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

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

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.

Highlights

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production
Sorghum could be used as a guide to identify a minimum tiling path (MTP) of BACs covering the euchromatin of a monoploid genome of sugarcane
All seven cosegregation groups (CGs) that aligned with two sorghum chromosomes were assigned to S. spontaneum chromosomes or to recombinant chromosomes between S. spontaneum and S. officinarum (Fig. 5). These results suggested that a few large chromosome rearrangements differentiate S. spontaneum on one side and S. officinarum and sorghum on the other

Summary

Introduction

Aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. While sugarcane breeding is still essentially focused on conventional methods since sugarcane genetics knowledge has lagged behind that of other major crops[2] This is due to the interspecific, polyploid, and aneuploid nature of modern sugarcane cultivar genomes, a complexity that exceeds that of most if not all other crops. Modern sugarcane cultivars are derived from a few interspecific hybridizations performed a century ago between S. officinarum and S. spontaneum, two highly polyploid species. One haplotype sequence would provide a good reference for the other haplotypes (=hom(oe)ologous chromosomes) These studies revealed a high level of microcolinearity between sorghum and sugarcane[47,48,49,50,51]. While new sequencing and assembling methods tailored for complex genomes continue to be developed, we deployed this original strategy to produce a first sugarcane reference genome sequence assembly

Methods

Results

Conclusion