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Research: Continuous infiltration and evolutionary trajectory of nuclear organelle DNA in Oryza
- Chenbo Gong,
- Yicheng Huang,
- Mengmeng Liu,
- Yong Zhou,
- Yinwei Xu,
- Nahed Mohammed,
- Xintong Qiao,
- Andrea Zuccolo,
- Weibo Xie,
- Rod A. Wing,
- Jianwei Zhang,
- Fei Zhou,
- and Yongjun Lin
Genome Res. June 2025 35: 1349-1363; Published in Advance April 25, 2025, doi:10.1101/gr.279609.124
...their general abundance and activity within the , rather than a NORG-specific association.Based on their original and derived forms, we further interpreted the dynamic change process of NORGs. For example, ONG0400870 appears to have been a 66 kb insertion of mtDNA along with >10 kb sequences from chromosomal...
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Research: Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages
- Jennifer F. Hughes,
- Helen Skaletsky,
- Tatyana Pyntikova,
- Natalia Koutseva,
- Terje Raudsepp,
- Laura G. Brown,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Shannon Dugan-Rocha,
- Ziad Khan,
- Colin Kremitzki,
- Catrina Fronick,
- Tina A. Graves-Lindsay,
- Lucinda Fulton,
- Wesley C. Warren,
- Richard K. Wilson,
- Elaine Owens,
- James E. Womack,
- William J. Murphy,
- Donna M. Muzny,
- Kim C. Worley,
- Bhanu P. Chowdhary,
- Richard A. Gibbs,
- and David C. Page
Genome Res. December 2020 30: 1716-1726; Published in Advance November 18, 2020, doi:10.1101/gr.269902.120
...as revealed by high-throughput sequencing of individual chromosomes. Cytogenet Genome Res 157: 115–122. doi:10.1159/000497091 ↵Liu Z, Moore PH, Ma H, Ackerman CM, Ragiba M, Yu Q, Pearl HM, Kim MS, Charlton JW, Stiles JI, et al. 2004. A primitive Y chromosome in papaya marks incipient sex chromosome evolution...
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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
..., Carica (papaya), and Theobroma (cacao) experienced hexaploidization ∼110 million years ago (mya) with no further WGD thereafter (Jaillon et al. 2007). Three ancient WGDs shaped the ancestral lineage of grasses (Jiao et al. 2014); however, Oryza sativa (rice) and Sorghum bicolor (sorghum) experienced...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
.... There were 34 contigs containing large proportions of genes originating in two or more of the ancient chromosomes that were discarded, as were any contigs containing four or fewer genes from a Brassica . Although the 9712 contigs so omitted represent 89% of all contigs, they represent only 55% of the genes...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...ability to identify conserved regulatory elements, as well our knowledge of the extent to which different types of selection act to maintain genes within this unique genomic environment. Here, we present the first MSY (male-specific region of the Y chromosome) sequences from two carnivores, the domestic...
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Resource: The genome of the pear (Pyrus bretschneideri Rehd.)
- Jun Wu,
- Zhiwen Wang,
- Zebin Shi,
- Shu Zhang,
- Ray Ming,
- Shilin Zhu,
- M. Awais Khan,
- Shutian Tao,
- Schuyler S. Korban,
- Hao Wang,
- Nancy J. Chen,
- Takeshi Nishio,
- Xun Xu,
- Lin Cong,
- Kaijie Qi,
- Xiaosan Huang,
- Yingtao Wang,
- Xiang Zhao,
- Juyou Wu,
- Cao Deng,
- Caiyun Gou,
- Weili Zhou,
- Hao Yin,
- Gaihua Qin,
- Yuhui Sha,
- Ye Tao,
- Hui Chen,
- Yanan Yang,
- Yue Song,
- Dongliang Zhan,
- Juan Wang,
- Leiting Li,
- Meisong Dai,
- Chao Gu,
- Yuezhi Wang,
- Daihu Shi,
- Xiaowei Wang,
- Huping Zhang,
- Liang Zeng,
- Danman Zheng,
- Chunlei Wang,
- Maoshan Chen,
- Guangbiao Wang,
- Lin Xie,
- Valpuri Sovero,
- Shoufeng Sha,
- Wenjiang Huang,
- Shujun Zhang,
- Mingyue Zhang,
- Jiangmei Sun,
- Linlin Xu,
- Yuan Li,
- Xing Liu,
- Qingsong Li,
- Jiahui Shen,
- Junyi Wang,
- Robert E. Paull,
- Jeffrey L. Bennetzen,
- Jun Wang,
- and Shaoling Zhang
Genome Res. February 2013 23: 396-408; Published in Advance November 13, 2012, doi:10.1101/gr.144311.112
...in the apple draft using theWGS strategy. As for the nine ancestral chromosomes reported in apple, we infer that these nine chromosomes not only are the origin of the Pyreae tribe but also serve as the ancestors of thewhole Rosaceae family. The sequence of the pear provides an invaluable new resource...
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Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
...that these annotations remained approximately static over the course of the simulation. We examined repeat content of the simulated s (see legend to Table 2) and found a comparable portion of annotated repeats to that in the original human chromosome13, but a reduction of slightly more than half in the proportion...
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