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

Garsmeur, Olivier; Droc, Gaetan; Antonise, Rudie; Grimwood, Jane; Potier, Bernard; Aitken, Karen; Jenkins, Jerry; Martin, Guillaume; Charron, Carine; Hervouet, Catherine; Costet, Laurent; Yahiaoui, Nabila; Healey, Adam; Sims, David; Cherukuri, Yesesri; Sreedasyam, Avinash; Kilian, Andrzej; Chan, Agnes; Van Sluys, Marie -Anne; Swaminathan, Kankshita; Town, Christopher; Bergès, Hélène; Simmons, Blake; Glaszmann, Jean Christophe; van der Vossen, Edwin; Henry, Robert; Schmutz, Jeremy; D’Hont, Angélique

doi:10.1038/s41467-018-05051-5

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

Journal Article · 06 July 2018 · Nature Communications

DOI: https://doi.org/10.1038/s41467-018-05051-5 · OSTI ID:1543745

^[1];

^[1]; Antonise, Rudie ^[2]; Grimwood, Jane ^[3];

^[4]; Aitken, Karen ^[5]; Jenkins, Jerry ^[3];

^[1];

^[1]; Hervouet, Catherine ^[1];

^[6]; Yahiaoui, Nabila ^[1]; Healey, Adam ^[3]; Sims, David ^[3]; Cherukuri, Yesesri ^[3]; Sreedasyam, Avinash ^[3]; Kilian, Andrzej ^[7]; Chan, Agnes ^[8];

^[9]; Swaminathan, Kankshita ^[3] more »

CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), Montpellier (France); Univ. Montpellier, Montpellier (France)
KEYGENE N.V., Wageningen (The Netherlands)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
SASRI (South African Sugarcane Research Institute), Mount Edgecombe (South Africa)
CSIRO (Commonwealth Scientific and Industrial Research Organisation), St. Lucia (Australia)
CIRAD, La Reunion (France)
Diversity Arrays Technology, Yarralumla (Australia)
J. Craig Venter Institute, Rockville, MD (United States)
Univ. de Sao Paulo, Sao Paulo (Brazil)
INRA-CNRGV, Castanet-Tolosan (France)
JBEI Joint BioEnergy Inst., Emeryville, CA (United States)
Univ. of Queensland, St. Lucia (Australia)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1543745

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 9; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Genome-wide alternative splicing landscapes modulated by biotrophic sugarcane smut pathogen Bedre, Renesh; Irigoyen, Sonia; Schaker, Patricia D. C. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-45184-1	journal	June 2019
Genotype × environment interaction by AMMI and GGE-biplot analysis for sugar yield in three crop cycles of sugarcane (Saccharum officinirum L.) clones in Ethiopia Tena, Esayas; Goshu, Frehiwot; Mohamad, Hussein Cogent Food & Agriculture, Vol. 5, Issue 1 https://doi.org/10.1080/23311932.2019.1651925	journal	January 2019
The endemic ‘sugar canes’ of Madagascar (Poaceae, Saccharinae: Lasiorhachis) are close relatives of sorghum Vorontsova, Maria S.; Besnard, Guillaume; Razanatsoa, Jacqueline Botanical Journal of the Linnean Society, Vol. 192, Issue 1 https://doi.org/10.1093/botlinnean/boz067	journal	November 2019
Assembly of the 373k gene space of the polyploid sugarcane genome reveals reservoirs of functional diversity in the world's leading biomass crop Souza, Glaucia Mendes; Van Sluys, Marie-Anne; Lembke, Carolina Gimiliani GigaScience, Vol. 8, Issue 12 https://doi.org/10.1093/gigascience/giz129	journal	November 2019
Comparative analysis of glyoxalase pathway genes in Erianthus arundinaceus and commercial sugarcane hybrid under salinity and drought conditions Manoj, Vadakkancherry Mohanan; Anunanthini, Pushpanathan; Swathik, Peter Clarancia BMC Genomics, Vol. 19, Issue S9 https://doi.org/10.1186/s12864-018-5349-7	journal	April 2019
Comparative genomics revealed the gene evolution and functional divergence of magnesium transporter families in Saccharum Wang, Yongjun; Hua, Xiuting; Xu, Jingsheng BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-5437-3	journal	January 2019
Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype Rody, Hugo V. S.; Bombardelli, Renato G. H.; Creste, Silvana BMC Genomics, Vol. 20, Issue 1 https://doi.org/10.1186/s12864-019-6207-y	journal	November 2019
A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses Brottier, Laurent; Chaintreuil, Clémence; Simion, Paul BMC Plant Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12870-018-1567-z	journal	December 2018
Genome-wide systematic characterization of the HAK/KUP/KT gene family and its expression profile during plant growth and in response to low-K+ stress in Saccharum Feng, Xiaomin; Wang, Yongjun; Zhang, Nannan BMC Plant Biology, Vol. 20, Issue 1 https://doi.org/10.1186/s12870-019-2227-7	journal	January 2020
Silencing of a BAHD acyltransferase in sugarcane increases biomass digestibility de Souza, Wagner Rodrigo; Pacheco, Thályta Fraga; Duarte, Karoline Estefani Biotechnology for Biofuels, Vol. 12, Issue 1 https://doi.org/10.1186/s13068-019-1450-7	journal	May 2019
A genome-wide association study identified loci for yield component traits in sugarcane (Saccharum spp.) Barreto, Fernanda Zatti; Rosa, João Ricardo Bachega Feijó; Balsalobre, Thiago Willian Almeida PLOS ONE, Vol. 14, Issue 7 https://doi.org/10.1371/journal.pone.0219843	journal	July 2019
Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane Dantas, Luíza L. B.; Calixto, Cristiane P. G.; Dourado, Maira M. Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01614	journal	December 2019
The Role of Sugarcane Catalase Gene ScCAT2 in the Defense Response to Pathogen Challenge and Adversity Stress Sun, Tingting; Liu, Feng; Wang, Wenju International Journal of Molecular Sciences, Vol. 19, Issue 9 https://doi.org/10.3390/ijms19092686	journal	September 2018
Comparative Analysis of two Sugarcane Ancestors Saccharum officinarum and S. spontaneum based on Complete Chloroplast Genome Sequences and Photosynthetic Ability in Cold Stress Xu, Fu; He, Lilian; Gao, Shiwu International Journal of Molecular Sciences, Vol. 20, Issue 15 https://doi.org/10.3390/ijms20153828	journal	August 2019
Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis Chu, Na; Zhou, Jing-Ru; Fu, Hua-Ying Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010010	journal	December 2019
Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics Meng, Jian-Yu; Ntambo, Mbuya Sylvain; Rott, Philippe C. Microorganisms, Vol. 8, Issue 1 https://doi.org/10.3390/microorganisms8010076	journal	January 2020
Sugarcane Omics: An Update on the Current Status of Research and Crop Improvement Ali, Ahmad; Khan, Mehran; Sharif, Rahat Plants, Vol. 8, Issue 9 https://doi.org/10.3390/plants8090344	journal	September 2019

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

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