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

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its genome poses challenges that have not been addressed in any prior sequencing project due to its highly polyploid, aneuploid, heterozygous and interspecific genome structure (2n ~ 12x ~ 120, ~10Gb). We exploited the colinearity with sorghum to produce a monoploid genome sequence of sugarcane. We applied whole genome profiling (WGPTM) to 20,736 sugarcane BAC clones and anchored 11,732 of them onto the sorghum genome. A minimum tiling path of 4,660 sugarcane BAC clones that best cover the gene-rich part of the sorghum genome was selected, sequenced and assembled in a 382 Mb single tiling path (STP) of high quality sequence. A total of 25,316 protein-coding gene models were predicted on the STP, 17% of which displayed no colinearity with their sorghum orthologs. A 12,468 SNP-based sugarcane genetic map revealed a few large chromosomal rearrangements in S. spontaneum as compared to S. officinarum and sorghum, which explain their distinct basic chromosome numbers and suggest that polyploidization in S. spontaneum and S. officinarum lineages arose after their divergence.This BAC-based monoploid sugarcane reference sequence represents a crucial resource for genetic and functional genomic studies while providing an essential framework for future whole genome sequence assembly programmes.

甘蔗（Saccharum spp.）是用于蔗糖及生物能源生产的重要经济作物。其基因组兼具高度多倍性、非整倍性、杂合性及种间嵌合结构（2n≈12x≈120，基因组大小约10Gb），是此前所有测序项目均未攻克的技术难题。本研究借助甘蔗与高粱的基因组共线性关系，成功构建了甘蔗单倍体基因组序列。我们对20736个甘蔗细菌人工染色体（Bacterial Artificial Chromosome，BAC）克隆开展全基因组分析（Whole Genome Profiling，WGPTM），并将其中11732个克隆锚定至高粱基因组。随后筛选出4660个可最优覆盖高粱基因富集区域的甘蔗BAC克隆，对其进行测序并组装得到总长382 Mb的高质量单叠连路径（Single Tiling Path，STP）序列。该STP序列中共预测得到25316个蛋白质编码基因模型，其中17%的基因与高粱直系同源基因未表现出共线性特征。我们构建了基于12468个单核苷酸多态性（Single Nucleotide Polymorphism，SNP）的甘蔗遗传图谱，对比分析发现，相较于S. officinarum与高粱，S. spontaneum存在多处大型染色体重排事件，这一现象解释了二者基础染色体数目的差异，并表明S. spontaneum与S. officinarum谱系的多倍化过程发生于二者分化之后。本项基于BAC的甘蔗单倍体参考基因组序列，可为遗传与功能基因组学研究提供关键资源，同时也为未来全基因组测序组装项目提供了重要的框架支撑。