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  1. AU="Maldonado, Carlos Ernesto"
  2. AU="Trujillo Hernández, Angélica"
  3. AU="Song, MinGyu"
  4. AU="Liu, Qigong"
  5. AU="Darlene Dela Cruz"
  6. AU="Gorog, Diana A"
  7. AU="Fan, Yuan"
  8. AU="Cho, Yong Sang"
  9. AU="Silveira, Amanda Bortolini"
  10. AU="Carugati, Manuela"
  11. AU="Jurriaans, Suzanne"
  12. AU="Tsai, Kelvin K"
  13. AU=Nana Melanie
  14. AU=Mojet Barbara Louise AU=Mojet Barbara Louise
  15. AU=Alessandri-Haber Nicole AU=Alessandri-Haber Nicole
  16. AU="Alan White"
  17. AU="Rutherford, Anna"
  18. AU="Habrant, Anouck"
  19. AU="Barrejón, Myriam"
  20. AU="Mussatyé Elorza Parra"
  21. AU="Agnarelli, Alessandro"
  22. AU="Rill, Nathaniel O"
  23. AU="Sarah Lyon-Caen"
  24. AU="Endharti, Agustina Tri"
  25. AU="Baez-Noyer, Nelson"
  26. AU="Kucherlapati, Raju S."
  27. AU="Loyaux, Romain"
  28. AU="Yaxin Long"
  29. AU="Vlasenkova, Ramilia"
  30. AU="Taheri, Fateme"
  31. AU="Berman, Robert F"
  32. AU="Resnick, Cory M"
  33. AU=Freeman Gordon J AU=Freeman Gordon J
  34. AU="Fangru Zhou"

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  1. Artikel ; Online: Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data.

    Zhang, Jianwei / Chen, Ling-Ling / Sun, Shuai / Kudrna, Dave / Copetti, Dario / Li, Weiming / Mu, Ting / Jiao, Wen-Biao / Xing, Feng / Lee, Seunghee / Talag, Jayson / Song, Jia-Ming / Du, Bogu / Xie, Weibo / Luo, Meizhong / Maldonado, Carlos Ernesto / Goicoechea, Jose Luis / Xiong, Lizhong / Wu, Changyin /
    Xing, Yongzhong / Zhou, Dao-Xiu / Yu, Sibin / Zhao, Yu / Wang, Gongwei / Yu, Yeisoo / Luo, Yijie / Hurtado, Beatriz Elena Padilla / Danowitz, Ann / Wing, Rod A / Zhang, Qifa

    Scientific data

    2016  Band 3, Seite(n) 160076

    Abstract: Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality ... ...

    Abstract Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology. With these data, we successfully assembled two platinum standard reference genomes that have been publicly released. Here we provide the full sets of raw data used to generate these two reference genome assemblies. These data sets can be used to test new programs for better genome assembly and annotation, aid in the discovery of new insights into genome structure, function, and evolution, and help to provide essential support to biological research in general.
    Mesh-Begriff(e) Genome ; Oryza/genetics
    Sprache Englisch
    Erscheinungsdatum 2016-09-13
    Erscheinungsland England
    Dokumenttyp Comment ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2775191-0
    ISSN 2052-4463 ; 2052-4463
    ISSN (online) 2052-4463
    ISSN 2052-4463
    DOI 10.1038/sdata.2016.76
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

    Zhang, Jianwei / Chen, Ling-Ling / Xing, Feng / Kudrna, David A / Yao, Wen / Copetti, Dario / Mu, Ting / Li, Weiming / Song, Jia-Ming / Xie, Weibo / Lee, Seunghee / Talag, Jayson / Shao, Lin / An, Yue / Zhang, Chun-Liu / Ouyang, Yidan / Sun, Shuai / Jiao, Wen-Biao / Lv, Fang /
    Du, Bogu / Luo, Meizhong / Maldonado, Carlos Ernesto / Goicoechea, Jose Luis / Xiong, Lizhong / Wu, Changyin / Xing, Yongzhong / Zhou, Dao-Xiu / Yu, Sibin / Zhao, Yu / Wang, Gongwei / Yu, Yeisoo / Luo, Yijie / Zhou, Zhi-Wei / Hurtado, Beatriz Elena Padilla / Danowitz, Ann / Wing, Rod A / Zhang, Qifa

    Proceedings of the National Academy of Sciences of the United States of America

    2016  Band 113, Heft 35, Seite(n) E5163–71

    Abstract: Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality ... ...

    Abstract Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) contigs, with an accuracy >99.99%, and covered 90.6% and 93.2% of their estimated genome sizes. Comparative analyses of these two indica genomes uncovered surprising structural differences, especially with respect to inversions, translocations, presence/absence variations, and segmental duplications. Approximately 42% of nontransposable element related genes were identical between the two genomes. Transcriptome analysis of three tissues showed that 1,059-2,217 more genes were expressed in the hybrid than in the parents and that the expressed genes in the hybrid were much more diverse due to their divergence between the parental genomes. The public availability of two high-quality reference genomes for the indica subspecies of rice will have large-ranging implications for plant biology and crop genetic improvement.
    Sprache Englisch
    Erscheinungsdatum 2016-08-30
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1611012113
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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