UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia.
The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Int J Mol Sci. 2021 Apr 21;22(9):4326. doi: 10.3390/ijms22094326.
Legumes are of great interest for sustainable agricultural production as they fix atmospheric nitrogen to improve the soil. is a well-established model legume, and extensive studies in fundamental molecular, physiological, and developmental biology have been undertaken to translate into trait improvements in economically important legume crops worldwide. However, reference genome was generated in the accession Jemalong A17, which is highly recalcitrant to transformation. R108 is more attractive for genetic studies due to its high transformation efficiency and -insertion population resource for functional genomics. The need to perform accurate synteny analysis and comprehensive genome-scale comparisons necessitates a chromosome-length genome assembly for cv. R108. Here, we performed in situ Hi-C (48×) to anchor, order, orient scaffolds, and correct misjoins of contigs in a previously published genome assembly (R108 v1.0), resulting in an improved genome assembly containing eight chromosome-length scaffolds that span 97.62% of the sequenced bases in the input assembly. The long-range physical information data generated using Hi-C allowed us to obtain a chromosome-length ordering of the genome assembly, better validate previous draft misjoins, and provide further insights accurately predicting synteny between A17 and R108 regions corresponding to the known chromosome 4/8 translocation. Furthermore, mapping the insertion landscape on this reference assembly presents an important resource for functional genomics by supporting efficient mutant gene identification in insertion lines. Our data provide a much-needed foundational resource that supports functional and molecular research into the Leguminosae for sustainable agriculture and feeding the future.
豆类对于可持续农业生产具有重要意义，因为它们可以固定大气氮，从而改善土壤。 是一种成熟的模式豆科植物，为了在全球范围内将其转化为经济上重要的豆科作物的性状改良，已经进行了广泛的基础分子、生理和发育生物学研究。然而， 参考基因组是在高度转化抗性的 Jemalong A17 品系中生成的。 由于其高效的转化效率和 -插入群体资源，用于功能基因组学，因此 R108 更适合进行遗传研究。需要进行准确的同线性分析和全面的基因组规模比较，这就需要对 cv. R108 进行染色体长度基因组组装。在这里，我们使用原位 Hi-C（48×）来固定、排序、定向支架，并纠正先前发表的基因组组装（R108 v1.0）中 contigs 的错误连接，从而得到一个改进的基因组组装，包含 8 个染色体长度的支架，涵盖了输入组装中 97.62%的测序碱基。使用 Hi-C 生成的长程物理信息数据使我们能够获得基因组组装的染色体长度排序，更好地验证以前的草案连接错误，并提供更准确的预测，以准确预测对应已知第 4/8 号染色体易位的 A17 和 R108 区域之间的同线性。此外，在这个参考组装上绘制 插入景观为 功能基因组学提供了一个重要的资源，通过支持在 插入系中高效鉴定突变基因，为 功能基因组学提供了一个重要的资源。我们的数据提供了一个急需的基础资源，支持可持续农业和未来粮食供应的豆类功能和分子研究。
