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Research: Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing
- Yingjia Shen,
- R.C. Venu,
- Kan Nobuta,
- Xiaohui Wu,
- Varun Notibala,
- Caghan Demirci,
- Blake C. Meyers,
- Guo-Liang Wang,
- Guoli Ji,
- and Qingshun Q. Li
Genome Res. September 2011 21: 1478-1486; Published in Advance August 3, 2011, doi:10.1101/gr.114744.110
...www..org Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H, Decola S. 2004b. The use of MPSS for whole- transcriptional analysis in Arabidopsis. Genome Res 14: 1641–1653. Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V, Ning J, Haudenschild CD. 2004c. Analysis...
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Research: Differences in activity and stability drive transposable element variation in tropical and temperate maize
- Shujun Ou,
- Armin Scheben,
- Tyler Collins,
- Yinjie Qiu,
- Arun S. Seetharam,
- Claire C. Menard,
- Nancy Manchanda,
- Jonathan I. Gent,
- Michael C. Schatz,
- Sarah N. Anderson,
- Matthew B. Hufford,
- and Candice N. Hirsch
Genome Res. August 2024 34: 1140-1153; Published in Advance September 9, 2024, doi:10.1101/gr.278131.123
...to a single reference (Quadrana et al. 2016; Carpentier et al. 2019; Domínguez et al. 2020; Wyler et al. 2020; Qiu et al. 2021). With continued advancements in long-read sequencing technologies and improved assembly algorithms, there is a growing movement in genomics toward pangenomic-based approaches (Bayer...
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Research: Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations
- Caifu Jiang,
- Aziz Mithani,
- Eric J. Belfield,
- Richard Mott,
- Laurence D. Hurst,
- and Nicholas P. Harberd
Genome Res. November 2014 24: 1821-1829; Published in Advance October 14, 2014, doi:10.1101/gr.177659.114
...directly address this issue and show that A. thaliana (The Arabidopsis Genome Initiative 2000) MA lineages grown for 10 successive generations on saline soil display an increased frequency of accumulated de novo mutations and epimutations (differentially methylated cytosine positions, DMPs). We also show...
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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
..., wherein a recent twofold increase in LTR numbers must have occurred, compared with that of other sequenced plant species (The Arabidopsis Genome Initiative 2000; Ming et al. 2008; Shulaev et al. 2010; Velasco et al. 2010). This suggests that the pear is in continuous expansion (Supplemental Fig. 10...
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COMMENTARY: Life with 25,000 Genes
- R. Scott Poethig
Genome Res. March 1, 2001 11: 313-316; doi:10.1101/gr
...to look at, fun to grow, and intellectually interesting. Given all of this, it is surprising that they remain so poorly understood. The completion of the Arabidopsis sequence will do much to change this ( Arabidopsis Genome Initiative 2000 ; Lin et al. 1999 ; Mayer et al. 1999 ; Salanoubat et al. 2000...
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PERSPECTIVE: The Arabidopsis genome: A foundation for plant research
- Michael Bevan and
- Sean Walsh
Genome Res. December 2005 15: 1632-1642; doi:10.1101/gr.3723405
...was the first plant, and the third multicellular organism after Caenorhabditis elegans ( The C. elegans Sequencing Consortium 1998 ) and Drosophila melanogaster ( Adams et al. 2000 ), to be completely sequenced ( The Arabidopsis Genome Initiative 2000 ). At the time, it was claimed that the Arabidopsis sequence...
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Research: Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population
- Robert J. Schmitz,
- Yupeng He,
- Oswaldo Valdés-López,
- Saad M. Khan,
- Trupti Joshi,
- Mark A. Urich,
- Joseph R. Nery,
- Brian Diers,
- Dong Xu,
- Gary Stacey,
- and Joseph R. Ecker
Genome Res. October 2013 23: 1663-1674; Published in Advance June 5, 2013, doi:10.1101/gr.152538.112
...,000 protein-coding genes (Schmutz et al. 2010) in contrast to the ;27,000 protein-coding genes present in the Arabidopsis thaliana Col-0 (The Arabidopsis Genome Initiative 2000), which reflects recent whole duplications (Schmutz et al. 2010). The soybean LD contains higher amounts of all three types of DNA...
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PERSPECTIVE: Grains of knowledge: Genomics of model cereals
- Andrew H. Paterson,
- Michael Freeling,
- and Takuji Sasaki
Genome Res. December 2005 15: 1643-1650; doi:10.1101/gr.3725905
...,000, implying a much lower gene density than the 4.5/kb value for Arabidopsis ( Arabidopsis Genome Initiative 2000 ). The map-based sequence also provides accurate positional information of components characterized by the presence of repeat or exogenous sequences. Widespread gene transfer from the organelles...
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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
...at http://www..org. The sequence data from this study have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE23756.] It is generally assumed that the s of different individuals of the same species are similar in content. However, there is growing...
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RESOURCE: A global assembly of cotton ESTs
- Joshua A. Udall,
- Jordan M. Swanson,
- Karl Haller,
- Ryan A. Rapp,
- Michael E. Sparks,
- Jamie Hatfield,
- Yeisoo Yu,
- Yingru Wu,
- Caitriona Dowd,
- Aladdin B. Arpat,
- Brad A. Sickler,
- Thea A. Wilkins,
- Jin Ying Guo,
- Xiao Ya Chen,
- Jodi Scheffler,
- Earl Taliercio,
- Ricky Turley,
- Helen McFadden,
- Paxton Payton,
- Natalya Klueva,
- Randell Allen,
- Deshui Zhang,
- Candace Haigler,
- Curtis Wilkerson,
- Jinfeng Suo,
- Stefan R. Schulze,
- Margaret L. Pierce,
- Margaret Essenberg,
- HyeRan Kim,
- Danny J. Llewellyn,
- Elizabeth S. Dennis,
- David Kudrna,
- Rod Wing,
- Andrew H. Paterson,
- Cari Soderlund,
- and Jonathan F. Wendel
Genome Res. March 2006 16: 441-450; Published in Advance February 14, 2006, doi:10.1101/gr.4602906
...., Wu, C.H., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. 2004 . UniProt: The universal protein knowledgebase. Nucleic Acids Res. 32 : D115 –D119. ↵ The Arabidopsis Genome Initiative. 2000 . Analysis of the sequence of the flowering plant Arabidopsis...

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