Institute of Computational Biology, Department of Biotechnology, University of Life Sciences and Natural Resources, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia.
J Biotechnol. 2021 Jun 10;333:67-76. doi: 10.1016/j.jbiotec.2021.04.007. Epub 2021 Apr 28.
Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. While the genome of sugar beet, the most prominent beet crop, has been studied extensively, molecular data on other beet cultivars is scant. Here, we present a genome assembly of chard, a vegetable crop grown for its fleshy leaves. We report a de novo genome assembly of 604 Mbp, slightly larger than sugar beet assemblies presented so far. About 57 % of the assembly was annotated as repetitive sequence, of which LTR retrotransposons were the most abundant. Based on the presence of conserved genes, the chard assembly was estimated to be at least 96 % complete regarding its gene space. We predicted 34,521 genes of which 27,582 genes were supported by evidence from transcriptomic sequencing reads, and 5503 of the evidence-supported genes had multiple isoforms. We compared the chard gene set with gene sets from sugar beet and two wild beets (i.e. Beta vulgaris ssp. maritima and Beta patula) to find orthology relationships and identified genome-wide syntenic regions between chard and sugar beet. Lastly, we determined genomic variants that distinguish sugar beet and chard. Assessing the variation distribution along the chard chromosomes, we found extensive haplotype sharing between the two cultivars. In summary, our work provides a foundation for the molecular analysis of Beta vulgaris cultigroups as a basis for chard genomics and to unravel the domestication history of beet crops.
莙荙菜（Beta vulgaris ssp. vulgaris var. cicla）是甜菜四个不同栽培种之一。虽然已对糖用甜菜（最主要的甜菜作物）的基因组进行了广泛研究，但其他甜菜品种的分子数据却很少。在这里，我们呈现了一个莙荙菜的基因组组装，它是一种因其肉质叶片而种植的蔬菜作物。我们报告了一个 604 Mbp 的从头基因组组装，略大于迄今为止呈现的糖用甜菜组装。大约 57%的组装被注释为重复序列，其中 LTR 反转录转座子最为丰富。基于保守基因的存在，该莙荙菜组装估计在其基因空间方面至少有 96%是完整的。我们预测了 34521 个基因，其中 27582 个基因得到了转录组测序reads 的证据支持，证据支持的基因中有 5503 个有多个同工型。我们将莙荙菜基因集与糖用甜菜和两种野生甜菜（即 Beta vulgaris ssp. maritima 和 Beta patula）的基因集进行了比较，以发现同源关系，并确定了莙荙菜和糖用甜菜之间的全基因组共线性区域。最后，我们确定了区分糖用甜菜和莙荙菜的基因组变异。评估莙荙菜染色体上的变异分布，我们发现这两个品种之间存在广泛的单倍型共享。总之，我们的工作为甜菜栽培种的分子分析提供了基础，为莙荙菜的基因组学研究和揭示甜菜作物的驯化历史提供了基础。
