Journal articles: 'Genome comparison'

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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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Mori, K., K. Horimoto, S. Fukuchi, and K. Nishikawa. "Genome comparison based on gene locations : I Comparison between microbial genomes." Seibutsu Butsuri 41, supplement (2001): S81. http://dx.doi.org/10.2142/biophys.41.s81_1.

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Uras, Tansel, and Esra Erdem. "Genome Rearrangement and Planning: Revisited." Proceedings of the International Conference on Automated Planning and Scheduling 20 (May 25, 2021): 250–53. http://dx.doi.org/10.1609/icaps.v20i1.13434.

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Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier formulated the pairwise comparison of entire genomes as the problem of planning rearrangement events that transform one genome to the other. We reformulate this problem as a planning problem to extend its applicability to genomes with multiple copies of genes and with unequal gene content, and illustrate its applicability and effectiveness on three real datasets: mitochondrial genomes of Metazoa, chloroplast genomes of Campanulaceae, chloroplast genomes of various land plants and green algae.

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Uras, Tansel, and Esra Erdem. "Genome Rearrangement: A Planning Approach." Proceedings of the AAAI Conference on Artificial Intelligence 24, no. 1 (July 5, 2010): 1963–64. http://dx.doi.org/10.1609/aaai.v24i1.7787.

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Evolutionary trees of species can be reconstructed by pairwise comparison of their entire genomes. Such a comparison can be quantified by determining the number of events that change the order of genes in a genome. Earlier Erdem and Tillier formulated the pairwise comparison of entire genomes as the problem of planning rearrangement events that transform one genome to the other. We reformulate this problem as a planning problem to extend its applicability to genomes with multiple copies of genes and with unequal gene content, and illustrate its applicability and effectiveness on three real datasets: mitochondrial genomes of Metazoa, chloroplast genomes of Campanulaceae, chloroplast genomes of various land plants and green algae.

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Bao, Jingyue, Yong Zhang, Chuan Shi, Qinghua Wang, Shujuan Wang, Xiaodong Wu, Shengbo Cao, Fengping Xu, and Zhiliang Wang. "Genome-Wide Diversity Analysis of African Swine Fever Virus Based on a Curated Dataset." Animals 12, no. 18 (September 16, 2022): 2446. http://dx.doi.org/10.3390/ani12182446.

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African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has had serious effects on the global pig industry. Virus genome sequencing and comparison play an important role in tracking the outbreaks of the disease and tracing the transmission of the virus. Although more than 140 ASFV genome sequences have been deposited in the public databases, the genome-wide diversity of ASFV remains unclear. Here we prepared a curated dataset of ASFV genome sequences by filtering genomes with sequencing errors as well as duplicated genomes. A total of 123 ASFV genome sequences were included in the dataset, representing 10 genotypes collected between 1949 and 2020. Phylogenetic analysis based on whole-genome sequences provided high-resolution topology in differentiating closely related ASFV isolates, and drew new clues in the classification of some ASFV isolates. Genome-wide diversity of ASFV genomes was explored by pairwise sequence similarity comparison and ORF distribution comparison. Tandem repeat sequences were found widely distributed and highly varied in ASFV genomes. Structural variation and highly variable poly G or poly C tracts also contributed to the genome diversity. This study expanded our knowledge on the patterns of genetic diversity and evolution of ASFV, and provided valuable information for diagnosis improvement and vaccine development.

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LAM, WINNIE W. M., KEITH C. C. CHAN, DAVID K. Y. CHIU, and ANDREW K. C. WONG. "A GRAPH-BASED ALGORITHM FOR MINING MULTI-LEVEL PATTERNS IN GENOMIC DATA." Journal of Bioinformatics and Computational Biology 08, no. 05 (October 2010): 789–807. http://dx.doi.org/10.1142/s0219720010005002.

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Comparative genomics is concerned with the study of genome structure and function of different species. It can provide useful information for the derivation of evolutionary and functional relationships between genomes. Previous work on genome comparison focuses mainly on comparing the entire genomes for visualization without further analysis. As many interesting patterns may exist between genomes and may lead to the discovering of functional gene segments (groups of genes), we propose an algorithm called Multi-Level Genome Comparison Algorithm (MGC) that can be used to facilitate the analysis of genomes at multi-levels during the comparison process to discover sequential and regional consistency in gene segments. Different genomes may have common sub-sequences that differ from each other due to mutations, lateral gene transfers, gene rearrangements, etc., and these sub-sequences are usually not easily identified. Not all the genes can have a perfect one-to-one matching with each other. It is quite possible for one-to-many or many-to-many ambiguous relationships to exist between them. To perform the tasks effectively, MGC takes such ambiguity into consideration during genome comparison by representing genomes in a graph and then make use of a graph mining algorithm called the Multi-Level Attributed Graph Mining Algorithm (MAGMA) to build a hierarchical multi-level graph structure to facilitate genome comparison. To determine the effectiveness of these proposed algorithms, experiments were performed using intra- and inter-species of Microbial genomes. The results show that the proposed algorithms are able to discover multiple level matching patterns that show the similarities and dissimilarities among different genomes, in addition to confirming the specific role of the genes in the genomes.

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Digiampietri, Luciano Antonio, Vivian Mayumi Yamassaki Pereira, Geraldo José Santos-Júnior, Giovani Sousa-Leite, Priscilla Koch Wagner, Leandro Márcio Moreira, and Caio Rafael do Nascimento Santiago. "A gene based bacterial whole genome comparison toolkit." Revista de Informática Teórica e Aplicada 26, no. 1 (April 14, 2019): 36. http://dx.doi.org/10.22456/2175-2745.84814.

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Most of the computational biology analysis is made comparing genomic features. The nucleotide and amino acid sequence alignments are frequently used in gene function identification and genome comparison. Despite its widespread use, there are limitations in their analysis capabilities that need to be considered but are often overlooked or unknown by many researchers. This paper presents a gene based whole genome comparison toolkit which can be used not only as an alternative and more robust way to compare a set of whole genomes, but, also, to understand the tradeoff of the use of sequence local alignment in this kind of comparison. A study case was performed considering fifteen whole genomes of the Xanthomonas genus. The results were compared with the 16S rRNA-processing protein RimM phylogeny and some thresholds for the use of sequence alignments in this kind of analysis were discussed.

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Tanaka, Mami, Sayaka Mino, Yoshitoshi Ogura, Tetsuya Hayashi, and Tomoo Sawabe. "Availability of Nanopore sequences in the genome taxonomy for Vibrionaceae systematics: Rumoiensis clade species as a test case." PeerJ 6 (June 18, 2018): e5018. http://dx.doi.org/10.7717/peerj.5018.

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Whole genome sequence comparisons have become essential for establishing a robust scheme in bacterial taxonomy. To generalize this genome-based taxonomy, fast, reliable, and cost-effective genome sequencing methodologies are required. MinION, the palm-sized sequencer from Oxford Nanopore Technologies, enables rapid sequencing of bacterial genomes using minimal laboratory resources. Here we tested the ability of Nanopore sequences for the genome-based taxonomy of Vibrionaceae and compared Nanopore-only assemblies to complete genomes of five Rumoiensis clade species: Vibrio aphrogenes, V. algivorus, V. casei, V. litoralis, and V. rumoiensis. Comparison of overall genome relatedness indices (OGRI) and multilocus sequence analysis (MLSA) based on Nanopore-only assembly and Illumina or hybrid assemblies revealed that errors in Nanopore-only assembly do not influence average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, or MLSA tree topology in Vibrionaceae. Our results show that the genome sequences from Nanopore-based approach can be used for rapid species identification based on the OGRI and MLSA.

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Rouchka, E. C. "Comparison of whole genome assemblies of the human genome." Nucleic Acids Research 30, no. 22 (November 15, 2002): 5004–14. http://dx.doi.org/10.1093/nar/gkf633.

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Sullivan, M. J., N. K. Petty, and S. A. Beatson. "Easyfig: a genome comparison visualizer." Bioinformatics 27, no. 7 (January 28, 2011): 1009–10. http://dx.doi.org/10.1093/bioinformatics/btr039.

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FU, ZHENG, and TAO JIANG. "CLUSTERING OF MAIN ORTHOLOGS FOR MULTIPLE GENOMES." Journal of Bioinformatics and Computational Biology 06, no. 03 (June 2008): 573–84. http://dx.doi.org/10.1142/s0219720008003540.

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The identification of orthologous genes shared by multiple genomes is critical for both functional and evolutionary studies in comparative genomics. While it is usually done by sequence similarity search and reconciled tree construction in practice, recently a new combinatorial approach and high-throughput system MSOAR for ortholog identification between closely related genomes based on genome rearrangement and gene duplication has been proposed in Fu et al.1 MSOAR assumes that orthologous genes correspond to each other in the most parsimonious evolutionary scenario, minimizing the number of genome rearrangement and (postspeciation) gene duplication events. However, the parsimony approach used by MSOAR limits it to pairwise genome comparisons. In this paper, we extend MSOAR to multiple (closely related) genomes and propose an ortholog clustering method, called MultiMSOAR, to infer main orthologs in multiple genomes. As a preliminary experiment, we apply MultiMSOAR to rat, mouse, and human genomes, and validate our results using gene annotations and gene function classifications in the public databases. We further compare our results to the ortholog clusters predicted by MultiParanoid, which is an extension of the well-known program InParanoid for pairwise genome comparisons. The comparison reveals that MultiMSOAR gives more detailed and accurate orthology information, since it can effectively distinguish main orthologs from inparalogs.

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Diaz-del-Pino, Sergio, Pablo Rodriguez-Brazzarola, Esteban Perez-Wohlfeil, and Oswaldo Trelles. "Combining Strengths for Multi-genome Visual Analytics Comparison." Bioinformatics and Biology Insights 13 (January 2019): 117793221882512. http://dx.doi.org/10.1177/1177932218825127.

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The eclosion of data acquisition technologies has shifted the bottleneck in molecular biology research from data acquisition to data analysis. Such is the case in Comparative Genomics, where sequence analysis has transitioned from genes to genomes of several orders of magnitude larger. This fact has revealed the need to adapt software to work with huge experiments efficiently and to incorporate new data-analysis strategies to manage results from such studies. In previous works, we presented GECKO, a software to compare large sequences; now we address the representation, browsing, data exploration, and post-processing of the massive amount of information derived from such comparisons. GECKO-MGV is a web-based application organized as client-server architecture. It is aimed at visual analysis of the results from both pairwise and multiple sequences comparison studies combining a set of common commands for image exploration with improved state-of-the-art solutions. In addition, GECKO-MGV integrates different visualization analysis tools while exploiting the concept of layers to display multiple genome comparison datasets. Moreover, the software is endowed with capabilities for contacting external-proprietary and third-party services for further data post-processing and also presents a method to display a timeline of large-scale evolutionary events. As proof-of-concept, we present 2 exercises using bacterial and mammalian genomes which depict the capabilities of GECKO-MGV to perform in-depth, customizable analyses on the fly using web technologies. The first exercise is mainly descriptive and is carried out over bacterial genomes, whereas the second one aims to show the ability to deal with large sequence comparisons. In this case, we display results from the comparison of the first Homo sapiens chromosome against the first 5 chromosomes of Mus musculus.

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Field, Dawn, Edward J. Feil, and Gareth A. Wilson. "Databases and software for the comparison of prokaryotic genomes." Microbiology 151, no. 7 (July 1, 2005): 2125–32. http://dx.doi.org/10.1099/mic.0.28006-0.

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The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics. To exploit the full potential of this approach requires the development of novel algorithms, databases and software which are sophisticated enough to draw meaningful comparisons between complete genome sequences and are widely accessible to the scientific community at large. This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes.

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Swidan, Firas, and Ron Shamir. "Assessing the Quality of Whole Genome Alignments in Bacteria." Advances in Bioinformatics 2009 (November 15, 2009): 1–8. http://dx.doi.org/10.1155/2009/749027.

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Comparing genomes is an essential preliminary step to solve many problems in biology. Matching long similar segments between two genomes is a precondition for their evolutionary, genetic, and genome rearrangement analyses. Though various comparison methods have been developed in recent years, a quantitative assessment of their performance is lacking. Here, we describe two families of assessment measures whose purpose is to evaluate bacteria-oriented comparison tools. The first measure is based on how well the genome segmentation fits the gene annotation of the studied organisms; the second uses the number of segments created by the segmentation and the percentage of the two genomes that are conserved. The effectiveness of the two measures is demonstrated by applying them to the results of genome comparison tools obtained on 41 pairs of bacterial species. Despite the difference in the nature of the two types of measurements, both show consistent results, providing insights into the subtle differences between the mapping tools.

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Lukens, Lewis, Fei Zou, Derek Lydiate, Isobel Parkin, and Tom Osborn. "Comparison of a Brassica oleracea Genetic Map With the Genome of Arabidopsis thaliana." Genetics 164, no. 1 (May 1, 2003): 359–72. http://dx.doi.org/10.1093/genetics/164.1.359.

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Abstract Brassica oleracea is closely related to the model plant, Arabidopsis thaliana. Despite this relationship, it has been difficult to both identify the most closely related segments between the genomes and determine the degree of genome replication within B. oleracea relative to A. thaliana. These difficulties have arisen in part because both species have replicated genomes, and the criteria used to identify orthologous regions between the genomes are often ambiguous. In this report, we compare the positions of sequenced Brassica loci with a known position on a B. oleracea genetic map to the positions of their putative orthologs within the A. thaliana genome. We use explicit criteria to distinguish orthologous from paralogous loci. In addition, we develop a conservative algorithm to identify collinear loci between the genomes and a permutation test to evaluate the significance of these regions. The algorithm identified 34 significant A. thaliana regions that are collinear with >28% of the B. oleracea genetic map. These regions have a mean of 3.3 markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Our findings are consistent with the hypothesis that the B. oleracea genome has been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.

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Khaja, Razi, Junjun Zhang, Jeffrey R. MacDonald, Yongshu He, Ann M. Joseph-George, John Wei, Muhammad A. Rafiq, et al. "Genome assembly comparison identifies structural variants in the human genome." Nature Genetics 38, no. 12 (November 22, 2006): 1413–18. http://dx.doi.org/10.1038/ng1921.

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Istrail, Sorin, Granger G. Sutton, Liliana Florea, Aaron L. Halpern, Clark M. Mobarry, Ross Lippert, Brian Walenz, et al. "Whole-genome shotgun assembly and comparison of human genome assemblies." Proceedings of the National Academy of Sciences 101, no. 7 (February 9, 2004): 1916–21. http://dx.doi.org/10.1073/pnas.0307971100.

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Yang, Youngik, Donald Gilbert, and Sun Kim. "Annotation confidence score for genome annotation: a genome comparison approach." Bioinformatics 26, no. 1 (October 24, 2009): 22–29. http://dx.doi.org/10.1093/bioinformatics/btp613.

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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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ŞAHİNGİL, Mehmet Cihan, and Yakup OZKAZANC. "Comparison of SARS-CoV-2 Virus Variant Genomes Detected in China and the USA." Genetics & Applications 4, no. 2 (December 24, 2020): 10. http://dx.doi.org/10.31383/ga.vol4iss2pp10-26.

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In the spreading period of the SARS-CoV-2 virus which is the cause of COVID-19 in the world, it is seen that the genome of the virus mutates and this mutation processes create new SARS-CoV-2 variants. In this study, we examined two variant genome groups. The first group includes the genomes of variants detected in China, while the second includes those detected in the USA. We applied the multiple sequence alignment process on these publicly available SARS-CoV-2 virus genomes and reported the obtained results. There are 87 genomes for China variants and 200 for USA variants in the used data. The analyses were made for each domain of the genomes. The results of the analysis show that the variant genomes in the two SARS-CoV-2 groups examined have some similar mutation features as well as different characteristics. It is also one of the results obtained in this study that the domains where the most mutations are detected on the genome are regions that have properties that affect the interaction of the virus with the host.

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Schirawski, Jan, Gertrud Mannhaupt, Karin Münch, Thomas Brefort, Kerstin Schipper, Gunther Doehlemann, Maurizio Di Stasio, et al. "Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison." Science 330, no. 6010 (December 9, 2010): 1546–48. http://dx.doi.org/10.1126/science.1195330.

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Biotrophic pathogens, such as the related maize pathogenic fungi Ustilago maydis and Sporisorium reilianum, establish an intimate relationship with their hosts by secreting protein effectors. Because secreted effectors interacting with plant proteins should rapidly evolve, we identified variable genomic regions by sequencing the genome of S. reilianum and comparing it with the U. maydis genome. We detected 43 regions of low sequence conservation in otherwise well-conserved syntenic genomes. These regions primarily encode secreted effectors and include previously identified virulence clusters. By deletion analysis in U. maydis, we demonstrate a role in virulence for four previously unknown diversity regions. This highlights the power of comparative genomics of closely related species for identification of virulence determinants.

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Zhang, Pengfei, Dike Jiang, Yin Wang, Xueping Yao, Yan Luo, and Zexiao Yang. "Comparison of De Novo Assembly Strategies for Bacterial Genomes." International Journal of Molecular Sciences 22, no. 14 (July 17, 2021): 7668. http://dx.doi.org/10.3390/ijms22147668.

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(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes, particularly when combined with short-read Illumina data. However, it is not clear how different assembly strategies affect genomic accuracy, completeness, and protein prediction. (2) Methods: we compare different assembly strategies for Haemophilus parasuis, which causes Glässer’s disease, characterized by fibrinous polyserositis and arthritis, in swine by using Illumina sequencing and long reads from the sequencing platforms of either Oxford Nanopore Technologies (ONT) or SMRT Pacific Biosciences (PacBio). (3) Results: Assembly with either PacBio or ONT reads, followed by polishing with Illumina reads, facilitated high-quality genome reconstruction and was superior to the long-read-only assembly and hybrid-assembly strategies when evaluated in terms of accuracy and completeness. An equally excellent method was correction with Homopolish after the ONT-only assembly, which had the advantage of avoiding hybrid sequencing with Illumina. Furthermore, by aligning transcripts to assembled genomes and their predicted CDSs, the sequencing errors of the ONT assembly were mainly indels that were generated when homopolymer regions were sequenced, thus critically affecting protein prediction. Polishing can fill indels and correct mistakes. (4) Conclusions: The assembly of bacterial genomes can be directly achieved by using long-read sequencing techniques. To maximize assembly accuracy, it is essential to polish the assembly with homologous sequences of related genomes or sequencing data from short-read technology.

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Stothard, Paul, Jason R. Grant, and Gary Van Domselaar. "Visualizing and comparing circular genomes using the CGView family of tools." Briefings in Bioinformatics 20, no. 4 (July 26, 2017): 1576–82. http://dx.doi.org/10.1093/bib/bbx081.

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Abstract Graphical genome maps are widely used to assess genome features and sequence characteristics. The CGView (Circular Genome Viewer) software family is a popular collection of tools for generating genome maps for bacteria, organelles and viruses. In this review, we describe the capabilities of the original CGView program along with those of subsequent companion applications, including the CGView Server and the CGView Comparison Tool. We also discuss GView, a graphical user interface-enabled rewrite of CGView, and the GView Server, which offers several integrated analyses for identifying shared or unique genome regions relative to a collection of comparison genomes. We conclude with some remarks about our current development efforts related to CGView aimed at adding new functionality while increasing ease of use.

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Bacusmo, Jo Marie, Julie Bokor, Kathy Savage, and Valérie de Crécy-Lagard. "Identifying Pathogenic Islands through Genome Comparison." American Biology Teacher 81, no. 8 (October 1, 2019): 577–81. http://dx.doi.org/10.1525/abt.2019.81.8.577.

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Bioinformatics, the study of biological data using various computational techniques, is a very important aspect of biology, and its integration would greatly benefit current high school curricula. However, because most bioinformatics tools have not been readily accessible until recently, most high school instructors were not exposed to them during their formative years. We describe a bioinformatics-based module that introduces the application of genome comparison in the identification of “pathogenic islands.” The module also introduces foundational concepts of horizontal gene transfer and the genetic basis of virulence, with a special focus on antibiotic resistance – a theme teachers and students alike can easily connect and relate to. The module takes students on a journey: from conceptualizing the perfect pathogen, to an immersive experience of being a pathogen, and finally the experience of being a research scientist identifying drug-resistant genes and other virulence factors using the bioinformatics tool of genome comparison.

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Alekshun, Michael N. "Beyond comparison—antibiotics from genome data?" Nature Biotechnology 19, no. 12 (December 2001): 1124–25. http://dx.doi.org/10.1038/nbt1201-1124.

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Payne, G. A., W. C. Nierman, J. R. Wortman, B. L. Pritchard, D. Brown, R. A. Dean, D. Bhatnagar, T. E. Cleveland, Masayuki Machida, and J. Yu. "Whole genome comparison ofAspergillus flavusandA. oryzae." Medical Mycology 44, s1 (January 2006): 9–11. http://dx.doi.org/10.1080/13693780600835716.

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Wortman, J. R., N. Fedorova, J. Crabtree, V. Joardar, R. Maiti, B. J. Haas, P. Amedeo, et al. "Whole genome comparison of theA. fumigatusfamily." Medical Mycology 44, s1 (January 2006): 3–7. http://dx.doi.org/10.1080/13693780600835799.

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Abouelhoda, Mohamed Ibrahim, and Enno Ohlebusch. "Chaining algorithms for multiple genome comparison." Journal of Discrete Algorithms 3, no. 2-4 (June 2005): 321–41. http://dx.doi.org/10.1016/j.jda.2004.08.011.

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Fu, Li M., and Casey S. Fu-Liu. "Genome Comparison ofMycobacterium tuberculosisand Other Bacteria." OMICS: A Journal of Integrative Biology 6, no. 2 (April 2002): 199–206. http://dx.doi.org/10.1089/153623102760092797.

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Davison, Andrew J., Aidan Dolan, Parvis Akter, Clare Addison, Derrick J. Dargan, Donald J. Alcendor, Duncan J. McGeoch, and Gary S. Hayward. "The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome." Journal of General Virology 84, no. 4 (April 1, 2003): 1053. http://dx.doi.org/10.1099/0022-1317-84-4-1053.

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Liu, Hongshan, Zhihai Su, Shuiqing Yu, Jialin Liu, Xiaojuan Yin, Guowei Zhang, Wei Liu, and Bin Li. "Genome Comparison Reveals Mutation Hotspots in the Chloroplast Genome and Phylogenetic Relationships of Ormosia Species." BioMed Research International 2019 (August 21, 2019): 1–11. http://dx.doi.org/10.1155/2019/7265030.

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The papilionoid legume genus Ormosia comprises approximately 130 species, which are distributed mostly in the Neotropics, with some species in eastern Asia and northeastern Australia. The taxonomy and evolutionary history remain unclear due to the lack of a robust species-level phylogeny. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. In this study, we determined the complete chloroplast genome sequences of five Ormosia species by Illumina sequencing. The Ormosia chloroplast genomes displayed the typical quadripartite structure of angiosperms, which consisted of a pair of inverted regions separated by a large single-copy region and a small single-copy region. The location and distribution of repeat sequences and microsatellites were determined. Comparative analyses highlighted a wide spectrum of variation, with trnK-rbcL, atpE-trnS-rps4, trnC-petN, trnS-psbZ-trnG, trnP-psaJ-rpl33, and clpP intron being the most variable regions. Phylogenetic analysis revealed that Ormosia is in the Papilionoideae clade and is sister to the Lupinus clade. Overall, this study, which provides Ormosia chloroplast genomic resources and a comparative analysis of Ormosia chloroplast genomes, will be beneficial for the evolutionary study and phylogenetic reconstruction of the genus Ormosia and molecular barcoding in population genetics and will provide insight into the chloroplast genome evolution of legumes.

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Svitashev, Sergei, Tomas Bryngelsson, Xiaomei Li, and Richard RC Wang. "Genome-specific repetitive DNA and RAPD markers for genome identification in Elymus and Hordelymus." Genome 41, no. 1 (February 1, 1998): 120–28. http://dx.doi.org/10.1139/g97-108.

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We have developed RFLP and RAPD markers specific for the genomes involved in the evolution of Elymus species, i.e., the St, Y, H, P, and W genomes. Two P genome specific repetitive DNA sequences, pAgc1 (350 bp) and pAgc30 (458 bp), and three W genome specific sequences, pAuv3 (221 bp), pAuv7 (200 bp), and pAuv13 (207 bp), were isolated from the genomes of Agropyron cristatum and Australopyrum velutinum, respectively. Attempts to find Y genome specific sequences were not successful. Primary-structure analysis demonstrated that pAgc1 (P genome) and pAgc30 (P genome) share 81% similarity over a 227-bp stretch. The three W genome specific sequences were also highly homologous. Sequence comparison analysis revealed no homology to sequences in the EMBL- GenBank databases. Three to four genome-specific RAPD markers were found for each of the five genomes. Genome-specific bands were cloned and demonstrated to be mainly low-copy sequences present in various Triticeae species. The RFLP and RAPD markers obtained, together with the previously described H and St genome specific clones pHch2 and pPlTaq2.5 and the Ns genome specific RAPD markers were used to investigate the genomic composition of a few Elymus species and Hordelymus europaeus, whose genome formulas were unknown. Our results demonstrate that only three of eight Elymus species examined (the tetraploid species Elymus grandis and the hexaploid speciesElymus caesifolius and Elymus borianus) really belong to Elymus.

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Sedlazeck, Fritz J., Andi Dhroso, Dale L. Bodian, Justin Paschall, Farrah Hermes, and Justin M. Zook. "Tools for annotation and comparison of structural variation." F1000Research 6 (October 3, 2017): 1795. http://dx.doi.org/10.12688/f1000research.12516.1.

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The impact of structural variants (SVs) on a variety of organisms and diseases like cancer has become increasingly evident. Methods for SV detection when studying genomic differences across cells, individuals or populations are being actively developed. Currently, just a few methods are available to compare different SVs callsets, and no specialized methods are available to annotate SVs that account for the unique characteristics of these variant types. Here, we introduce SURVIVOR_ant, a tool that compares types and breakpoints for candidate SVs from different callsets and enables fast comparison of SVs to genomic features such as genes and repetitive regions, as well as to previously established SV datasets such as from the 1000 Genomes Project. As proof of concept we compared 16 SV callsets generated by different SV calling methods on a single genome, the Genome in a Bottle sample HG002 (Ashkenazi son), and annotated the SVs with gene annotations, 1000 Genomes Project SV calls, and four different types of repetitive regions. Computation time to annotate 134,528 SVs with 33,954 of annotations was 22 seconds on a laptop.

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Shao-Qing, Tang, Zhang Yuan, Xu Qing, Sun Dong-Xiao, and Yu Ying. "Comparison of methylation level of genomes among different animal species and various tissues." Chinese Journal of Agricultural Biotechnology 4, no. 1 (April 2007): 75–79. http://dx.doi.org/10.1017/s1479236207001179.

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AbstractThe methylation levels of genomes were compared in swine, cattle, sheep, rat, chicken and duck, using the methylation-sensitive amplification polymorphism technique (MSAP). The results showed that the methylation levels in genomes of the species investigated were mostly about 40–50% (except cattle); the methylation level varied in different species; the methylation pattern in various tissues of each species was specific; for the same species, the methylation level of the tissue genome was mostly higher than that of the blood genome; the difference of methylation level between birds and mammals was not significant, however mammals appeared to have a lower hemi-methylation frequency and higher full methylation frequency than birds.

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McCann, Angela, James A. Cotton, and James O. McInerney. "The tree of genomes: An empirical comparison of genome phylogeny reconstruction methods." BMC Evolutionary Biology 8, no. 1 (2008): 312. http://dx.doi.org/10.1186/1471-2148-8-312.

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Cheng, Hui, Jinfeng Li, Hong Zhang, Binhua Cai, Zhihong Gao, Yushan Qiao, and Lin Mi. "The complete chloroplast genome sequence of strawberry (Fragaria × ananassaDuch.) and comparison with related species of Rosaceae." PeerJ 5 (October 12, 2017): e3919. http://dx.doi.org/10.7717/peerj.3919.

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Compared with other members of the family Rosaceae, the chloroplast genomes ofFragariaspecies exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing ofFragariaspecies is needed. In this study, we sequenced the complete chloroplast genome ofF. × ananassa‘Benihoppe’ using the Illumina HiSeq 2500-PE150 platform and then performed a combination ofde novoassembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of theF. × ananassa‘Benihoppe’ chloroplast genome is 155,549 bp, representing the smallestFragariachloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content inFragaria, particularly among three octoploid strawberries which wereF. × ananassa‘Benihoppe’,F.chiloensis(GP33) andF.virginiana(O477). However, when the sequences of the coding and non-coding regions ofF. × ananassa‘Benihoppe’ were compared in detail with those ofF.chiloensis(GP33) andF.virginiana(O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK,trnS-trnG,atpF-atpH,trnC-petN,trnT-psbDandtrnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genusFragaria.

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Zhang, Tong, Weiqing Xing, Aoming Wang, Na Zhang, Ling Jia, Sanyuan Ma, and Qingyou Xia. "Comparison of Long-Read Methods for Sequencing and Assembly of Lepidopteran Pest Genomes." International Journal of Molecular Sciences 24, no. 1 (December 30, 2022): 649. http://dx.doi.org/10.3390/ijms24010649.

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Lepidopteran species are mostly pests, causing serious annual economic losses. High-quality genome sequencing and assembly uncover the genetic foundation of pest occurrence and provide guidance for pest control measures. Long-read sequencing technology and assembly algorithm advances have improved the ability to timeously produce high-quality genomes. Lepidoptera includes a wide variety of insects with high genetic diversity and heterozygosity. Therefore, the selection of an appropriate sequencing and assembly strategy to obtain high-quality genomic information is urgently needed. This research used silkworm as a model to test genome sequencing and assembly through high-coverage datasets by de novo assemblies. We report the first nearly complete telomere-to-telomere reference genome of silkworm Bombyx mori (P50T strain) produced by Pacific Biosciences (PacBio) HiFi sequencing, and highly contiguous and complete genome assemblies of two other silkworm strains by Oxford Nanopore Technologies (ONT) or PacBio continuous long-reads (CLR) that were unrepresented in the public database. Assembly quality was evaluated by use of BUSCO, Inspector, and EagleC. It is necessary to choose an appropriate assembler for draft genome construction, especially for low-depth datasets. For PacBio CLR and ONT sequencing, NextDenovo is superior. For PacBio HiFi sequencing, hifiasm is better. Quality assessment is essential for genome assembly and can provide better and more accurate results. For chromosome-level high-quality genome construction, we recommend using 3D-DNA with EagleC evaluation. Our study references how to obtain and evaluate high-quality genome assemblies, and is a resource for biological control, comparative genomics, and evolutionary studies of Lepidopteran pests and related species.

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Temel, Melih, Yasin Kaymaz, Duygu Ateş, Abdullah Kahraman, and Muhammed Bahattin Tanyolaç. "The Complete Chloroplast Genome Sequence of Cicer bijugum, Genome Organization, and Comparison with Related Species." Current Genomics 23, no. 1 (January 2022): 50–65. http://dx.doi.org/10.2174/1389202923666220211113708.

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Background: Chickpea is one of the legumes that is very important for Turkey and is frequently preferred especially in human nourishment thanks to its rich nutritional content. Chloroplasts, which have their own genetic material, are organelles responsible for photosynthesis in plant cells and their genome contains non-trivial information about the molecular features and evolutionary process of plants. Objective: Current study aimed at revealing complete chloroplast genome sequence of one of the wild type Cicer species Cicer bijugum and comparing its genome with cultivated Cicer species Cicer arietinum by using bioinformatics analysis tools. There are no study about revealing chloroplast genome sequence of Cicer species except the cultivated one Cicer arietinum. Therefore, we targeted to reveal the complete chloroplast genome sequence of wild type Cicer species Cicer bijugum and compare the chloroplast genome of Cicer bijugum with the cultivated one Cicer arietinum. Methods: In this study, we sequenced the whole chloroplast genome of Cicer bijugum, one of the wild types of chickpea species, with the help Next Generation Sequencing platform and compared it with the chloroplast genome of the cultivated chickpea species, Cicer arietinum by using online bioinformatics analysis tools. Results: We determined the size of the chloroplast genome of C. bijugum as 124,804 bp and found that C. bijugum did not contain an inverted repeat region in its chloroplast genome. Comparative analysis of the C. bijugum chloroplast genome uncovered thirteen hotspot regions (psbA, matK, rpoB, rpoC1, rpoC2, psbI, psbK, accD, rps19, ycf2, ycf1, rps15 and ndhF) and seven of them (matK, accD, rps19, ycf1, ycf2, rps15 and ndhF) could potentially be used as strong molecular markers for species identification. It has been determined that C. bijugum was phylogenetically closer to cultivated chickpea as compared to the other species. Conclusion: It is aimed that the data obtained from this study, which is the first study in which whole chloroplast genomes of wild chickpea species were sequenced, will guide researchers in future molecular, evolutionary and genetic engineering studies with chickpea species.

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Ren, Jie, Xin Bai, Yang Young Lu, Kujin Tang, Ying Wang, Gesine Reinert, and Fengzhu Sun. "Alignment-Free Sequence Analysis and Applications." Annual Review of Biomedical Data Science 1, no. 1 (July 20, 2018): 93–114. http://dx.doi.org/10.1146/annurev-biodatasci-080917-013431.

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Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads. Alignment-free approaches based on the counts of word patterns in NGS data do not depend on the complete genome and are generally computationally efficient. Thus, they contribute significantly to genome and metagenome comparison. Recently, novel statistical approaches have been developed for the comparison of both long and shotgun sequences. These approaches have been applied to many problems, including the comparison of gene regulatory regions, genome sequences, metagenomes, binning contigs in metagenomic data, identification of virus–host interactions, and detection of horizontal gene transfers. We provide an updated review of these applications and other related developments of word count–based approaches for alignment-free sequence analysis.

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Takeshita, Kazutaka, and Yoshitomo Kikuchi. "Genomic Comparison of Insect Gut Symbionts from Divergent Burkholderia Subclades." Genes 11, no. 7 (July 3, 2020): 744. http://dx.doi.org/10.3390/genes11070744.

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Stink bugs of the superfamilies Coreoidea and Lygaeoidea establish gut symbioses with environmentally acquired bacteria of the genus Burkholderia sensu lato. In the genus Burkholderia, the stink bug-associated strains form a monophyletic clade, named stink bug-associated beneficial and environmental (SBE) clade (or Caballeronia). Recently, we revealed that members of the family Largidae of the superfamily Pyrrhocoroidea are associated with Burkholderia but not specifically with the SBE Burkholderia; largid bugs harbor symbionts that belong to a clade of plant-associated group of Burkholderia, called plant-associated beneficial and environmental (PBE) clade (or Paraburkholderia). To understand the genomic features of Burkholderia symbionts of stink bugs, we isolated two symbiotic Burkholderia strains from a bordered plant bug Physopellta gutta (Pyrrhocoroidea: Largidae) and determined their complete genomes. The genome sizes of the insect-associated PBE (iPBE) are 9.5 Mb and 11.2 Mb, both of which are larger than the genomes of the SBE Burkholderia symbionts. A whole-genome comparison between two iPBE symbionts and three SBE symbionts highlighted that all previously reported symbiosis factors are shared and that 282 genes are specifically conserved in the five stink bug symbionts, over one-third of which have unknown function. Among the symbiont-specific genes, about 40 genes formed a cluster in all five symbionts; this suggests a “symbiotic island” in the genome of stink bug-associated Burkholderia.

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Yan, Kan, Juan Ran, Songming Bao, Yimeng Li, Rehmat Islam, Nai Zhang, Wei Zhao, Yanni Ma, and Chao Sun. "The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species." Genes 14, no. 1 (December 25, 2022): 64. http://dx.doi.org/10.3390/genes14010064.

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Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

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Tsai, Ming-Hsin, Yen-Yi Liu, Von-Wun Soo, and Chih-Chieh Chen. "A New Genome-to-Genome Comparison Approach for Large-Scale Revisiting of Current Microbial Taxonomy." Microorganisms 7, no. 6 (June 3, 2019): 161. http://dx.doi.org/10.3390/microorganisms7060161.

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Microbial diversity has always presented taxonomic challenges. With the popularity of next-generation sequencing technology, more unculturable bacteria have been sequenced, facilitating the discovery of additional new species and complicated current microbial classification. The major challenge is to assign appropriate taxonomic names. Hence, assessing the consistency between taxonomy and genomic relatedness is critical. We proposed and applied a genome comparison approach to a large-scale survey to investigate the distribution of genomic differences among microorganisms. The approach applies a genome-wide criterion, homologous coverage ratio (HCR), for describing the homology between species. The survey included 7861 microbial genomes that excluded plasmids, and 1220 pairs of genera exhibited ambiguous classification. In this study, we also compared the performance of HCR and average nucleotide identity (ANI). The results indicated that HCR and ANI analyses yield comparable results, but a few examples suggested that HCR has a superior clustering effect. In addition, we used the Genome Taxonomy Database (GTDB), the gold standard for taxonomy, to validate our analysis. The GTDB offers 120 ubiquitous single-copy proteins as marker genes for species classification. We determined that the analysis of the GTDB still results in classification boundary blur between some genera and that the marker gene-based approach has limitations. Although the choice of marker genes has been quite rigorous, the bias of marker gene selection remains unavoidable. Therefore, methods based on genomic alignment should be considered for use for species classification in order to avoid the bias of marker gene selection. On the basis of our observations of microbial diversity, microbial classification should be re-examined using genome-wide comparisons.

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Muravenko, Olga V., Alexander R. Fedotov, Elizabeth O. Punina, Ludmila I. Fedorova, Valerii G. Grif, and Alexander V. Zelenin. "Comparison of chromosome BrdU-Hoechst-Giemsa banding patterns of the A1 and (AD)2 genomes of cotton." Genome 41, no. 4 (August 1, 1998): 616–25. http://dx.doi.org/10.1139/g98-049.

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The karyotypes of diploid cotton, Gossypium herbaceum L. var. africanum (Watt) Mauer, and tetraploid cotton, Gossypium barbadense L., were studied by BrdU-Hoechst-Giemsa banding, using a specially developed image-analysis system. The patterns obtained are represented by the slightly and intensively stained bands that correspond, respectively, to the early replicating DNA and the DNA replicating in the mid and late S period. The number of main Giemsa-positive bands varies from 2 to 9 per chromosome. The banding patterns of all homologous pairs are specific in both the A1 and (AD)2 genomes. This made possible the complete classification of the chromosomes. Based on the similarity of the BrdU-Hoechst-Giemsa banding patterns and the sizes of the chromosomes in the A1 and (AD)2 genomes, we divided the (AD)2 genome into Ab and Db subgenomes and classified their chromosomes according to the A1 genome chromosome classification. The BrdU-Hoechst-Giemsa banding pattern of the Db subgenome is basically similar to that of the A1 genome and Ab subgenome, but the differences between it and the banding patterns of the A1 genome and Ab subgenome are more significant than the differences between the latter two genomes. The similarity of the intragenomic banding patterns between nonhomologous chromosomes a and b, c and g, d and e, f and j, h and i, and l and m was revealed. Based on our results, we suggest that the ancestral cotton genome contained 7 homologous pairs of chromosomes. The results prove the feasibility of image-analysis techniques for identification and quantitative analysis of chromosomes, especially with regard to small-chromosome species.Key words: cotton, A1 and (AD)2 genomes, chromosome identification, BrdU-Hoechst-Giemsa banding, image analysis.

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Davison, Andrew J., Aidan Dolan, Parvis Akter, Clare Addison, Derrick J. Dargan, Donald J. Alcendor, Duncan J. McGeoch, and Gary S. Hayward. "The human cytomegalovirus genome revisited: comparison with the chimpanzee cytomegalovirus genome FN1." Journal of General Virology 84, no. 1 (January 1, 2003): 17–28. http://dx.doi.org/10.1099/vir.0.18606-0.

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Livingstone, Kevin D., Vincent K. Lackney, James R. Blauth, Rik van Wijk, and Molly Kyle Jahn. "Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae." Genetics 152, no. 3 (July 1, 1999): 1183–202. http://dx.doi.org/10.1093/genetics/152.3.1183.

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Abstract We have created a genetic map of Capsicum (pepper) from an interspecific F2 population consisting of 11 large (76.2–192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7 cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes included in this study to positions throughout the pepper map suggests that no major losses have occurred during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed that 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome. Through these maps and the potato map, we determined the number and types of rearrangements that differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there have been 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that differentiate the two pepper mapping parents.

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Kawai, Mikihiko, Keiichiro Nakao, Ikuo Uchiyama, and Ichizo Kobayashi. "How genomes rearrange: Genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms." Gene 383 (November 2006): 52–63. http://dx.doi.org/10.1016/j.gene.2006.07.013.

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Pei, Jialong, Yong Wang, Juan Zhuo, Huibin Gao, Naresh Vasupalli, Dan Hou, and Xinchun Lin. "Complete Chloroplast Genome Features of Dendrocalamusfarinosus and Its Comparison and Evolutionary Analysis with Other Bambusoideae Species." Genes 13, no. 9 (August 24, 2022): 1519. http://dx.doi.org/10.3390/genes13091519.

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Dendrocalamus farinosus is one of the essential bamboo species mainly used for food and timber in the southwestern region of China. In this study, the complete chloroplast (cp) genome of D. farinosus is sequenced, assembled, and the phylogenetic relationship analyzed. The cp genome has a circular and quadripartite structure, has a total length of 139,499 bp and contains 132 genes: 89 protein-coding genes, eight rRNAs and 35 tRNAs. The repeat analyses showed that three types of repeats (palindromic, forward and reverse) are present in the genome. A total of 51 simple sequence repeats are identified in the cp genome. The comparative analysis between different species belonging to Dendrocalamus revealed that although the cp genomes are conserved, many differences exist between the genomes. The analysis shows that the non-coding regions were more divergent than the coding regions, and the inverted repeat regions are more conserved than the single-copy regions. Moreover, these results also indicate that rpoC2 may be used to distinguish between different bamboo species. Phylogenetic analysis results supported that D. farinosus was closely related to D. latiflorus. Furthermore, these bamboo species’ geographical distribution and rhizome types indicate two evolutionary pathways: one is from the tropics to the alpine zone, and the other is from the tropics to the warm temperate zone. Our study will be helpful in the determination of the cp genome sequences of D. farinosus, and provides new molecular data to understand the Bambusoideae evolution.

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Androsiuk, Piotr, Jan Paweł Jastrzębski, Łukasz Paukszto, Adam Okorski, Agnieszka Pszczółkowska, Katarzyna Joanna Chwedorzewska, Justyna Koc, Ryszard Górecki, and Irena Giełwanowska. "The complete chloroplast genome ofColobanthus apetalus(Labill.) Druce: genome organization and comparison with related species." PeerJ 6 (May 23, 2018): e4723. http://dx.doi.org/10.7717/peerj.4723.

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Colobanthus apetalusis a member of the genusColobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genusColobanthusconsists of 25 species, includingColobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome ofC. apetalus.The complete cp genome ofC. apetalushas the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison ofC. apetalusandC. quitensiscp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae andC. apetalus,and it revealed thatC. apetalusandC. quitensisform a clade that is closely related toSilenespecies andAgrostemma githago. Moreover, the genusSileneappeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

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Lam, Hugo Y. K., Michael J. Clark, Rui Chen, Rong Chen, Georges Natsoulis, Maeve O'Huallachain, Frederick E. Dewey, et al. "Performance comparison of whole-genome sequencing platforms." Nature Biotechnology 30, no. 1 (December 18, 2011): 78–82. http://dx.doi.org/10.1038/nbt.2065.

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Zhou, Leming, Jonathan Stanton, and Liliana Florea. "Universal seeds for cDNA-to-genome comparison." BMC Bioinformatics 9, no. 1 (2008): 36. http://dx.doi.org/10.1186/1471-2105-9-36.

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Journal articles on the topic 'Genome comparison'

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