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

Published in:

Nat Commun 9(1) , 2638 (Jul 6 2018)

Author(s):

Garsmeur, O., Droc, G., Antonise, R., Grimwood, J., Potier, B., Aitken, K., Jenkins, J., Martin, G., Charron, C., Hervouet, C., Costet, L., Yahiaoui, N., Healey, A., Sims, D., Cherukuri, Y., Sreedasyam, A., Kilian, A., Chan, A., Van Sluys, M. A., Swaminathan, K., Town, C., Berges, H., Simmons, B., Glaszmann, J. C., van der Vossen, E., Henry, R., Schmutz, J., D'Hont, A.

DOI:

10.1038/s41467-018-05051-5

Abstract:

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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