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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...Tracey4, Brendan R.E. Ansell5, Aaron R. Jex5, Garrett W. Cooper6, Ethan D. Smith6, Rui Xiao2, Jennifer E. Dumaine3, Peter Georgeson6,7,8, Bernard J. Pope6,7,9,10, Matthew Berriman4, Boris Striepen3, James A. Cotton4 and Jessica C. Kissinger1,2,11 1Center for Tropical and Emerging Global Diseases...
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LETTER: Incongruent Patterns of Local and Global Genome Size Evolution in Cotton
- Corrinne E. Grover,
- HyeRan Kim,
- Rod A. Wing,
- Andrew H. Paterson,
- and Jonathan F. Wendel
Genome Res. August 2004 14: 1474-1482; Published in Advance July 15, 2004, doi:10.1101/gr.2673204
...Incongruent Patterns of Local and Global Genome Size Evolution in Cotton Corrinne E. Grover 1 , HyeRan Kim 2 , Rod A. Wing 2 , Andrew H. Paterson 3 , and Jonathan F. Wendel 1 , 4 1 Department of Ecology, Evolution...
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Research: Transposon accumulation at xenobiotic gene family loci in aphids
- Tobias Baril,
- Adam Pym,
- Chris Bass,
- and Alex Hayward
Genome Res. October 2023 33: 1718-1733; Published in Advance October 18, 2023, doi:10.1101/gr.277820.123
...insects to evolve resistance to multiple insecticide classes (Li et al. 2007; Bradshaw et al. 2016), severely affecting our ability to control target insects (Singh et al. 2021). The emergence of multiple-insecticide resistance is a major global challenge, threatening global food security in the case...
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Research: A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia
- Sivaranjani Namasivayam,
- Rodrigo P. Baptista,
- Wenyuan Xiao,
- Erica M. Hall,
- Joseph S. Doggett,
- Karin Troell,
- and Jessica C. Kissinger
Genome Res. May 2021 31: 852-865; Published in Advance April 27, 2021, doi:10.1101/gr.266403.120
...of Georgia, Athens, Georgia 30602, USA; 2Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA; 3Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA; 4Division of Infectious Diseases, Oregon Health Sciences University, Portland, Oregon...
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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
...genes could be mapped to the 3K-RG (Supplemental Table S7). Overall, the gene level mapping rates were lower than genomic sequence level mapping rates for pan- comparison (Supplemental Table S8). Similar results were obtained at the protein level comparison of the pan-s at the global identity cutoffs...
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ARTICLE: Comparative genomics of Gossypium and Arabidopsis: Unraveling the consequences of both ancient and recent polyploidy
- Junkang Rong,
- John E. Bowers,
- Stefan R. Schulze,
- Vijay N. Waghmare,
- Carl J. Rogers,
- Gary J. Pierce,
- Hua Zhang,
- James C. Estill,
- and Andrew H. Paterson
Genome Res. September 2005 15: 1198-1210; Published in Advance August 18, 2005, doi:10.1101/gr.3907305
...with dashed lines. Ancient duplication in the cotton since its divergence from a common ancestor shared with Arabidopsis Previously ( Rong et al. 2004 ), we noted some hints of segmental duplication within individual cotton subs. We further investigated this in two ways. First, 39,079 ESTs for G. arboreum (a...
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Method: Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants
- Dongqing Shi,
- Jun Wu,
- Haibao Tang,
- Hao Yin,
- Hongtao Wang,
- Ran Wang,
- Runze Wang,
- Ming Qian,
- Juyou Wu,
- Kaijie Qi,
- Zhihua Xie,
- Zhiwen Wang,
- Xiang Zhao,
- and Shaoling Zhang
Genome Res. November 2019 29: 1889-1899; Published in Advance October 24, 2019, doi:10.1101/gr.251033.119
....1739 ↵Germanà MA. 2011. Anther culture for haploid and doubled haploid production. Plant Cell Tiss Org 104: 283–300. doi:10.1007/s11240-010-9852-z ↵He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, et al. 2010. Global epigenetic and transcriptional trends among two rice...
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LETTER: Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium
- Jennifer S. Hawkins,
- HyeRan Kim,
- John D. Nason,
- Rod A. Wing,
- and Jonathan F. Wendel
Genome Res. October 2006 16: 1252-1261; Published in Advance September 5, 2006, doi:10.1101/gr.5282906
...over &gt;75 bp to Gorge3 (e-value cut-off of e-20, data not shown). Based on this high level of sequence identity to G45 and G84, presence in the Gossypium EST libraries, and overabundance of Gorge3 in the WGS libraries, we believe Gorge3 is a recently active, major constituent of the cotton that, like...
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RESEARCH: Computational and Biological Analysis of 680 kb of DNA Sequence from the Human 5q31 Cytokine Gene Cluster Region
- Kelly A. Frazer,
- Yukihiko Ueda,
- Yiwen Zhu,
- Vincent R. Gifford,
- Maria R. Garofalo,
- Narla Mohandas,
- Christopher H. Martin,
- Michael J. Palazzolo,
- Jan-Fang Cheng,
- and Edward M. Rubin
Genome Res. May 1, 1997 7: 495-512; doi:10.1101/gr.7.5.495
...identified and verified expression of 16 new genes, as well as 7 previously known genes. Of the total of 23 genes in this region, 78% had similarity matches to sequences in protein databases and 83% had exact expressed sequence tag (EST) database matches. Comparative mapping studies of eight of the new human...
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Methods: Targeted discovery of novel human exons by comparative genomics
- Adam Siepel,
- Mark Diekhans,
- Broňa Brejová,
- Laura Langton,
- Michael Stevens,
- Charles L.G. Comstock,
- Colleen Davis,
- Brent Ewing,
- Shelly Oommen,
- Christopher Lau,
- Hung-Chun Yu,
- Jianfeng Li,
- Bruce A. Roe,
- Phil Green,
- Daniela S. Gerhard,
- Gary Temple,
- David Haussler,
- and Michael R. Brent
Genome Res. December 2007 17: 1763-1773; Published in Advance November 7, 2007, doi:10.1101/gr.7128207
...difficult to achieve. In response to declining yields from methods based on random expressed sequence tag (EST) sequencing ( Gerhard et al. 2004 ), several years ago the MGC adopted a more directed strategy, by which candidate genes not in the collection were amplified by RT–PCR, then were cloned...

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