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New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica

M.C. Schatz, L.G. Maron, J.C. Stein, Wences A. Hernandez, J. Gurtowski, E. Biggers, H. Lee, M. Kramer, E. Antoniou, E. Ghiban, M.H. Wright, J.H. Chia, D. Ware, S.R. McCouch, W.R. McCombie
doi: https://doi.org/10.1101/003764
M.C. Schatz
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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L.G. Maron
2Department of Plant Breeding and Genetics, Cornell University Ithaca, NY 14853
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J.C. Stein
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Wences A. Hernandez
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
3Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos México
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J. Gurtowski
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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E. Biggers
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
4Macalester College St. Paul, MN, 55105
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H. Lee
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
5Stony Brook UniversityStony Brook, NY, 11794
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M. Kramer
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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E. Antoniou
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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E. Ghiban
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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M.H. Wright
2Department of Plant Breeding and Genetics, Cornell University Ithaca, NY 14853
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J.H. Chia
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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D. Ware
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
6USDA Agricultural Research Service
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S.R. McCouch
2Department of Plant Breeding and Genetics, Cornell University Ithaca, NY 14853
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W.R. McCombie
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
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Abstract

The use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. Currently, when the genomes of different strains of a given organism are compared, whole genome resequencing data are aligned to an established reference sequence. However when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate. Here, we use rice as a model to explore the extent of structural variation among strains adapted to different ecologies and geographies, and show that this variation can be significant, often matching or exceeding the variation present in closely related human populations or other mammals. We demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared to provide an unbiased assessment. Using this approach, we are able to accurately assess the “pan-genome” of three divergent rice varieties and document several megabases of each genome absent in the other two. Many of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard resequencing approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.

Footnotes

  • ↵† Co-Corresponding Authors: SRM: srm4{at}cornell.edu; WRM: mccombie{at}cshl.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 02, 2014.
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New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica
M.C. Schatz, L.G. Maron, J.C. Stein, Wences A. Hernandez, J. Gurtowski, E. Biggers, H. Lee, M. Kramer, E. Antoniou, E. Ghiban, M.H. Wright, J.H. Chia, D. Ware, S.R. McCouch, W.R. McCombie
bioRxiv 003764; doi: https://doi.org/10.1101/003764
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New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica
M.C. Schatz, L.G. Maron, J.C. Stein, Wences A. Hernandez, J. Gurtowski, E. Biggers, H. Lee, M. Kramer, E. Antoniou, E. Ghiban, M.H. Wright, J.H. Chia, D. Ware, S.R. McCouch, W.R. McCombie
bioRxiv 003764; doi: https://doi.org/10.1101/003764

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