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Prusokiene A, Boonham N, Fox A, Howard TP. Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent. PLoS One 2024; 19:e0298834. [PMID: 38512939 PMCID: PMC10956839 DOI: 10.1371/journal.pone.0298834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024] Open
Abstract
Current tools for estimating the substitution distance between two related sequences struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as false seeding and over-alignment, create a high barrier for the development of a stable estimator. This is especially true for viral genomes, which carry a high rate of mutation, small size, and sparse taxonomy. Developing an accurate substitution distance measure would help to elucidate the relationship between highly divergent sequences, interrogate their evolutionary history, and better facilitate the discovery of new viral genomes. To tackle these problems, we propose an approach that uses short-read mappers to create whole-genome maps, and gradient descent to isolate the homologous fraction and calculate the final distance value. We implement this approach as Mottle. With the use of simulated and biological sequences, Mottle was able to remain stable to 0.66-0.96 substitutions per base pair and identify viral outgroup genomes with 95% accuracy at the family-order level. Our results indicate that Mottle performs as well as existing programs in identifying taxonomic relationships, with more accurate numerical estimation of genomic distance over greater divergences. By contrast, one limitation is a reduced numerical accuracy at low divergences, and on genomes where insertions and deletions are uncommon, when compared to alternative approaches. We propose that Mottle may therefore be of particular interest in the study of viruses, viral relationships, and notably for viral discovery platforms, helping in benchmarking of homology search tools and defining the limits of taxonomic classification methods. The code for Mottle is available at https://github.com/tphoward/Mottle_Repo.
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Affiliation(s)
- Alisa Prusokiene
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
| | - Neil Boonham
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
| | - Adrian Fox
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
- Fera Ltd., Biotech Campus, York, United Kingdom
| | - Thomas P. Howard
- Faculty of Science, Agriculture and Engineering, School of Natural and Environmental Sciences, Newcastle University, United Kingdom
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2
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Lallemand T, Leduc M, Landès C, Rizzon C, Lerat E. An Overview of Duplicated Gene Detection Methods: Why the Duplication Mechanism Has to Be Accounted for in Their Choice. Genes (Basel) 2020; 11:E1046. [PMID: 32899740 PMCID: PMC7565063 DOI: 10.3390/genes11091046] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Gene duplication is an important evolutionary mechanism allowing to provide new genetic material and thus opportunities to acquire new gene functions for an organism, with major implications such as speciation events. Various processes are known to allow a gene to be duplicated and different models explain how duplicated genes can be maintained in genomes. Due to their particular importance, the identification of duplicated genes is essential when studying genome evolution but it can still be a challenge due to the various fates duplicated genes can encounter. In this review, we first describe the evolutionary processes allowing the formation of duplicated genes but also describe the various bioinformatic approaches that can be used to identify them in genome sequences. Indeed, these bioinformatic approaches differ according to the underlying duplication mechanism. Hence, understanding the specificity of the duplicated genes of interest is a great asset for tool selection and should be taken into account when exploring a biological question.
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Affiliation(s)
- Tanguy Lallemand
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Martin Leduc
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Claudine Landès
- IRHS, Agrocampus-Ouest, INRAE, Université d’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France; (T.L.); (M.L.); (C.L.)
| | - Carène Rizzon
- Laboratoire de Mathématiques et Modélisation d’Evry (LaMME), Université d’Evry Val d’Essonne, Université Paris-Saclay, UMR CNRS 8071, ENSIIE, USC INRAE, 23 bvd de France, CEDEX, 91037 Evry Paris, France;
| | - Emmanuelle Lerat
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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Abstract
Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make most effective use of our rapidly growing databases of whole genomes.
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Affiliation(s)
- Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA.
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4
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Lee J, Hong WY, Cho M, Sim M, Lee D, Ko Y, Kim J. Synteny Portal: a web-based application portal for synteny block analysis. Nucleic Acids Res 2016; 44:W35-40. [PMID: 27154270 PMCID: PMC4987893 DOI: 10.1093/nar/gkw310] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/12/2016] [Indexed: 11/12/2022] Open
Abstract
Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomic regions conserved among multiple species, is key to understanding genomic architecture and the evolutionary history of genomes. However, the construction and visualization of such synteny blocks from multiple species are very challenging, especially for biologists with a lack of computational skills. Here, we present Synteny Portal, a versatile web-based application portal for constructing, visualizing and browsing synteny blocks. With Synteny Portal, users can easily (i) construct synteny blocks among multiple species by using prebuilt alignments in the UCSC genome browser database, (ii) visualize and download syntenic relationships as high-quality images, (iii) browse synteny blocks with genetic information and (iv) download the details of synteny blocks to be used as input for downstream synteny-based analyses, all in an intuitive and easy-to-use web-based interface. We believe that Synteny Portal will serve as a highly valuable tool that will enable biologists to easily perform comparative genomics studies by compensating limitations of existing tools. Synteny Portal is freely available at http://bioinfo.konkuk.ac.kr/synteny_portal.
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Affiliation(s)
- Jongin Lee
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
| | - Woon-Young Hong
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
| | - Minah Cho
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
| | - Mikang Sim
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
| | - Daehwan Lee
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
| | - Younhee Ko
- Department of Clinical Genetics, Department of Pediatrics, Yonsei University College of Medicine, Seoul 03722, South Korea
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Seoul 05029, South Korea
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Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:812-23. [PMID: 25953741 DOI: 10.1111/1758-2229.12297] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 04/13/2015] [Indexed: 05/07/2023]
Abstract
Bdellovibrio bacteriovorus are small Deltaproteobacteria that invade, kill and assimilate their prey. Metagenomic assembly analysis of the microbial mats of an arsenic rich, hot spring was performed to describe the genotypes of the predator Bdellovibrio and the ecogenetically adapted taxa Enterobacter. The microbial mats were enriched with Bdellovibrio (1.3%) and several Gram-negative bacteria including Bordetella (16%), Enterobacter (6.8%), Burkholderia (4.8%), Acinetobacter (2.3%) and Yersinia (1%). A high-quality (47 contigs, 25X coverage; 3.5 Mbp) draft genome of Bdellovibrio (strain ArHS; Arsenic Hot Spring) was reassembled, which lacked the marker gene Bd0108 associated with the usual method of prey interaction and invasion for this genus, while maintaining genes coding for the hydrolytic enzymes necessary for prey assimilation. By filtering microbial mat samples (< 0.45 μm) to enrich for small predatory cell sizes, we observed Bdellovibrio-like cells attached side-on to E. coli through electron microscopy. Furthermore, a draft pan-genome of the dominant potential host taxon, Enterobacter cloacae ArHS (4.8 Mb), along with three of its viral genotypes (n = 3; 42 kb, 49 kb and 50 kb), was assembled. These data were further used to analyse the population level evolutionary dynamics (taxonomical and functional) of reconstructed genotypes.
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Affiliation(s)
- Naseer Sangwan
- Department of Zoology, University of Delhi, Delhi, 110007, India
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Carey Lambert
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Anukriti Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - R Elizabeth Sockett
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India
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Sharma A, Sangwan N, Negi V, Kohli P, Khurana JP, Rao DLN, Lal R. Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite. BMC Genomics 2015; 16:313. [PMID: 25898829 PMCID: PMC4405911 DOI: 10.1186/s12864-015-1488-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 03/25/2015] [Indexed: 11/16/2022] Open
Abstract
Background Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g−1 sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient. Results Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g−1 of soil). Conclusions Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anukriti Sharma
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Naseer Sangwan
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Vivek Negi
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Puneet Kohli
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
| | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India.
| | - Desiraju Lakshmi Narsimha Rao
- All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038, India.
| | - Rup Lal
- Department of Zoology, University of Delhi, New Delhi, 110007, India.
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7
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Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data. ISME JOURNAL 2013; 8:398-408. [PMID: 24030592 PMCID: PMC3906814 DOI: 10.1038/ismej.2013.153] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 11/14/2022]
Abstract
Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the ‘upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes.
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8
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Abstract
MOTIVATION The exponential growth of protein sequence databases has increasingly made the fundamental question of searching for homologs a computational bottleneck. The amount of unique data, however, is not growing nearly as fast; we can exploit this fact to greatly accelerate homology search. Acceleration of programs in the popular PSI/DELTA-BLAST family of tools will not only speed-up homology search directly but also the huge collection of other current programs that primarily interact with large protein databases via precisely these tools. RESULTS We introduce a suite of homology search tools, powered by compressively accelerated protein BLAST (CaBLASTP), which are significantly faster than and comparably accurate with all known state-of-the-art tools, including HHblits, DELTA-BLAST and PSI-BLAST. Further, our tools are implemented in a manner that allows direct substitution into existing analysis pipelines. The key idea is that we introduce a local similarity-based compression scheme that allows us to operate directly on the compressed data. Importantly, CaBLASTP's runtime scales almost linearly in the amount of unique data, as opposed to current BLASTP variants, which scale linearly in the size of the full protein database being searched. Our compressive algorithms will speed-up many tasks, such as protein structure prediction and orthology mapping, which rely heavily on homology search. AVAILABILITY CaBLASTP is available under the GNU Public License at http://cablastp.csail.mit.edu/ CONTACT bab@mit.edu.
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Affiliation(s)
- Noah M Daniels
- Department of Computer Science, Tufts University, Medford, MA 02451, USA
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9
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Kim B, Yu HJ, Park SG, Shin JY, Oh M, Kim N, Mun JH. Identification and profiling of novel microRNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC PLANT BIOLOGY 2012; 12:218. [PMID: 23163954 PMCID: PMC3554443 DOI: 10.1186/1471-2229-12-218] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 11/14/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are one of the functional non-coding small RNAs involved in the epigenetic control of the plant genome. Although plants contain both evolutionary conserved miRNAs and species-specific miRNAs within their genomes, computational methods often only identify evolutionary conserved miRNAs. The recent sequencing of the Brassica rapa genome enables us to identify miRNAs and their putative target genes. In this study, we sought to provide a more comprehensive prediction of B. rapa miRNAs based on high throughput small RNA deep sequencing. RESULTS We sequenced small RNAs from five types of tissue: seedlings, roots, petioles, leaves, and flowers. By analyzing 2.75 million unique reads that mapped to the B. rapa genome, we identified 216 novel and 196 conserved miRNAs that were predicted to target approximately 20% of the genome's protein coding genes. Quantitative analysis of miRNAs from the five types of tissue revealed that novel miRNAs were expressed in diverse tissues but their expression levels were lower than those of the conserved miRNAs. Comparative analysis of the miRNAs between the B. rapa and Arabidopsis thaliana genomes demonstrated that redundant copies of conserved miRNAs in the B. rapa genome may have been deleted after whole genome triplication. Novel miRNA members seemed to have spontaneously arisen from the B. rapa and A. thaliana genomes, suggesting the species-specific expansion of miRNAs. We have made this data publicly available in a miRNA database of B. rapa called BraMRs. The database allows the user to retrieve miRNA sequences, their expression profiles, and a description of their target genes from the five tissue types investigated here. CONCLUSIONS This is the first report to identify novel miRNAs from Brassica crops using genome-wide high throughput techniques. The combination of computational methods and small RNA deep sequencing provides robust predictions of miRNAs in the genome. The finding of numerous novel miRNAs, many with few target genes and low expression levels, suggests the rapid evolution of miRNA genes. The development of a miRNA database, BraMRs, enables us to integrate miRNA identification, target prediction, and functional annotation of target genes. BraMRs will represent a valuable public resource with which to study the epigenetic control of B. rapa and other closely related Brassica species. The database is available at the following link: http://bramrs.rna.kr [1].
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Affiliation(s)
- Bumjin Kim
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Hee-Ju Yu
- Department of Life Sciences, The Catholic University of Korea, 43 Jibong-ro Wonmi-gu, Bucheon, 420-743, Korea
| | - Sin-Gi Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Ja Young Shin
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Mijin Oh
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
| | - Namshin Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-gu, Daejeon, 305-806, Korea
| | - Jeong-Hwan Mun
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro Gwonseon-gu, Suwon, 441-707, Korea
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10
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Abstract
Whole-genome alignment (WGA) is the prediction of evolutionary relationships at the nucleotide level between two or more genomes. It combines aspects of both colinear sequence alignment and gene orthology prediction, and is typically more challenging to address than either of these tasks due to the size and complexity of whole genomes. Despite the difficulty of this problem, numerous methods have been developed for its solution because WGAs are valuable for genome-wide analyses, such as phylogenetic inference, genome annotation, and function prediction. In this chapter, we discuss the meaning and significance of WGA and present an overview of the methods that address it. We also examine the problem of evaluating whole-genome aligners and offer a set of methodological challenges that need to be tackled in order to make the most effective use of our rapidly growing databases of whole genomes.
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Affiliation(s)
- Colin N Dewey
- Biostatistics and Medical Informatics and Computer Sciences, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA.
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11
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Audemard E, Schiex T, Faraut T. Detecting long tandem duplications in genomic sequences. BMC Bioinformatics 2012; 13:83. [PMID: 22568762 PMCID: PMC3464658 DOI: 10.1186/1471-2105-13-83] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 05/08/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. RESULTS In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. CONCLUSIONS ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.
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Affiliation(s)
- Eric Audemard
- Unité de Biométrie et Intelligence Artificielle, UR 875, INRA, Toulouse, France.
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Mahmood K, Webb GI, Song J, Whisstock JC, Konagurthu AS. Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acids Res 2011; 40:e44. [PMID: 22210858 PMCID: PMC3315314 DOI: 10.1093/nar/gkr1261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Broadly, computational approaches for ortholog assignment is a three steps process: (i) identify all putative homologs between the genomes, (ii) identify gene anchors and (iii) link anchors to identify best gene matches given their order and context. In this article, we engineer two methods to improve two important aspects of this pipeline [specifically steps (ii) and (iii)]. First, computing sequence similarity data [step (i)] is a computationally intensive task for large sequence sets, creating a bottleneck in the ortholog assignment pipeline. We have designed a fast and highly scalable sort-join method (afree) based on k-mer counts to rapidly compare all pairs of sequences in a large protein sequence set to identify putative homologs. Second, availability of complex genomes containing large gene families with prevalence of complex evolutionary events, such as duplications, has made the task of assigning orthologs and co-orthologs difficult. Here, we have developed an iterative graph matching strategy where at each iteration the best gene assignments are identified resulting in a set of orthologs and co-orthologs. We find that the afree algorithm is faster than existing methods and maintains high accuracy in identifying similar genes. The iterative graph matching strategy also showed high accuracy in identifying complex gene relationships. Standalone afree available from http://vbc.med.monash.edu.au/∼kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/∼kmahmood/EGM2.
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Affiliation(s)
- Khalid Mahmood
- Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
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13
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Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K. i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res 2011; 40:e11. [PMID: 22102584 PMCID: PMC3258164 DOI: 10.1093/nar/gkr955] [Citation(s) in RCA: 138] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Comparative genomics is a powerful means to gain insight into the evolutionary processes that shape the genomes of related species. As the number of sequenced genomes increases, the development of software to perform accurate cross-species analyses becomes indispensable. However, many implementations that have the ability to compare multiple genomes exhibit unfavorable computational and memory requirements, limiting the number of genomes that can be analyzed in one run. Here, we present a software package to unveil genomic homology based on the identification of conservation of gene content and gene order (collinearity), i-ADHoRe 3.0, and its application to eukaryotic genomes. The use of efficient algorithms and support for parallel computing enable the analysis of large-scale data sets. Unlike other tools, i-ADHoRe can process the Ensembl data set, containing 49 species, in 1 h. Furthermore, the profile search is more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive homology. From ultra-conserved collinear regions between mammals and birds, by integrating coexpression information and protein–protein interactions, we identified more than 400 regions in the human genome showing significant functional coherence. The different algorithmical improvements ensure that i-ADHoRe 3.0 will remain a powerful tool to study genome evolution.
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14
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Dewey CN. Positional orthology: putting genomic evolutionary relationships into context. Brief Bioinform 2011; 12:401-12. [PMID: 21705766 PMCID: PMC3178058 DOI: 10.1093/bib/bbr040] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Orthology is a powerful refinement of homology that allows us to describe more precisely the evolution of genomes and understand the function of the genes they contain. However, because orthology is not concerned with genomic position, it is limited in its ability to describe genes that are likely to have equivalent roles in different genomes. Because of this limitation, the concept of ‘positional orthology’ has emerged, which describes the relation between orthologous genes that retain their ancestral genomic positions. In this review, we formally define this concept, for which we introduce the shorter term ‘toporthology’, with respect to the evolutionary events experienced by a gene’s ancestors. Through a discussion of recent studies on the role of genomic context in gene evolution, we show that the distinction between orthology and toporthology is biologically significant. We then review a number of orthology prediction methods that take genomic context into account and thus that may be used to infer the important relation of toporthology.
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Affiliation(s)
- Colin N Dewey
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 5785 Medical Sciences Center, 1300 University Ave, Madison, WI 53706, USA.
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Kristensen DM, Wolf YI, Mushegian AR, Koonin EV. Computational methods for Gene Orthology inference. Brief Bioinform 2011; 12:379-91. [PMID: 21690100 DOI: 10.1093/bib/bbr030] [Citation(s) in RCA: 150] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Accurate inference of orthologous genes is a pre-requisite for most comparative genomics studies, and is also important for functional annotation of new genomes. Identification of orthologous gene sets typically involves phylogenetic tree analysis, heuristic algorithms based on sequence conservation, synteny analysis, or some combination of these approaches. The most direct tree-based methods typically rely on the comparison of an individual gene tree with a species tree. Once the two trees are accurately constructed, orthologs are straightforwardly identified by the definition of orthology as those homologs that are related by speciation, rather than gene duplication, at their most recent point of origin. Although ideal for the purpose of orthology identification in principle, phylogenetic trees are computationally expensive to construct for large numbers of genes and genomes, and they often contain errors, especially at large evolutionary distances. Moreover, in many organisms, in particular prokaryotes and viruses, evolution does not appear to have followed a simple 'tree-like' mode, which makes conventional tree reconciliation inapplicable. Other, heuristic methods identify probable orthologs as the closest homologous pairs or groups of genes in a set of organisms. These approaches are faster and easier to automate than tree-based methods, with efficient implementations provided by graph-theoretical algorithms enabling comparisons of thousands of genomes. Comparisons of these two approaches show that, despite conceptual differences, they produce similar sets of orthologs, especially at short evolutionary distances. Synteny also can aid in identification of orthologs. Often, tree-based, sequence similarity- and synteny-based approaches can be combined into flexible hybrid methods.
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Affiliation(s)
- David M Kristensen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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Cai B, Yang X, Tuskan GA, Cheng ZM. MicroSyn: a user friendly tool for detection of microsynteny in a gene family. BMC Bioinformatics 2011; 12:79. [PMID: 21418570 PMCID: PMC3072343 DOI: 10.1186/1471-2105-12-79] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 03/18/2011] [Indexed: 12/04/2022] Open
Abstract
Background The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. For the normal protein-coding gene families, low bootstrap values are frequently encountered in some nodes, suggesting low confidence or likely inappropriateness of placement of those members in those nodes. Results We introduce MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface. MicroSyn is available from: http://fcsb.njau.edu.cn/microsyn/. Conclusions Case studies of the microRNA167 genes in plants and Xyloglucan ndotransglycosylase/Hydrolase family in Populus trichocarpa were presented to show the utility of the software. The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis.
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Affiliation(s)
- Bin Cai
- College of Horticulture, Nanjing Agricultural University, China
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Soderlund C, Bomhoff M, Nelson WM. SyMAP v3.4: a turnkey synteny system with application to plant genomes. Nucleic Acids Res 2011; 39:e68. [PMID: 21398631 PMCID: PMC3105427 DOI: 10.1093/nar/gkr123] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
SyMAP (Synteny Mapping and Analysis Program) was originally developed to compute synteny blocks between a sequenced genome and a FPC map, and has been extended to support pairs of sequenced genomes. SyMAP uses MUMmer to compute the raw hits between the two genomes, which are then clustered and filtered using the optional gene annotation. The filtered hits are input to the synteny algorithm, which was designed to discover duplicated regions and form larger-scale synteny blocks, where intervening micro-rearrangements are allowed. SyMAP provides extensive interactive Java displays at all levels of resolution along with simultaneous displays of multiple aligned pairs. The synteny blocks from multiple chromosomes may be displayed in a high-level dot plot or three-dimensional view, and the user may then drill down to see the details of a region, including the alignments of the hits to the gene annotation. These capabilities are illustrated by showing their application to the study of genome duplication, differential gene loss and transitive homology between sorghum, maize and rice. The software may be used from a website or standalone for the best performance. A project manager is provided to organize and automate the analysis of multi-genome groups. The software is freely distributed at http://www.agcol.arizona.edu/software/symap.
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Affiliation(s)
- Carol Soderlund
- BIO5 Institute, 1657 Helen Street, University of Arizona, Tucson, AZ 85721, USA.
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Synonymous Codon Usage, GC3, and Evolutionary Patterns Across Plastomes of Three Pooid Model Species: Emerging Grass Genome Models for Monocots. Mol Biotechnol 2011; 49:116-28. [DOI: 10.1007/s12033-011-9383-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Raffaele S, Win J, Cano LM, Kamoun S. Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans. BMC Genomics 2010; 11:637. [PMID: 21080964 PMCID: PMC3091767 DOI: 10.1186/1471-2164-11-637] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Accepted: 11/16/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation. RESULTS We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors. CONCLUSIONS This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.
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Affiliation(s)
- Sylvain Raffaele
- The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK
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Popendorf K, Tsuyoshi H, Osana Y, Sakakibara Y. Murasaki: a fast, parallelizable algorithm to find anchors from multiple genomes. PLoS One 2010; 5:e12651. [PMID: 20885980 PMCID: PMC2945767 DOI: 10.1371/journal.pone.0012651] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 08/06/2010] [Indexed: 12/24/2022] Open
Abstract
Background With the number of available genome sequences increasing rapidly, the magnitude of sequence data required for multiple-genome analyses is a challenging problem. When large-scale rearrangements break the collinearity of gene orders among genomes, genome comparison algorithms must first identify sets of short well-conserved sequences present in each genome, termed anchors. Previously, anchor identification among multiple genomes has been achieved using pairwise alignment tools like BLASTZ through progressive alignment tools like TBA, but the computational requirements for sequence comparisons of multiple genomes quickly becomes a limiting factor as the number and scale of genomes grows. Methodology/Principal Findings Our algorithm, named Murasaki, makes it possible to identify anchors within multiple large sequences on the scale of several hundred megabases in few minutes using a single CPU. Two advanced features of Murasaki are (1) adaptive hash function generation, which enables efficient use of arbitrary mismatch patterns (spaced seeds) and therefore the comparison of multiple mammalian genomes in a practical amount of computation time, and (2) parallelizable execution that decreases the required wall-clock and CPU times. Murasaki can perform a sensitive anchoring of eight mammalian genomes (human, chimp, rhesus, orangutan, mouse, rat, dog, and cow) in 21 hours CPU time (42 minutes wall time). This is the first single-pass in-core anchoring of multiple mammalian genomes. We evaluated Murasaki by comparing it with the genome alignment programs BLASTZ and TBA. We show that Murasaki can anchor multiple genomes in near linear time, compared to the quadratic time requirements of BLASTZ and TBA, while improving overall accuracy. Conclusions/Significance Murasaki provides an open source platform to take advantage of long patterns, cluster computing, and novel hash algorithms to produce accurate anchors across multiple genomes with computational efficiency significantly greater than existing methods. Murasaki is available under GPL at http://murasaki.sourceforge.net.
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Affiliation(s)
- Kris Popendorf
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Hachiya Tsuyoshi
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Yasunori Osana
- Department of Computer and Informatics Science, Seikei University, Musashino-shi, Tokyo, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
- * E-mail:
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Mahmood K, Konagurthu AS, Song J, Buckle AM, Webb GI, Whisstock JC. EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes. Bioinformatics 2010; 26:2076-84. [DOI: 10.1093/bioinformatics/btq339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Pierri CL, Parisi G, Porcelli V. Computational approaches for protein function prediction: a combined strategy from multiple sequence alignment to molecular docking-based virtual screening. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1695-712. [PMID: 20433957 DOI: 10.1016/j.bbapap.2010.04.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 03/04/2010] [Accepted: 04/14/2010] [Indexed: 12/12/2022]
Abstract
The functional characterization of proteins represents a daily challenge for biochemical, medical and computational sciences. Although finally proved on the bench, the function of a protein can be successfully predicted by computational approaches that drive the further experimental assays. Current methods for comparative modeling allow the construction of accurate 3D models for proteins of unknown structure, provided that a crystal structure of a homologous protein is available. Binding regions can be proposed by using binding site predictors, data inferred from homologous crystal structures, and data provided from a careful interpretation of the multiple sequence alignment of the investigated protein and its homologs. Once the location of a binding site has been proposed, chemical ligands that have a high likelihood of binding can be identified by using ligand docking and structure-based virtual screening of chemical libraries. Most docking algorithms allow building a list sorted by energy of the lowest energy docking configuration for each ligand of the library. In this review the state-of-the-art of computational approaches in 3D protein comparative modeling and in the study of protein-ligand interactions is provided. Furthermore a possible combined/concerted multistep strategy for protein function prediction, based on multiple sequence alignment, comparative modeling, binding region prediction, and structure-based virtual screening of chemical libraries, is described by using suitable examples. As practical examples, Abl-kinase molecular modeling studies, HPV-E6 protein multiple sequence alignment analysis, and some other model docking-based characterization reports are briefly described to highlight the importance of computational approaches in protein function prediction.
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Affiliation(s)
- Ciro Leonardo Pierri
- Department of Pharmaco-Biology, Laboratory of Biochemistry and Molecular Biology, University of Bari, Va E. Orabona, 4 - 70125 Bari, Italy.
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Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y. Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genomics 2010; 11:243. [PMID: 20398357 PMCID: PMC2867830 DOI: 10.1186/1471-2164-11-243] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 04/16/2010] [Indexed: 11/21/2022] Open
Abstract
Background Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length. Results We applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1. These are specific for γ-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases. Conclusions The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks. Multiple genome-level comparisons among five closely related Bacillus species were also carried out. The determined genome sequence of B. subtilis natto and gene annotations are available from the Natto genome browser http://natto-genome.org/.
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Affiliation(s)
- Yukari Nishito
- Department of Biosciences and Informatics, Keio University, Hiyoshi, Kohoku-ku, Yokohama, Japan
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Salse J, Abrouk M, Murat F, Quraishi UM, Feuillet C. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics. Brief Bioinform 2009; 10:619-30. [DOI: 10.1093/bib/bbp037] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Peng Q, Alekseyev MA, Tesler G, Pevzner PA. Decoding Synteny Blocks and Large-Scale Duplications in Mammalian and Plant Genomes. LECTURE NOTES IN COMPUTER SCIENCE 2009. [DOI: 10.1007/978-3-642-04241-6_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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