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Research: Comparative transcriptomics of primary cells in vertebrates
- Tanvir Alam,
- Saumya Agrawal,
- Jessica Severin,
- Robert S. Young,
- Robin Andersson,
- Erik Arner,
- Akira Hasegawa,
- Marina Lizio,
- Jordan A. Ramilowski,
- Imad Abugessaisa,
- Yuri Ishizu,
- Shohei Noma,
- Hiroshi Tarui,
- Martin S. Taylor,
- Timo Lassmann,
- Masayoshi Itoh,
- Takeya Kasukawa,
- Hideya Kawaji,
- Luigi Marchionni,
- Guojun Sheng,
- Alistair R.R. Forrest,
- Levon M. Khachigian,
- Yoshihide Hayashizaki,
- Piero Carninci,
- and Michiel J.L. de Hoon
Genome Res. July 2020 30: 951-961; Published in Advance July 27, 2020, doi:10.1101/gr.255679.119
...with it in the Ensembl Compara multi-species database (Vilella et al. 2009). This yielded 16,217 (human-mouse), 15,486 (human-rat), 15,861 (human-dog), 11,950 (human-chicken), and 10,237 (in all five species) pairs of orthologous genes, of which 15,893 (human-mouse), 15,207 (human-rat), 15,482 (human-dog), 11,873 (human...
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Method: Genome-scale coestimation of species and gene trees
- Bastien Boussau,
- Gergely J. Szöllősi,
- Laurent Duret,
- Manolo Gouy,
- Eric Tannier,
- and Vincent Daubin
Genome Res. February 2013 23: 323-330; Published in Advance November 6, 2012, doi:10.1101/gr.141978.112
...evolution from the gorilla sequence. Nature 483: 169–175. doi. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2008. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327–335. Waddell PJ, Okada N, HasegawaM. 1999. Towards resolving...
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Method: Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees
- Yi-Chieh Wu,
- Matthew D. Rasmussen,
- Mukul S. Bansal,
- and Manolis Kellis
Genome Res. March 2014 24: 475-486; Published in Advance December 5, 2013, doi:10.1101/gr.161968.113
...common ancestry, or a gene family, these histories are often inferred by comparing two kinds of phylogenetic trees: a gene tree that depicts the evolutionary relationships among the genes within the gene family, and a species tree that depicts the evolutionary relationships of a set of species. The gene...
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Resource: A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
..., Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327–335. Xue Y, Wang Q, Long Q , Ng BL, Swerdlow H, Burton J, Skuce C, Taylor R, Abdellah Z, Zhao Y, et al. 2009. Human Y chromosome base...
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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
...contains over 2100 complete s. We compare OMA standalone to other methods in the context of phylogenetic tree inference, by inferring a phylogeny of Lophotrochozoa, a challenging clade within the protostomes. We also discuss other potential applications of OMA standalone, including identifying gene...
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Research: The evolution of duplicate gene expression in mammalian organs
- Katerina Guschanski,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. September 2017 27: 1461-1474; Published in Advance July 25, 2017, doi:10.1101/gr.215566.116
.... 2012) and employed a rigorousmultistep filtering procedure that removed poorly supported duplications, misannotations, and intronless genes (Supplemental Fig. S1; Supplemental Methods). Inference of duplication age was based on gene tree topology and validated by measuring the rate of synonymous...
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Method: Unified modeling of gene duplication, loss, and coalescence using a locus tree
- Matthew D. Rasmussen and
- Manolis Kellis
Genome Res. April 2012 22: 755-765; Published in Advance January 23, 2012, doi:10.1101/gr.123901.111
...al. 2009; Datta et al. 2009; Vilella et al. 2009; Mi et al. 2010). The key idea in many of these approaches is that gene duplications and losses lead to incongruence (topological differences) between two important kinds of phylogenetic trees, the gene tree and the species tree (Goodman et al. 1979...
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Research: An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication
- Elise Parey,
- Alexandra Louis,
- Jérôme Montfort,
- Yann Guiguen,
- Hugues Roest Crollius,
- and Camille Berthelot
Genome Res. September 2022 32: 1685-1697; Published in Advance August 12, 2022, doi:10.1101/gr.276953.122
...://doi.org/10.5281/zenodo.5776772).Phylogenetic gene treesInitial gene trees were built using the Ensembl Compara pipeline (Vilella et al. 2009). Briefly, starting from the sets of proteins derived from the longest transcripts in each , we performed an all-against-all BLASTP+ (Altschul et al. 1990...
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Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
- Xingyan Liu,
- Qunlun Shen,
- and Shihua Zhang
Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
...of reference data, which limits the use of CAME in unsupervised scenarios. We expect it will be solved in the future.It should be noted that the inter-species gene homology mapping is still developing, and different methods like Ensembl_Compara (Vilella et al. 2009), Domainoid (Persson et al. 2019...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...molecular basis underlying the genomic recombination and chromosomal evolution.View larger version: In this window In a new window Figure 1. Research framework, hybridization scheme, karyotype and chromosomal painting, statistics of homologs and gene families, phylogenetic tree, and synteny landscape. (A...
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