A mosaic monoploid reference sequence for the highly complex genome of sugarcane.

Autor:	Garsmeur O; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Droc G; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Antonise R; KEYGENE N.V., 6708 PW, Wageningen, The Netherlands., Grimwood J; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Potier B; SASRI (South African Sugarcane Research Institute), Mount Edgecombe, 4300, South Africa., Aitken K; CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia, QLD, 4067, Australia., Jenkins J; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Martin G; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Charron C; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Hervouet C; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Costet L; CIRAD, UMR PVBMT, F-97410, Saint-Pierre, La Réunion, France., Yahiaoui N; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., Healey A; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Sims D; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Cherukuri Y; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Sreedasyam A; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Kilian A; Diversity Arrays Technology, Yarralumla, ACT, 2600, Australia., Chan A; J. Craig Venter Institute, Rockville, MD, 20850, USA., Van Sluys MA; Universidade de Sao Paulo, Sao Paulo, 05508-090, SP, Brazil., Swaminathan K; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA., Town C; J. Craig Venter Institute, Rockville, MD, 20850, USA., Bergès H; INRA-CNRGV, 31326, Toulouse, Castanet-Tolosan, France., Simmons B; JBEI Joint BioEnergy Institute, Emeryville, CA, 94608, USA., Glaszmann JC; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France., van der Vossen E; KEYGENE N.V., 6708 PW, Wageningen, The Netherlands., Henry R; QAAFI (Queensland Alliance for Agriculture and Food Innovation), University of Queensland, St. Lucia, QLD, 4072, Australia., Schmutz J; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35801, USA.; Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA., D'Hont A; CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398, Montpellier, France. dhont@cirad.fr.; AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060, Montpellier, France. dhont@cirad.fr.
Jazyk:	angličtina
Zdroj:	Nature communications [Nat Commun] 2018 Jul 06; Vol. 9 (1), pp. 2638. Date of Electronic Publication: 2018 Jul 06.
DOI:	10.1038/s41467-018-05051-5
Abstrakt:	Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
Databáze:	MEDLINE
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