Table_2_Unraveling the Genome of a High Yielding Colombian Sugarcane Hybrid.XLSX

Recent developments in High Throughput Sequencing (HTS) technologies and bioinformatics, including improved read lengths and genome assemblers allow the reconstruction of complex genomes with unprecedented quality and contiguity. Sugarcane has one of the most complicated genomes among grassess with a haploid length of 1Gbp and a ploidies between 8 and 12. In this work, we present a genome assembly of the Colombian sugarcane hybrid CC 01-1940. Three types of sequencing technologies were combined for this assembly: PacBio long reads, Illumina paired short reads, and Hi-C reads. We achieved a median contig length of 34.94 Mbp and a total genome assembly of 903.2 Mbp. We annotated a total of 63,724 protein coding genes and performed a reconstruction and comparative analysis of the sucrose metabolism pathway. Nucleotide evolution measurements between orthologs with close species suggest that divergence between Saccharum officinarum and Saccharum spontaneum occurred <2 million years ago. Synteny analysis between CC 01-1940 and the S. spontaneum genome confirms the presence of translocation events between the species and a random contribution throughout the entire genome in current sugarcane hybrids. Analysis of RNA-Seq data from leaf and root tissue of contrasting sugarcane genotypes subjected to water stress treatments revealed 17,490 differentially expressed genes, from which 3,633 correspond to genes expressed exclusively in tolerant genotypes. We expect the resources presented here to serve as a source of information to improve the selection processes of new varieties of the breeding programs of sugarcane.

高通量测序（High Throughput Sequencing, HTS）技术与生物信息学领域的最新进展，包括优化后的测序读长与基因组组装工具，使得我们能够以空前的质量与连续性重建复杂基因组。甘蔗是禾本科中基因组最为复杂的物种之一，其单倍体基因组长度为1吉碱基对（Gbp），倍性介于8至12之间。本研究针对哥伦比亚甘蔗杂交品种CC 01-1940构建了基因组组装结果，本次组装整合了三类测序技术：PacBio长读长测序数据、Illumina双端短读长测序数据以及Hi-C测序数据。最终获得的重叠群（contig）中位长度为34.94兆碱基对（Mbp），组装得到的总基因组大小为903.2 Mbp。我们共注释得到63724个蛋白质编码基因，并对蔗糖代谢通路开展了重建与比较分析。通过对近缘物种间直系同源基因（orthologs）的核苷酸进化特征分析，我们推测甘蔗（Saccharum officinarum）与割手密（Saccharum spontaneum）的分化事件发生于距今不足200万年前。对CC 01-1940与割手密基因组进行的同线性分析（synteny analysis）证实，两类物种间存在染色体易位事件，且当前甘蔗杂交品种的整个基因组中均存在来自两个祖先物种的随机基因组片段渗入。对经水分胁迫处理的表型差异显著的甘蔗基因型（耐旱与敏感型）的叶片与根系组织的RNA测序（RNA-Seq）数据进行分析，共鉴定得到17490个差异表达基因，其中3633个仅在耐旱基因型中特异性表达。本研究所提供的各类组学资源，有望为甘蔗育种项目中的新品种选育流程提供关键的信息支撑。