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Research: Long-read sequencing of 111 rice genomes reveals significantly larger pan-genomes
- Fan Zhang,
- Hongzhang Xue,
- Xiaorui Dong,
- Min Li,
- Xiaoming Zheng,
- Zhikang Li,
- Jianlong Xu,
- Wensheng Wang,
- and Chaochun Wei
Genome Res. May 2022 32: 853-863; Published in Advance April 8, 2022, doi:10.1101/gr.276015.121
...,624 clusters were identified. Of these, 19,319 novel genes were identified.For the gene family-level analysis, the protein sequences of the longest gene transcript isoforms were clustered using Markov Chain-based algorithm OrthoMCL v2.0.9 (Li et al. 2003) with the parameter “percentMatchCutoff = 50, evalue...
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Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
..., small-scale pipeline (OrthoMCL [Li et al. 2003]).It is important to examine multiple aspects of genomic diversity for these comparisons because the evolutionary history of bacterial pans can be highly complex. However, we are not aware of any prepackaged simulation tools that can encompass the entire...
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Research: Gene duplication and genetic innovation in cereal genomes
- Hui Guo,
- Yuannian Jiao,
- Xu Tan,
- Xiyin Wang,
- Xianzhong Huang,
- Huizhe Jin,
- and Andrew H. Paterson
Genome Res. February 2019 29: 261-269; Published in Advance January 16, 2019, doi:10.1101/gr.237511.118
...orthologous gene families (see Methods), that have at least one paralog with Ks < 0.05, suggesting recent duplication (Fig. 4A). To further examine gene family size, we sampled 18 species across the angiosperm phylogeny and constructed orthologous groups using OrthoMCL (Li et al. 2003). The expansion...
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Method: OMA standalone: orthology inference among public and custom genomes and transcriptomes
- Adrian M. Altenhoff,
- Jeremy Levy,
- Magdalena Zarowiecki,
- Bartłomiej Tomiczek,
- Alex Warwick Vesztrocy,
- Daniel A. Dalquen,
- Steven Müller,
- Maximilian J. Telford,
- Natasha M. Glover,
- David Dylus,
- and Christophe Dessimoz
Genome Res. July 2019 29: 1152-1163; Published in Advance June 24, 2019, doi:10.1101/gr.243212.118
...of the orthologous markers.We first consider the amount of orthology information recovered by the various methods. OMA inferred 2162 orthologous groups containing 15 or more species (Fig. 3A). By comparison, the HaMStR pipeline inferred 1241 orthologous groups, the OrthoMCL pipeline inferred 484 orthologous groups...
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Research: Pangolin genomes and the evolution of mammalian scales and immunity
- Siew Woh Choo,
- Mike Rayko,
- Tze King Tan,
- Ranjeev Hari,
- Aleksey Komissarov,
- Wei Yee Wee,
- Andrey A. Yurchenko,
- Sergey Kliver,
- Gaik Tamazian,
- Agostinho Antunes,
- Richard K. Wilson,
- Wesley C. Warren,
- Klaus-Peter Koepfli,
- Patrick Minx,
- Ksenia Krasheninnikova,
- Antoinette Kotze,
- Desire L. Dalton,
- Elaine Vermaak,
- Ian C. Paterson,
- Pavel Dobrynin,
- Frankie Thomas Sitam,
- Jeffrine J. Rovie-Ryan,
- Warren E. Johnson,
- Aini Mohamed Yusoff,
- Shu-Jin Luo,
- Kayal Vizi Karuppannan,
- Gang Fang,
- Deyou Zheng,
- Mark B. Gerstein,
- Leonard Lipovich,
- Stephen J. O'Brien,
- and Guat Jah Wong
Genome Res. October 2016 26: 1312-1322; Published in Advance August 10, 2016, doi:10.1101/gr.203521.115
...classification. Bioinformatics 30: 1236–1240. Jurka J. 2000. Repbase update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418–420. Li L, Stoeckert CJ Jr, Roos DS. 2003. OrthoMCL: identification of ortholog groups for eukaryotic s. Genome Res 13: 2178–2189. Li H, Handsaker B...
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Research: Complete avian malaria parasite genomes reveal features associated with lineage-specific evolution in birds and mammals
- Ulrike Böhme,
- Thomas D. Otto,
- James A. Cotton,
- Sascha Steinbiss,
- Mandy Sanders,
- Samuel O. Oyola,
- Antoine Nicot,
- Sylvain Gandon,
- Kailash P. Patra,
- Colin Herd,
- Ellen Bushell,
- Katarzyna K. Modrzynska,
- Oliver Billker,
- Joseph M. Vinetz,
- Ana Rivero,
- Chris I. Newbold,
- and Matthew Berriman
Genome Res. April 2018 28: 547-560; Published in Advance March 2, 2018, doi:10.1101/gr.218123.116
...noncoding RNA genes. OrthoMCL 38 (Li et al. 2003) was used to identify orthologs and paralogs.Phylogenetic analysisOrthoMCL v2.0 (default parameters and an inflation parameter of 1.5) was used to identify a total of 881 cluster proteins that were single-copy and present in 19 species of Apicomplexan...
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Research: Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication
- Andrew J. Heidel,
- Hajara M. Lawal,
- Marius Felder,
- Christina Schilde,
- Nicholas R. Helps,
- Budi Tunggal,
- Francisco Rivero,
- Uwe John,
- Michael Schleicher,
- Ludwig Eichinger,
- Matthias Platzer,
- Angelika A. Noegel,
- Pauline Schaap,
- and Gernot Glöckner
Genome Res. November 2011 21: 1882-1891; Published in Advance July 14, 2011, doi:10.1101/gr.121137.111
...the OrthoMCL analysis, and these proteins are also part of the common core set (Supplemental Fig. S3.6). The OrthoMCL analysis suggests that species-specific duplications and deletions leave ;3600 genes per species without oneto-one orthologs, while 5604 of the remaining 7054 genes have no assigned function...
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RESOURCE: Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi
- Michael J. Cornell,
- Intikhab Alam,
- Darren M. Soanes,
- Han Min Wong,
- Cornelia Hedeler,
- Norman W. Paton,
- Magnus Rattray,
- Simon J. Hubbard,
- Nicholas J. Talbot,
- and Stephen G. Oliver
Genome Res. December 2007 17: 1809-1822; Published in Advance November 5, 2007, doi:10.1101/gr.6531807
.... It is interesting to note that there appears to be little parallel duplication between S. pombe and R. oryzae . View this table: In this window In a new window Table 2. Chi-squared scores for coduplication in OrthoMCL clusters To investigate the genetic basis of the yeast and filamentous growth habits by fungi, we...
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Methods: Systematic identification of functional orthologs based on protein network comparison
- Sourav Bandyopadhyay,
- Roded Sharan,
- and Trey Ideker
Genome Res. March 2006 16: 428-435; Published in Advance April 4, 2006, doi:10.1101/gr.4526006
...: 239 –247. ↵ Letovsky, S. and Kasif, S. 2003 . Predicting protein function from protein/protein interaction data: A probabilistic approach. Bioinformatics 19 (Suppl 1): I197 –I204. ↵ Li, L., Stoeckert Jr., C.J., and Roos, D.S. 2003 . OrthoMCL: Identification of ortholog groups for eukaryotic s. Genome...
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Research: Contiguous and complete assemblies of Blastocystis gut microbiome–associated protists reveal evolutionary diversification to host ecology
- Abigail L. Lind,
- Nathan A. McDonald,
- Elias R. Gerrick,
- Ami S. Bhatt,
- and Katherine S. Pollard
Genome Res. June 2025 35: 1377-1390; Published in Advance April 22, 2025, doi:10.1101/gr.279080.124
...identity of 56% AAI for the same 753 orthologs, suggesting substantial genetic distance within this group.Genomic diversity within BlastocystisWhen we compared sequenced Blastocystis s, we found substantial variation in the s between human Blastocystis isolates and the tortoise-associated clade, including...
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