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Method: Combining DNA and protein alignments to improve genome annotation with LiftOn
- Kuan-Hao Chao,
- Jakob M. Heinz,
- Celine Hoh,
- Alan Mao,
- Alaina Shumate,
- Mihaela Pertea,
- and Steven L. Salzberg
Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124
....48 million assemblies, of which 43,120 are eukaryotes, 2.20 million are bacteria, 24,050 are archaea, and 192,600 are viruses.Genome annotation—identifying genes and other biological features—is essential to understanding the biology of these s (Stein 2001). Annotating eukaryotic s presents particular...
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Resource: Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies
- Mingzhou Li,
- Lei Chen,
- Shilin Tian,
- Yu Lin,
- Qianzi Tang,
- Xuming Zhou,
- Diyan Li,
- Carol K.L. Yeung,
- Tiandong Che,
- Long Jin,
- Yuhua Fu,
- Jideng Ma,
- Xun Wang,
- Anan Jiang,
- Jing Lan,
- Qi Pan,
- Yingkai Liu,
- Zonggang Luo,
- Zongyi Guo,
- Haifeng Liu,
- Li Zhu,
- Surong Shuai,
- Guoqing Tang,
- Jiugang Zhao,
- Yanzhi Jiang,
- Lin Bai,
- Shunhua Zhang,
- Miaomiao Mai,
- Changchun Li,
- Dawei Wang,
- Yiren Gu,
- Guosong Wang,
- Hongfeng Lu,
- Yan Li,
- Haihao Zhu,
- Zongwen Li,
- Ming Li,
- Vadim N. Gladyshev,
- Zhi Jiang,
- Shuhong Zhao,
- Jinyong Wang,
- Ruiqiang Li,
- and Xuewei Li
Genome Res. May 2017 27: 865-874; Published in Advance September 19, 2016, doi:10.1101/gr.207456.116
...) (Supplemental Table S7) and covered most SNPs identified by resequencing as implemented in SAMtools (Li et al. 2009) (98.78%) and GATK (McKenna et al. 2010) (97.65%) and 3.12– 5.40 M SNPs (33.46%–35.25%) in divergent regions that failed to be cataloged by these algorithms, where unassembled short reads...
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LETTER: Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
- Deyou Zheng,
- Adam Frankish,
- Robert Baertsch,
- Philipp Kapranov,
- Alexandre Reymond,
- Siew Woh Choo,
- Yontao Lu,
- France Denoeud,
- Stylianos E. Antonarakis,
- Michael Snyder,
- Yijun Ruan,
- Chia-Lin Wei,
- Thomas R. Gingeras,
- Roderic Guigó,
- Jennifer Harrow,
- and Mark B. Gerstein
Genome Res. June 2007 17: 839-851; doi:10.1101/gr.5586307
...of pseudogene annotation in the ENCODE regions As a subgroup within the ENCODE project, our first goal is to obtain an accurate list of pseudogenes in order to facilitate the creation of a comprehensive catalog of structural and functional elements in the ENCODE regions ( The ENCODE Project Consortium 2004...
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RESOURCE: A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors
- Stuart Huntley,
- Daniel M. Baggott,
- Aaron T. Hamilton,
- Mary Tran-Gyamfi,
- Shan Yang,
- Joomyeong Kim,
- Laurie Gordon,
- Elbert Branscomb,
- and Lisa Stubbs
Genome Res. May 2006 16: 669-677; Published in Advance April 10, 2006, doi:10.1101/gr.4842106
...Elbert, Branscomb D Baggott Hamilton, A.T Stubbs Lisa Branscomb Elbert Elbert Baggott Laurie, Gordon Kim Joomyeong Baggott, Daniel M Tran-Gyamfi, M Hamilton, Aaron T S Yang DM Baggott Laurie Gordon Shan genome;gr.4842106 1088-9051 10.1101/gr.4842106 A comprehensive catalog of human KRAB-associated zinc...
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Research: The life history of retrocopies illuminates the evolution of new mammalian genes
- Francesco Nicola Carelli,
- Takashi Hayakawa,
- Yasuhiro Go,
- Hiroo Imai,
- Maria Warnefors,
- and Henrik Kaessmann
Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115
...established mRNA-derived gene duplicates, known as retrocopies, as models for the study of new gene origination. Here we combine mammalian transcriptomic and epigenomic data to unveil the processes underlying the evolution of stripped-down retrocopies into complex new genes. We show that although some...
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Research: Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification
- Robert K. Arthur,
- Lijia Ma,
- Matthew Slattery,
- Rebecca F. Spokony,
- Alexander Ostapenko,
- Nicolas Nègre,
- and Kevin P. White
Genome Res. July 2014 24: 1115-1124; Published in Advance July 1, 2014, doi:10.1101/gr.162008.113
...for deposition andmaintenance of H3K27me3 are known, it is likely that we do not have a complete catalog of all the elements of all PREs (Delest et al. 2012), nor dowe know the exact spatial or orientation requirements of the involved binding sites (if indeed there are any). However, the extreme conservation...
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Research: Birth and expression evolution of mammalian microRNA genes
- Julien Meunier,
- Frédéric Lemoine,
- Magali Soumillon,
- Angélica Liechti,
- Manuela Weier,
- Katerina Guschanski,
- Haiyang Hu,
- Philipp Khaitovich,
- and Henrik Kaessmann
Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
...al. 2011), provide detailed insights into the birth and evolution of mammalian miRNA genes and the associated selective forces. Results An unbiased miRNA catalog of mammals and birds We generated small RNA-seq data for brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart...
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Methods: Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons
- Yao-Ting Huang,
- Feng-Chi Chen,
- Chiuan-Jung Chen,
- Hsin-Liang Chen,
- and Trees-Juen Chuang
Genome Res. July 2008 18: 1163-1170; Published in Advance March 27, 2008, doi:10.1101/gr.075556.107
...) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models . Mol. Biol. Evol. 17 : 32 – 43 . ↵ Zhang, Z. , Harrison, P.M. , Liu, Y. , Gerstein, M. ( 2003 ) Millions of years of evolution preserved: A comprehensive catalog of the processed pseudogenes in the human . Genome...
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Perspective: Neanderthal genomics and the evolution of modern humans
- James P. Noonan
Genome Res. May 2010 20: 547-553; doi:10.1101/gr.076000.108
...et al. 2003; Chimpanzee Sequencing and Analysis Consortium 2005; Pollard et al. 2006a,b; Prabhakar et al. 2006, 2008; Haygood et al. 2007). The results from these analyses comprise a catalog of potential human-specific adaptive evolution on the molecular level. However, these studies are unable...
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Research: The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes
- Stephen B. Montgomery,
- David L. Goode,
- Erika Kvikstad,
- Cornelis A. Albers,
- Zhengdong D. Zhang,
- Xinmeng Jasmine Mu,
- Guruprasad Ananda,
- Bryan Howie,
- Konrad J. Karczewski,
- Kevin S. Smith,
- Vanessa Anaya,
- Rhea Richardson,
- Joe Davis,
- The 1000 Genomes Project Consortium,
- Daniel G. MacArthur,
- Arend Sidow,
- Laurent Duret,
- Mark Gerstein,
- Kateryna D. Makova,
- Jonathan Marchini,
- Gil McVean,
- and Gerton Lunter
Genome Res. May 2013 23: 749-761; Published in Advance March 11, 2013, doi:10.1101/gr.148718.112
.... The recent availability of affordable, high-throughput sequencing has made possible new catalogs of indels in individual s (Levy et al. 2007; Wheeler et al. 2008). However, due to differences in sequencing technology and indel calling methodology, vastly different numbers of indels have been reported...
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