. Baker. "Comparative Genomics Analysis of Trichoderma reesei Strains." Industrial Biotechnology 9, no. 6 (December 2013): 352–67. http://dx.doi.org/10.1089/ind.2013.0015.

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Leiting, W. U., and X. I. E. Jianping. "Comparative genomics analysis of Mycobacterium NrdH-redoxins." Microbial Pathogenesis 48, no. 3-4 (March 2010): 97–102. http://dx.doi.org/10.1016/j.micpath.2010.01.004.

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Sheth, Nihar, Xavier Roca, Michelle L. Hastings, Ted Roeder, Adrian R. Krainer, and Ravi Sachidanandam. "Comprehensive splice-site analysis using comparative genomics." Nucleic Acids Research 34, no. 14 (August 12, 2006): 3955–67. http://dx.doi.org/10.1093/nar/gkl556.

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Gillespie, Joseph J., Alice R. Wattam, Stephen A. Cammer, Joseph L. Gabbard, Maulik P. Shukla, Oral Dalay, Timothy Driscoll, et al. "PATRIC: the Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species." Infection and Immunity 79, no. 11 (September 6, 2011): 4286–98. http://dx.doi.org/10.1128/iai.00207-11.

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ABSTRACTFunded by the National Institute of Allergy and Infectious Diseases, thePathosystemsResourceIntegrationCenter (PATRIC) is a genomics-centric relational database and bioinformatics resource designed to assist scientists in infectious-disease research. Specifically, PATRIC provides scientists with (i) a comprehensive bacterial genomics database, (ii) a plethora of associated data relevant to genomic analysis, and (iii) an extensive suite of computational tools and platforms for bioinformatics analysis. While the primary aim of PATRIC is to advance the knowledge underlying the biology of human pathogens, all publicly available genome-scale data for bacteria are compiled and continually updated, thereby enabling comparative analyses to reveal the basis for differences between infectious free-living and commensal species. Herein we summarize the major features available at PATRIC, dividing the resources into two major categories: (i) organisms, genomes, and comparative genomics and (ii) recurrent integration of community-derived associated data. Additionally, we present two experimental designs typical of bacterial genomics research and report on the execution of both projects using only PATRIC data and tools. These applications encompass a broad range of the data and analysis tools available, illustrating practical uses of PATRIC for the biologist. Finally, a summary of PATRIC's outreach activities, collaborative endeavors, and future research directions is provided.

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Silva de Oliveira, Mônica, Jorianne Thyeska Castro Alves, Pablo Henrique Caracciolo Gomes de Sá, and Adonney Allan de Oliveira Veras. "PAN2HGENE–tool for comparative analysis and identifying new gene products." PLOS ONE 16, no. 5 (May 28, 2021): e0252414. http://dx.doi.org/10.1371/journal.pone.0252414.

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Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software

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Riley, Robert, Sajeet Haridas, Kenneth H. Wolfe, Mariana R. Lopes, Chris Todd Hittinger, Markus Göker, Asaf A. Salamov, et al. "Comparative genomics of biotechnologically important yeasts." Proceedings of the National Academy of Sciences 113, no. 35 (August 17, 2016): 9882–87. http://dx.doi.org/10.1073/pnas.1603941113.

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Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation.

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Beckstette, Michael, Jens T. Mailänder, Richard J. Marhöfer, Alexander Sczyrba, Enno Ohlebusch, Robert Giegerich, and Paul M. Selzer. "Genlight: Interactive high-throughput sequence analysis and comparative genomics." Journal of Integrative Bioinformatics 1, no. 1 (December 1, 2004): 90–107. http://dx.doi.org/10.1515/jib-2004-8.

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Abstract With rising numbers of fully sequenced genomes the importance of comparative genomics is constantly increasing. Although several software systems for genome comparison analyses do exist, their functionality and flexibility is still limited, compared to the manifold possible applications. Therefore, we developed Genlight(http://piranha.techfak.uni-bielefeld.de.), a Client/Server based program suite for large scale sequence analysis and comparative genomics. Genlight uses the object relational database system PostgreSQL together with a state of the art data representation and a distributed execution approach for large scale analysis tasks. The system includes a wide variety of comparison and sequence manipulation methods and supports the management of nucleotide sequences as well as protein sequences. The comparison methods are complemented by a large variety of visualization methods for the assessment of the generated results. In order to demonstrate the suitability of the system for the treatment of biological questions, Genlight was used to identify potential drug and vaccine targets of the pathogen Helicobacter pylori.

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Baumler, David J., Lois M. Banta, Kai F. Hung, Jodi A. Schwarz, Eric L. Cabot, Jeremy D. Glasner, and Nicole T. Perna. "Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis." CBE—Life Sciences Education 11, no. 1 (March 2012): 81–93. http://dx.doi.org/10.1187/cbe.10-04-0057.

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Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students' ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula.

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Barron-Montenegro, Rocío, Rodrigo García, Fernando Dueñas, Dácil Rivera, Andrés Opazo-Capurro, Stephen Erickson, and Andrea I. Moreno-Switt. "Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis." Antibiotics 10, no. 7 (July 2, 2021): 806. http://dx.doi.org/10.3390/antibiotics10070806.

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Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.

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Jia, Yan, Bo Yang, Paul Ross, Catherine Stanton, Hao Zhang, Jianxin Zhao, and Wei Chen. "Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches." Genes 11, no. 1 (January 14, 2020): 95. http://dx.doi.org/10.3390/genes11010095.

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The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.

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Liu, Jia, Liyu Ge, Huan Mei, Hailin Zheng, Jingwen Peng, Guanzhao Liang, and Weida Liu. "Comparative Genomics and Molecular Analysis of Epidermophyton floccosum." Mycopathologia 186, no. 4 (June 23, 2021): 487–97. http://dx.doi.org/10.1007/s11046-021-00567-9.

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Lindroos, H., and S. G. E. Andersson. "Visualizing metabolic pathways: comparative genomics and expression analysis." Proceedings of the IEEE 90, no. 11 (November 2002): 1793–802. http://dx.doi.org/10.1109/jproc.2002.804687.

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Ureta-Vidal, Abel, Laurence Ettwiller, and Ewan Birney. "Comparative genomics: genome-wide analysis in metazoan eukaryotes." Nature Reviews Genetics 4, no. 4 (April 2003): 251–62. http://dx.doi.org/10.1038/nrg1043.

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Zhou, Jinhua, Tao Zhu, Chunxia Hu, Hongyu Li, Gang Chen, Gang Xu, Shixuan Wang, Jianfeng Zhou, and Ding Ma. "Comparative genomics and function analysis on BI1 family." Computational Biology and Chemistry 32, no. 3 (June 2008): 159–62. http://dx.doi.org/10.1016/j.compbiolchem.2008.01.002.

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Bottacini, Francesca, Duccio Medini, Angelo Pavesi, Francesca Turroni, Elena Foroni, David Riley, Vanessa Giubellini, Hervé Tettelin, Douwe van Sinderen, and Marco Ventura. "Comparative genomics of the genus Bifidobacterium." Microbiology 156, no. 11 (November 1, 2010): 3243–54. http://dx.doi.org/10.1099/mic.0.039545-0.

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Whole-genome sequencing efforts have revolutionized the study of bifidobacterial genetics and physiology. Unfortunately, the sequence of a single genome does not provide information on bifidobacterial genetic diversity and on how genetic variability supports improved adaptation of these bacteria to the environment of the human gastrointestinal tract (GIT). Analysis of nine genomes from bifidobacterial species showed that such genomes display an open pan-genome structure. Mathematical extrapolation of the data indicates that the genome reservoir available to the bifidobacterial pan-genome consists of more than 5000 genes, many of which are uncharacterized, but which are probably important to provide adaptive abilities pertinent to the human GIT. We also define a core bifidobacterial gene set which will undoubtedly provide a new baseline from which one can examine the evolution of bifidobacteria. Phylogenetic investigation performed on a total of 506 orthologues that are common to nine complete bifidobacterial genomes allowed the construction of a Bifidobacterium supertree which is largely concordant with the phylogenetic tree obtained using 16S rRNA genes. Moreover, this supertree provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis. This comparative study of the genus Bifidobacterium thus presents a foundation for future functional analyses of this important group of GIT bacteria.

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Geballa-Koukoulas, Khalil, Hadjer Boudjemaa, Julien Andreani, Bernard La Scola, and Guillaume Blanc. "Comparative Genomics Unveils Regionalized Evolution of the Faustovirus Genomes." Viruses 12, no. 5 (May 24, 2020): 577. http://dx.doi.org/10.3390/v12050577.

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Faustovirus is a recently discovered genus of large DNA virus infecting the amoeba Vermamoeba vermiformis, which is phylogenetically related to Asfarviridae. To better understand the diversity and evolution of this viral group, we sequenced six novel Faustovirus strains, mined published metagenomic datasets and performed a comparative genomic analysis. Genomic sequences revealed three consistent phylogenetic groups, within which genetic diversity was moderate. The comparison of the major capsid protein (MCP) genes unveiled between 13 and 18 type-I introns that likely evolved through a still-active birth and death process mediated by intron-encoded homing endonucleases that began before the Faustovirus radiation. Genome-wide alignments indicated that despite genomes retaining high levels of gene collinearity, the central region containing the MCP gene together with the extremities of the chromosomes evolved at a faster rate due to increased indel accumulation and local rearrangements. The fluctuation of the nucleotide composition along the Faustovirus (FV) genomes is mostly imprinted by the consistent nucleotide bias of coding sequences and provided no evidence for a single DNA replication origin like in circular bacterial genomes.

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Wang, Qinghua, Huiyin Song, Xudong Liu, Huan Zhu, Zhengyu Hu, and Guoxiang Liu. "Deep genomic analysis of Coelastrella saipanensis (Scenedesmaceae, Chlorophyta): comparative chloroplast genomics of Scenedesmaceae." European Journal of Phycology 54, no. 1 (November 14, 2018): 52–65. http://dx.doi.org/10.1080/09670262.2018.1503334.

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Chen, Dai-Di, Ye Tian, Jian-Yu Jiao, Xiao-Tong Zhang, Yong-Guang Zhang, Zhou-Yan Dong, Meng-Jie Xiong, Min Xiao, Wen-Sheng Shu, and Wen-Jun Li. "Comparative genomics analysis of Nitriliruptoria reveals the genomic differences and salt adaptation strategies." Extremophiles 24, no. 2 (December 9, 2019): 249–64. http://dx.doi.org/10.1007/s00792-019-01150-3.

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Galperin, Michael Y., David M. Kristensen, Kira S. Makarova, Yuri I. Wolf, and Eugene V. Koonin. "Microbial genome analysis: the COG approach." Briefings in Bioinformatics 20, no. 4 (September 14, 2017): 1063–70. http://dx.doi.org/10.1093/bib/bbx117.

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Abstract For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis.

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Wixon, Jo. "Meeting Highlights: Genome Sequencing and Biology 2001." Comparative and Functional Genomics 2, no. 4 (2001): 243–51. http://dx.doi.org/10.1002/cfg.97.

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We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

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Kaur, Harpreet, Bhupinder Pal Singh, Harpreet Singh, and Avinash Kaur Nagpal. "Comparative Genomics of Ten Solanaceous Plastomes." Advances in Bioinformatics 2014 (November 17, 2014): 1–13. http://dx.doi.org/10.1155/2014/424873.

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Availability of complete plastid genomes of ten solanaceous species, Atropa belladonna, Capsicum annuum, Datura stramonium, Nicotiana sylvestris, Nicotiana tabacum, Nicotiana tomentosiformis, Nicotiana undulata, Solanum bulbocastanum, Solanum lycopersicum, and Solanum tuberosum provided us with an opportunity to conduct their in silico comparative analysis in depth. The size of complete chloroplast genomes and LSC and SSC regions of three species of Solanum is comparatively smaller than that of any other species studied till date (exception: SSC region of A. belladonna). AT content of coding regions was found to be less than noncoding regions. A duplicate copy of trnH gene in C. annuum and two alternative tRNA genes for proline in D. stramonium were observed for the first time in this analysis. Further, homology search revealed the presence of rps19 pseudogene and infA genes in A. belladonna and D. stramonium, a region identical to rps19 pseudogene in C. annum and orthologues of sprA gene in another six species. Among the eighteen intron-containing genes, 3 genes have two introns and 15 genes have one intron. The longest insertion was found in accD gene in C. annuum. Phylogenetic analysis using concatenated protein coding sequences gave two clades, one for Nicotiana species and another for Solanum, Capsicum, Atropa, and Datura.

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Grigoriev, Igor V., Richard D. Hayes, Sara Calhoun, Bishoy Kamel, Alice Wang, Steven Ahrendt, Sergey Dusheyko, et al. "PhycoCosm, a comparative algal genomics resource." Nucleic Acids Research 49, no. D1 (October 26, 2020): D1004—D1011. http://dx.doi.org/10.1093/nar/gkaa898.

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Abstract Algae are a diverse, polyphyletic group of photosynthetic eukaryotes spanning nearly all eukaryotic lineages of life and collectively responsible for ∼50% of photosynthesis on Earth. Sequenced algal genomes, critical to understanding their complex biology, are growing in number and require efficient tools for analysis. PhycoCosm (https://phycocosm.jgi.doe.gov) is an algal multi-omics portal, developed by the US Department of Energy Joint Genome Institute to support analysis and distribution of algal genome sequences and other ‘omics’ data. PhycoCosm provides integration of genome sequence and annotation for >100 algal genomes with available multi-omics data and interactive web-based tools to enable algal research in bioenergy and the environment, encouraging community engagement and data exchange, and fostering new sequencing projects that will further these research goals.

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Ulaszewski, Bartosz, Joanna Meger, and Jaroslaw Burczyk. "Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods." Forests 12, no. 2 (February 15, 2021): 222. http://dx.doi.org/10.3390/f12020222.

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Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.

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Wang, Shuo, Bo Yang, R. Paul Ross, Catherine Stanton, Jianxin Zhao, Hao Zhang, and Wei Chen. "Comparative Genomics Analysis of Lactobacillus ruminis from Different Niches." Genes 11, no. 1 (January 8, 2020): 70. http://dx.doi.org/10.3390/genes11010070.

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Lactobacillus ruminis is a commensal motile lactic acid bacterium living in the intestinal tract of humans and animals. Although a few genomes of L. ruminis were published, most of them were animal derived. To explore the genetic diversity and potential niche-specific adaptation changes of L. ruminis, in the current work, draft genomes of 81 L. ruminis strains isolated from human, bovine, piglet, and other animals were sequenced, and comparative genomic analysis was performed. The genome size and GC content of L. ruminis on average were 2.16 Mb and 43.65%, respectively. Both the origin and the sampling distance of these strains had a great influence on the phylogenetic relationship. For carbohydrate utilization, the human-derived L. ruminis strains had a higher consistency in the utilization of carbon source compared to the animal-derived strains. L. ruminis mainly increased the competitiveness of niches by producing class II bacteriocins. The type of clustered regularly interspaced short palindromic repeats /CRISPR-associated (CRISPR/Cas) system presented in L. ruminis was mainly subtype IIA. The diversity of CRISPR/Cas locus depended on the high denaturation of spacer number and sequence, although cas1 protein was relatively conservative. The genetic differences in those newly sequenced L. ruminis strains highlighted the gene gains and losses attributed to niche adaptations.

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Ronaghi, Mostafa, and Elahe Elahi. "Discovery of Single Nucleotide Polymorphisms and Mutations by Pyrosequencing." Comparative and Functional Genomics 3, no. 1 (2002): 51–56. http://dx.doi.org/10.1002/cfg.132.

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Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis.

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Xu, Zhuofei, Xiabing Chen, Lu Li, Tingting Li, Shengyue Wang, Huanchun Chen, and Rui Zhou. "Comparative Genomic Characterization of Actinobacillus pleuropneumoniae." Journal of Bacteriology 192, no. 21 (August 27, 2010): 5625–36. http://dx.doi.org/10.1128/jb.00535-10.

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ABSTRACT The Gram-negative bacterium Actinobacillus pleuropneumoniae is the etiologic agent of porcine contagious pleuropneumoniae, a lethal respiratory infectious disease causing great economic losses in the swine industry worldwide. In order to better interpret the genetic background of serotypic diversity, nine genomes of A. pleuropneumoniae reference strains of serovars 1, 2, 4, 6, 9, 10, 11, 12, and 13 were sequenced by using rapid high-throughput approach. Based on 12 genomes of corresponding serovar reference strains including three publicly available complete genomes (serovars 3, 5b, and 7) of this bacterium, we performed a comprehensive analysis of comparative genomics and first reported a global genomic characterization for this pathogen. Clustering of 26,012 predicted protein-coding genes showed that the pan genome of A. pleuropneumoniae consists of 3,303 gene clusters, which contain 1,709 core genome genes, 822 distributed genes, and 772 strain-specific genes. The genome components involved in the biogenesis of capsular polysaccharide and lipopolysaccharide O antigen relative to serovar diversity were compared, and their genetic diversity was depicted. Our findings shed more light on genomic features associated with serovar diversity of A. pleuropneumoniae and provide broader insight into both pathogenesis research and clinical/epidemiological application against the severe disease caused by this swine pathogen.

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Tsoy, Olga, Dmitry Ravcheev, and Arcady Mushegian. "Comparative Genomics of Ethanolamine Utilization." Journal of Bacteriology 191, no. 23 (September 25, 2009): 7157–64. http://dx.doi.org/10.1128/jb.00838-09.

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ABSTRACT Ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. Ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde and ammonia, is encoded by the gene tandem eutBC. Despite extensive studies of ethanolamine utilization in Salmonella enterica serovar Typhimurium, much remains to be learned about EutBC structure and catalytic mechanism, about the evolutionary origin of ethanolamine utilization, and about regulatory links between the metabolism of ethanolamine itself and the ethanolamine-ammonia lyase cofactor adenosylcobalamin. We used computational analysis of sequences, structures, genome contexts, and phylogenies of ethanolamine-ammonia lyases to address these questions and to evaluate recent data-mining studies that have suggested an association between bacterial food poisoning and the diol utilization pathways. We found that EutBC evolution included recruitment of a TIM barrel and a Rossmann fold domain and their fusion to N-terminal α-helical domains to give EutB and EutC, respectively. This fusion was followed by recruitment and occasional loss of auxiliary ethanolamine utilization genes in Firmicutes and by several horizontal transfers, most notably from the firmicute stem to the Enterobacteriaceae and from Alphaproteobacteria to Actinobacteria. We identified a conserved DNA motif that likely represents the EutR-binding site and is shared by the ethanolamine and cobalamin operons in several enterobacterial species, suggesting a mechanism for coupling the biosyntheses of apoenzyme and cofactor in these species. Finally, we found that the food poisoning phenotype is associated with the structural components of metabolosome more strongly than with ethanolamine utilization genes or with paralogous propanediol utilization genes per se.

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Carrillo, C., E. R. Tulman, G. Delhon, Z. Lu, A. Carreno, A. Vagnozzi, G. F. Kutish, and D. L. Rock. "Comparative Genomics of Foot-and-Mouth Disease Virus." Journal of Virology 79, no. 10 (May 15, 2005): 6487–504. http://dx.doi.org/10.1128/jvi.79.10.6487-6504.2005.

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ABSTRACT Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-and-mouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5′ and 3′ untranslated regions (UTR), as was tolerance for insertions/deletions in the 5′ UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins Lpro, 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural protein-encoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.

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Jung, Jaejoon, Eugene L. Madsen, Che Ok Jeon, and Woojun Park. "Comparative Genomic Analysis of Acinetobacter oleivorans DR1 To Determine Strain-Specific Genomic Regions and Gentisate Biodegradation." Applied and Environmental Microbiology 77, no. 20 (August 19, 2011): 7418–24. http://dx.doi.org/10.1128/aem.05231-11.

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ABSTRACTThe comparative genomics ofAcinetobacter oleivoransDR1 assayed withA. baylyiADP1,A. calcoaceticusPHEA-2, andA. baumanniiATCC 17978 revealed that the incorporation of phage-related genomic regions and the absence of transposable elements have contributed to the large size (4.15 Mb) of the DR1 genome. A horizontally transferred genomic region and a higher proportion of transcriptional regulator- and signal peptide-coding genes were identified as characteristics of the DR1 genome. Incomplete glucose metabolism, metabolic pathways of aromatic compounds, biofilm formation, antibiotics and metal resistance, and natural competence genes were conserved in four compared genomes. Interestingly, only strain DR1 possesses gentisate 1,2-dioxygenase (nagI) and grows on gentisate, whereas other species cannot. Expression of thenagIgene was upregulated during gentisate utilization, and four downstream open reading frames (ORFs) were cotranscribed, supporting the notion that gentisate metabolism is a unique characteristic of strain DR1. The genomic analysis of strain DR1 provides additional insights into the function, ecology, and evolution ofAcinetobacterspecies.

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Bykova, Nadezda A., Alexander V. Favorov, and Andrey A. Mironov. "Hidden Markov Models for Evolution and Comparative Genomics Analysis." PLoS ONE 8, no. 6 (June 7, 2013): e65012. http://dx.doi.org/10.1371/journal.pone.0065012.

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Cissé, Ousmane H., Liang Ma, Da Wei Huang, Pavel P. Khil, John P. Dekker, Geetha Kutty, Lisa Bishop, et al. "Comparative Population Genomics Analysis of the Mammalian Fungal PathogenPneumocystis." mBio 9, no. 3 (May 8, 2018): e00381-18. http://dx.doi.org/10.1128/mbio.00381-18.

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ABSTRACTPneumocystisspecies are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivablein vitro. HumanPneumocystisinfections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations ofPneumocystisinfecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations. Here, we detected reduced levels of recombination and variations in historical demography, which shape the global population structures. We report estimates of evolutionary rates, levels of genetic diversity, and population sizes. Molecular clock estimates indicate thatPneumocystisspecies diverged before their hosts, while the asynchronous timing of population declines suggests host shifts. Our results have uncovered complex patterns of genetic variation influenced by multiple factors that shaped the adaptation ofPneumocystispopulations during their spread across mammals.IMPORTANCEUnderstanding how natural pathogen populations evolve and identifying the determinants of genetic variation are central issues in evolutionary biology.Pneumocystis, a fungal pathogen which infects mammals exclusively, provides opportunities to explore these issues. In humans,Pneumocystiscan cause a life-threatening pneumonia in immunosuppressed individuals. In analysis of differentPneumocystisspecies infecting humans, rats, and mice, we found that there are high infection rates and that natural populations maintain a high level of genetic variation despite low levels of recombination. We found no evidence of population structuring by geography. Our comparisons of the times of divergence of these species to their respective hosts suggest thatPneumocystismay have undergone recent host shifts. The results demonstrate thatPneumocystisstrains are widely disseminated geographically and provide a new understanding of the evolution of these pathogens.

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YANG, E. "Comparative genomics and phylogenetic analysis of S. dysenteriae subgroup." Science in China Series C 48, no. 4 (2005): 406. http://dx.doi.org/10.1360/062004-96.

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Li, Yuan, Rui Wang, Wenjing Sun, Zhiqiang Song, Fan Bai, Huajun Zheng, and Jiuqing Xin. "Comparative genomics analysis of Mycoplasma capricolum subsp. capripneumoniae 87001." Genomics 112, no. 1 (January 2020): 615–20. http://dx.doi.org/10.1016/j.ygeno.2019.04.013.

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Guirola, María, Yandi Naranjo, Mercè Capdevila, and Sílvia Atrian. "Comparative genomics analysis of metallothioneins in twelve Drosophila species." Journal of Inorganic Biochemistry 105, no. 8 (August 2011): 1050–59. http://dx.doi.org/10.1016/j.jinorgbio.2011.05.004.

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McAuliffe, J. D., M. I. Jordan, and L. Pachter. "Subtree power analysis and species selection for comparative genomics." Proceedings of the National Academy of Sciences 102, no. 22 (May 23, 2005): 7900–7905. http://dx.doi.org/10.1073/pnas.0502790102.

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Bhati, Jyotika, Humira Sonah, Tripta Jhang, Nagender Kumar Singh, and Tilak Raj Sharma. "Comparative Analysis and EST Mining Reveals High Degree of Conservation among FiveBrassicaceaeSpecies." Comparative and Functional Genomics 2010 (2010): 1–13. http://dx.doi.org/10.1155/2010/520238.

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Brassicaceaeis an important family of the plant kingdom which includes several plants of major economic importance. TheBrassica spp.andArabidopsisshare much-conserved colinearity between their genomes which can be exploited for the genomic research inBrassicaceaecrops. In this study, 131,286 ESTs of fiveBrassicaceaespecies were assembled into unigene contigs and compared withArabidopsisgene indices. Almost all the unigenes ofBrassicaceaespecies showed high similarities withArabidopsisgenes except those ofB. napus,where 90% of unigenes were found similar. A total of 9,699 SSRs were identified in the unigenes. PCR primers were designed based on this information and amplified across species for validation. Functional annotation of unigenes showed that the majority of the genes are present in metabolism and energy functional classes. It is expected that comparative genome analysis betweenArabidopsisand related crop species will expedite research in the more complexBrassicagenomes. This would be helpful for genomics as well as evolutionary studies, and DNA markers developed can be used for mapping, tagging, and cloning of important genes inBrassicaceae.

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Carter, Ben, Guanghui Wu, Martin J. Woodward, and Muna F. Anjum. "A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes." BMC Genomics 9, no. 1 (2008): 53. http://dx.doi.org/10.1186/1471-2164-9-53.

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Winsor, G. L., D. K. W. Lam, L. Fleming, R. Lo, M. D. Whiteside, N. Y. Yu, R. E. W. Hancock, and F. S. L. Brinkman. "Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes." Nucleic Acids Research 39, Database (October 6, 2010): D596—D600. http://dx.doi.org/10.1093/nar/gkq869.

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Tang, Deyou, Yucheng Li, Daqiang Tan, Juan Fu, Yelei Tang, Jiabin Lin, Rong Zhao, Hongli Du, and Zhongming Zhao. "KCOSS: an ultra-fast k-mer counter for assembled genome analysis." Bioinformatics 38, no. 4 (November 26, 2021): 933–40. http://dx.doi.org/10.1093/bioinformatics/btab797.

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Abstract Motivation The k-mer frequency in whole genome sequences provides researchers with an insightful perspective on genomic complexity, comparative genomics, metagenomics and phylogeny. The current k-mer counting tools are typically slow, and they require large memory and hard disk for assembled genome analysis. Results We propose a novel and ultra-fast k-mer counting algorithm, KCOSS, to fulfill k-mer counting mainly for assembled genomes with segmented Bloom filter, lock-free queue, lock-free thread pool and cuckoo hash table. We optimize running time and memory consumption by recycling memory blocks, merging multiple consecutive first-occurrence k-mers into C-read, and writing a set of C-reads to disk asynchronously. KCOSS was comparatively tested with Jellyfish2, CHTKC and KMC3 on seven assembled genomes and three sequencing datasets in running time, memory consumption, and hard disk occupation. The experimental results show that KCOSS counts k-mer with less memory and disk while having a shorter running time on assembled genomes. KCOSS can be used to calculate the k-mer frequency not only for assembled genomes but also for sequencing data. Availabilityand implementation The KCOSS software is implemented in C++. It is freely available on GitHub: https://github.com/kcoss-2021/KCOSS. Supplementary information Supplementary data are available at Bioinformatics online.

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Samusik, Nikolay A., Yuriy P. Galachyants, and Andrey P. Kozlov. "Evolutionary analysis of sequences expressed in tumors." Ecological genetics 7, no. 2 (June 15, 2009): 26–37. http://dx.doi.org/10.17816/ecogen7226-37.

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Earlier we have identified a new class of human genomic sequences expressed preferentially in tumors. Here we use a comparative genomics approach and conservation analysis to study evolutionary specificity of nine human tumor-specific sequences, described previously. Three sequences had originated in the primate lineage. The other three had mammalian orthologs, but conservation analysis has shown that these sequences evolved neutrally. Three sequences were conservative. These data confirm previously formulated hypothesis that evolutionarily new genes are expressed in tumors.

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Bertelli, Claire, Keith E. Tilley, and Fiona S. L. Brinkman. "Microbial genomic island discovery, visualization and analysis." Briefings in Bioinformatics 20, no. 5 (June 3, 2018): 1685–98. http://dx.doi.org/10.1093/bib/bby042.

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Abstract Horizontal gene transfer (also called lateral gene transfer) is a major mechanism for microbial genome evolution, enabling rapid adaptation and survival in specific niches. Genomic islands (GIs), commonly defined as clusters of bacterial or archaeal genes of probable horizontal origin, are of particular medical, environmental and/or industrial interest, as they disproportionately encode virulence factors and some antimicrobial resistance genes and may harbor entire metabolic pathways that confer a specific adaptation (solvent resistance, symbiosis properties, etc). As large-scale analyses of microbial genomes increases, such as for genomic epidemiology investigations of infectious disease outbreaks in public health, there is increased appreciation of the need to accurately predict and track GIs. Over the past decade, numerous computational tools have been developed to tackle the challenges inherent in accurate GI prediction. We review here the main types of GI prediction methods and discuss their advantages and limitations for a routine analysis of microbial genomes in this era of rapid whole-genome sequencing. An assessment is provided of 20 GI prediction software methods that use sequence-composition bias to identify the GIs, using a reference GI data set from 104 genomes obtained using an independent comparative genomics approach. Finally, we present guidelines to assist researchers in effectively identifying these key genomic regions.

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Dhanapal, Arun Prabhu, and Mahalingam Govindaraj. "Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement." Genetics Research International 2015 (March 19, 2015): 1–15. http://dx.doi.org/10.1155/2015/684321.

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The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

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Journal articles on the topic 'Comparative Genomics Analysis'

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