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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...The pig pan provides insights into the roles of coding structural variations in genetic diversity and adaptation Zhengcao Li1, Xiaohong Liu1, Chen Wang1, Zhenyang Li1, Bo Jiang1, Ruifeng Zhang1, Lu Tong1, Youping Qu1, Sheng He1, Haifan Chen1, Yafei Mao2, Qingnan Li1, Torsten Pook3, Yu Wu1, Yanjun...
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Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
- Thomas E. Hughes,
- Jane A. Langdale,
- and Steven Kelly
Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
...Research The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole- duplication in maize Thomas E. Hughes, Jane A. Langdale, and Steven Kelly Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, United Kingdom Whole- duplications...
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Letter: Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
- Xiyin Wang,
- Haibao Tang,
- John E. Bowers,
- and Andrew H. Paterson
Genome Res. June 2009 19: 1026-1032; Published in Advance April 16, 2009, doi:10.1101/gr.087288.108
...sharing ancestry, but less similar in structure and sequence, are then referred to as homoeologous. Though widespread and frequent recombination between homoeologous DNA segments may have been restricted, occasional and small-scale recombination may persist for a long time. The present analysis in rice...
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Research: Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor
- Ruth A. Swanson-Wagner,
- Steven R. Eichten,
- Sunita Kumari,
- Peter Tiffin,
- Joshua C. Stein,
- Doreen Ware,
- and Nathan M. Springer
Genome Res. December 2010 20: 1689-1699; Published in Advance October 29, 2010, doi:10.1101/gr.109165.110
...variation The observation that many maize genes can vary in copy number or presence among genotypes leads to queries about the potential functional impacts. Two observations suggest that genes affected by structural variation are enriched for sequenceswith low levels of conservation among species. First...
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LETTER: Widespread genome duplications throughout the history of flowering plants
- Liying Cui,
- P. Kerr Wall,
- James H. Leebens-Mack,
- Bruce G. Lindsay,
- Douglas E. Soltis,
- Jeff J. Doyle,
- Pamela S. Soltis,
- John E. Carlson,
- Kathiravetpilla Arumuganathan,
- Abdelali Barakat,
- Victor A. Albert,
- Hong Ma,
- and Claude W. dePamphilis
Genome Res. June 2006 16: 738-749; Published in Advance May 15, 2006, doi:10.1101/gr.4825606
...Widespread genome duplications throughout the history of flowering plants Genome duplication in flowering plants Liying Cui 1 , 2 , 3 , P. Kerr Wall 1 , 2 , 3 , James H. Leebens-Mack 1 , 2 , 3 , Bruce G. Lindsay 5 , Douglas E. Soltis 6...
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Method: Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain
- Jenna Kalleberg,
- Jacob Rissman,
- and Robert D. Schnabel
Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
.... 2022; Liao et al. 2023; Smith et al. 2023; Kalbfleisch et al. 2024). Unfortunately, the development of species-agnostic tools has not kept pace with the exponential growth of sequenced biodiversity. Despite widespread variation in ploidy, chromosome number, or kinship, many bioinformatic tools expect...
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Perspective: Challenges in identifying mRNA transcript starts and ends from long-read sequencing data
- Ezequiel Calvo-Roitberg,
- Rachel F. Daniels,
- and Athma A. Pai
Genome Res. November 2024 34: 1719-1734; doi:10.1101/gr.279559.124
...to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS technologies for RNA-based applications, including concerns about low coverage, high...
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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
...based on this structure suggested a deaminase.View larger version: In this window In a new window Figure 5. A recently amplified sorghum retrotransposon. (A) Genomic distribution and structure. (B) Copy number variation in sorghum and outgroup species, estimated by the number of mapped reads normalized...
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Research: Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize
- Baoxing Song,
- Edward S. Buckler,
- Hai Wang,
- Yaoyao Wu,
- Evan Rees,
- Elizabeth A. Kellogg,
- Daniel J. Gates,
- Merritt Khaipho-Burch,
- Peter J. Bradbury,
- Jeffrey Ross-Ibarra,
- Matthew B. Hufford,
- and M. Cinta Romay
Genome Res. July 2021 31: 1245-1257; Published in Advance May 27, 2021, doi:10.1101/gr.266528.120
..., structural variation, and transposons. These contribute to the potential of Andropogoneae as a powerful system for studying CNSs and are factors we leverage to understand the function of maize CNSs. We found that 86% of CNSs were comprised of annotated features, including introns, UTRs, putative cis...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...RNA-like regions map to a higher diversity of smRNAs than regions without miRNA-like structure, explaining up to 27% of variation in smRNA mapping for some TE superfamilies. This mapping bias is more pronounced among putatively autonomous TEs relative to nonautonomous TEs. Genome-wide, miRNA-like regions are also...
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