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Resource: Genome-wide dynamics of alternative polyadenylation in rice
- Haihui Fu,
- Dewei Yang,
- Wenyue Su,
- Liuyin Ma,
- Yingjia Shen,
- Guoli Ji,
- Xinfu Ye,
- Xiaohui Wu,
- and Qingshun Q. Li
Genome Res. December 2016 26: 1753-1760; Published in Advance October 12, 2016, doi:10.1101/gr.210757.116
...of 3′-ends of -wide information at different stages of rice were also revealed. Many poly(A) sites in the intergenic regions were identified. While their authenticity as potentially unannotated gene transcripts remains to be tested, their existence at such a scale (∼23%) requires further investigation...
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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
...) and the International Rice Genome Sequencing Project ( 2005 ) recently estimated the number of genes in Arabidopsis and rice to be 28,952 and 37,544, respectively. In light of these gene number estimates and the fact that gene number inflation may be a common artifact within EST assemblies ( Close et al. 2004 ; Lazo et...
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Research: Genome and time-of-day transcriptome of Wolffia australiana link morphological minimization with gene loss and less growth control
- Todd P. Michael,
- Evan Ernst,
- Nolan Hartwick,
- Philomena Chu,
- Douglas Bryant,
- Sarah Gilbert,
- Stefan Ortleb,
- Erin L. Baggs,
- K. Sowjanya Sree,
- Klaus J. Appenroth,
- Joerg Fuchs,
- Florian Jupe,
- Justin P. Sandoval,
- Ksenia V. Krasileva,
- Ljudmylla Borisjuk,
- Todd C. Mockler,
- Joseph R. Ecker,
- Robert A. Martienssen,
- and Eric Lam
Genome Res. February 2021 31: 225-238; Published in Advance December 23, 2020, doi:10.1101/gr.266429.120
...signify an alternative defense system. Diurnal expression analysis revealed that only 13% of Wolffia genes are expressed in a time-of-day (TOD) fashion, which is less than the typical ∼40% found in several model plants under the same condition. In contrast to the model plants Arabidopsis and rice, many...
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LETTER: Diversification of transcriptional modulation: Large-scale identification and characterization of putative alternative promoters of human genes
- Kouichi Kimura,
- Ai Wakamatsu,
- Yutaka Suzuki,
- Toshio Ota,
- Tetsuo Nishikawa,
- Riu Yamashita,
- Jun-ichi Yamamoto,
- Mitsuo Sekine,
- Katsuki Tsuritani,
- Hiroyuki Wakaguri,
- Shizuko Ishii,
- Tomoyasu Sugiyama,
- Kaoru Saito,
- Yuko Isono,
- Ryotaro Irie,
- Norihiro Kushida,
- Takahiro Yoneyama,
- Rie Otsuka,
- Katsuhiro Kanda,
- Takahide Yokoi,
- Hiroshi Kondo,
- Masako Wagatsuma,
- Katsuji Murakawa,
- Shinichi Ishida,
- Tadashi Ishibashi,
- Asako Takahashi-Fujii,
- Tomoo Tanase,
- Keiichi Nagai,
- Hisashi Kikuchi,
- Kenta Nakai,
- Takao Isogai,
- and Sumio Sugano
Genome Res. January 2006 16: 55-65; Published in Advance December 12, 2005, doi:10.1101/gr.4039406
...molecular systems in humans. One of the most striking findings revealed by the Human Genome Project is that the human contains only 20,000-25,000 kinds of protein-coding genes ( International Human Genome Sequencing Consortium 2004 ). This number is unexpectedly small compared with the total gene numbers...
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RESEARCH: Alternate Polyadenylation in Human mRNAs: A Large-Scale Analysis by EST Clustering
- Daniel Gautheret,
- Olivier Poirot,
- Fabrice Lopez,
- Stéphane Audic,
- and Jean-Michel Claverie
Genome Res. May 1, 1998 8: 524-530; doi:10.1101/gr.8.5.524
...– 1699 . ↵ Schuler G. , Boguski M. , Stewart E. , Stein L. , Gyapay G. , Rice K. , White R. , Rodriguez-Tome P. , Aggarwal A. , Bajorek E. , et al. ( 1996 ) A gene map of the human . Science 274 : 540 – 546 . ↵ Senterre-Lesenfants S. , Alag A. , Sobel M. ( 1995 ) Multiple mRNA species are generated...
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Research: Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
.... Differentially expressed genes between two subspecies RNA-seq data analyses revealed extensive expression of the whole rice (Fig. 4).We further investigated the overall expression by alignment against theMSUgenemodels and found that 64.7%– 83.4% of the annotated genes (49,574 in 93-11, 43,038 in Gla4, and 55...
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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
...no evidence of conversion ( Zhang et al. 2002 ), however, using the same method, an exploration for conversion in rice revealed 377 events in 626 multigene families ( Xu et al. 2008 ). This controversy may result from the fact that Arabidopsis genes diverge faster than rice genes and may more frequently...
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LETTER: Comparative DNA Sequence Analysis of Wheat and Rice Genomes
- Mark E. Sorrells,
- Mauricio La Rota,
- Catherine E. Bermudez-Kandianis,
- Robert A. Greene,
- Ramesh Kantety,
- Jesse D. Munkvold,
- Miftahudin,
- Ahmed Mahmoud,
- Xuefeng Ma,
- Perry J. Gustafson,
- Lili L. Qi,
- Benjamin Echalier,
- Bikram S. Gill,
- David E. Matthews,
- Gerard R. Lazo,
- Shiaoman Chao,
- Olin D. Anderson,
- Hugh Edwards,
- Anna M. Linkiewicz,
- Jorge Dubcovsky,
- Eduard D. Akhunov,
- Jan Dvorak,
- Deshui Zhang,
- Henry T. Nguyen,
- Junhua Peng,
- Nora L.V. Lapitan,
- Jose L. Gonzalez-Hernandez,
- James A. Anderson,
- Khwaja Hossain,
- Venu Kalavacharla,
- Shahryar F. Kianian,
- Dong-Woog Choi,
- Timothy J. Close,
- Muharrem Dilbirligi,
- Kulvinder S. Gill,
- Camille Steber,
- Mary K. Walker-Simmons,
- Patrick E. McGuire,
- and Calvin O. Qualset
Genome Res. August 2003 13: 1818-1827; doi:10.1101/gr.1113003
...revealed by this analysis compared to the RFLP-based maps include a high frequency of breakdown in colinearity throughout the s, and localized homology between the s not previously reported. Prominent features of the rice–wheat comparison were grouped into four categories: (A) regions of conserved gene...
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LETTER: Patterns of Positive Selection in the Complete NBS-LRR Gene Family of Arabidopsis thaliana
- Mariana Mondragón-Palomino,
- Blake C. Meyers,
- Richard W. Michelmore,
- and Brandon S. Gaut
Genome Res. September 1, 2002 12: 1305-1315; doi:10.1101/gr.159402
.... 1999 , 2000 ). Comparative analyses of R genes from tomato, lettuce, rice, flax, and Arabidopsis have revealed that solvent-exposed positions of the LRRs are hypervariable and subject to positive natural selection ( Parniske et al. 1997 ; Meyers et al. 1998 ; Wang et al. 1998 ; Noel et al. 1999 ; Ellis...
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LETTER: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis
- Ligeng Ma,
- Chen Chen,
- Xigang Liu,
- Yuling Jiao,
- Ning Su,
- Lin Li,
- Xiangfeng Wang,
- Mengliang Cao,
- Ning Sun,
- Xiuqing Zhang,
- Jingyue Bao,
- Jian Li,
- Soren Pedersen,
- Lars Bolund,
- Hongyu Zhao,
- Longping Yuan,
- Gane Ka-Shu Wong,
- Jun Wang,
- Xing Wang Deng,
- and Jian Wang
Genome Res. September 2005 15: 1274-1283; doi:10.1101/gr.3657405
...provides expression evidence for the majority of LH gene models, and reveals a trend of changes in expression patterns of best-matched gene model pairs during plant evolution. This fundamental knowledge should provide a valuable basis for a more complete description of the rice . It is worth noting...

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