Searching journal content for articles similar to Feltus et al. 14 (9): 1812.

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  1. 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
    ...-nucleotide polymorphisms (SNPs).Wemade transcriptome comparisons between two rice subspecies, indica and japonica, using SNPs detected from 93-11 and Gla4 RNA-seq data. When referring to the japonicaNipponbare sequences, we identified 67,011 SNPs between 93-11 and Nipp, and 64,481 SNPs between Gla4 and Nipp. We also...
    OPEN ACCESS ARTICLE
  2. RESOURCE: The Oryza bacterial artificial chromosome library resource: Construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza
    • Jetty S.S. Ammiraju,
    • Meizhong Luo,
    • José L. Goicoechea,
    • Wenming Wang,
    • Dave Kudrna,
    • Christopher Mueller,
    • Jayson Talag,
    • HyeRan Kim,
    • Nicholas B. Sisneros,
    • Barbara Blackmon,
    • Eric Fang,
    • Jeffery B. Tomkins,
    • Darshan Brar,
    • David MacKill,
    • Susan McCouch,
    • Nori Kurata,
    • Georgina Lambert,
    • David W. Galbraith,
    • K. Arumuganathan,
    • Kiran Rao,
    • Jason G. Walling,
    • Navdeep Gill,
    • Yeisoo Yu,
    • Phillip SanMiguel,
    • Carol Soderlund,
    • Scott Jackson,
    • and Rod A. Wing
    Genome Res. January 2006 16: 140-147; Published in Advance December 12, 2005, doi:10.1101/gr.3766306
    ...resource for rice genetics and breeding based on subspecies indica and japonica alignments. Genome Res. 14 : 1812 -1819. ↵ Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al. 2002 . Sequence and analysis of rice chromosome 4. Nature 420 : 316 -320...
  3. 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
    ...of ONGs distinguishes well the Asian and African populations (Fig. 4A), O. glaberrima and O. barthii (Fig. 4B), four major groups of O. sativa (Fig. 4C), and three subpopulations of the japonica group (Fig. 4D) except for indica groups (Fig. 4E). PAV analysis of ONGs showed that there is considerable...
  4. 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
    ...of the sequence of the two major subspecies of cultivated rice, Oryza sativa ssp. japonica and ssp. indica . The sequence of the japonica cultivar Nipponbare was recently completed by a consortium of 10 countries, which comprised the International Rice Genome Sequencing Project (IRGSP), and represents a map-based...
  5. Method: Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation
    • Filipe G. Vieira,
    • Matteo Fumagalli,
    • Anders Albrechtsen,
    • and Rasmus Nielsen
    Genome Res. November 2013 23: 1852-1861; Published in Advance August 15, 2013, doi:10.1101/gr.157388.113
    .... s. indica, and O. s. japonica present significantly higher values around 0.6, 0.52, and 0.6, respectively (Fig. 4; Supplemental Table 1). To assess the impact of explicitly assuming inbreeding on SFS estimation, we estimated it for each of the four rice species/ subspecies. We used two different...
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