Ann Danowitz

University of Arizona

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Rod A. Wing

King Abdullah University of Science and Technology

Yeisoo Yu

DNACARE (South Korea)

Jianwei Zhang

Huazhong Agricultural University

Dario Copetti

ETH Zurich

Jayson Talag

University of Arizona

José Luis Goicoechea

University of Arizona

Seunghee Lee

Translational Genomics Research Institute

Dave Kudrna

University of Arizona

Carlos A. Machado

University of Maryland, College Park

Kshirod K. Jena

International Rice Research Institute

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University of Arizona

Huazhong Agricultural University

Translational Genomics Research Institute

International Rice Research Institute

Chinese Academy of Sciences

Centre National de la Recherche Scientifique

Joint Genome Institute

Cold Spring Harbor Laboratory

University of Georgia

University of Chicago

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Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63

Proceedings of the National Academy of Sciences (2016)

Jianwei Zhang Ling‐Ling Chen Feng Xing David Kudrna Wen Yao

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.

Elite

Divergence (linguistics)

Sequence (biology)

10.1073/pnas.1611012113

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Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Nature Genetics (2018)

Joshua C. Stein Yeisoo Yu Dario Copetti Derrick J. Zwickl Li Zhang

Oryza

10.1038/s41588-018-0261-2

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Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data

Scientific Data (2016)

Jianwei Zhang Ling‐Ling Chen Shuai Sun Dave Kudrna Dario Copetti

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.

Sequence assembly

Illumina dye sequencing

Hybrid genome assembly

10.1038/sdata.2016.76

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Citations (46)

Cyberspace across the Sahara

Communications of the ACM (1995)

Ann Danowitz Y. Nassef S. E. Goodman

Spanning 7.2 million square kilometers from the Atlantic Ocean to the Red Sea, and encompassing the Great Saharan Desert and Nile River Valley, North Africa embraces Mauritania, Western Sahara, Morocco, Algeria, Tunisia, Libya, and Egypt. Charting the development of information technology (IT) is as challenging as traversing the souks, the labyrinthine ancient marketplaces.

Desert (philosophy)

Traverse

Square (algebra)

10.1145/219663.219674

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Citations (93)

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Nature Genetics (2018)

Joshua C. Stein Yeisoo Yu Dario Copetti Derrick J. Zwickl Li Zhang

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago. Genome assemblies of 13 domesticated and wild rice relatives reveal salient features of genome evolution across the genus Oryza, especially rapid species diversification and turnover of transposons. This study also releases a complete long-read assembly of IR 8 'Miracle Rice'.

Introgression

Oryza

Oryza rufipogon

10.1038/s41588-018-0040-0

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Citations (470)

Explaining and alleviating information management indeterminism: A knowledge-based framework

Information Processing & Management (1994)

Hao Chen Ann Danowitz Kevin J. Lynch S. E. Goodman William K. McHenry

Indeterminism

10.1016/0306-4573(94)90039-6

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Citations (4)