Table_8_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）技术与生物信息学的最新进展，包括更长的测序读长与更完善的基因组组装工具，使得科研人员能够以前所未有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 Gbp，倍性范围介于8至12之间。本研究报道了哥伦比亚甘蔗杂交品种CC 01-1940的基因组组装结果。本次组装整合了三类测序技术：PacBio长读长测序、Illumina双端短读长测序以及Hi-C测序。本研究获得的重叠群（contig）中位长度为34.94 Mbp，总组装基因组大小为903.2 Mbp。我们共注释得到63,724个蛋白质编码基因，并对蔗糖代谢通路进行了重建与比较分析。通过对近缘物种间直系同源基因的核苷酸进化分析，结果显示栽培甘蔗（Saccharum officinarum）与甜根子草（Saccharum spontaneum）的分化事件发生于距今不足200万年的时期。对CC 01-1940与甜根子草（S. spontaneum）基因组的共线性分析证实，两物种间存在染色体易位事件，且现代甘蔗杂交品种的基因组来自两物种的贡献随机分布于整个基因组中。对经水分胁迫处理的不同抗旱性甘蔗基因型的叶片与根系组织的RNA-seq数据进行分析后，共鉴定得到17,490个差异表达基因，其中3,633个为耐旱基因型特异性表达的基因。本研究提供的相关资源有望为甘蔗育种项目中的新品种选育流程提供重要的信息支撑。