USDA-ARS Sugarbeet and Bean Research Unit, Michigan State University, 1066 Bogue St., East Lansing, MI 48824, USA.
Plant Breeding, Genetics, and Biotechnology Program, Michigan State University, East Lansing, MI 48824, USA.
DNA Res. 2023 Feb 1;30(1). doi: 10.1093/dnares/dsac033.
A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.
利用 PacBio 长读测序、BioNano 光学图谱、Hi-C 支架和 Illumina 短读纠错，构建了同源近交系 'EL10' 甜菜（Beta vulgaris ssp. vulgaris）基因组的连续组装。EL10.1 组装体为 540Mb，其中 96.2%包含在 9 个染色体大小的假染色体中，长度从 52 到 65Mb，31 个大小中位数为 282kb 的 contig 未组装。通过 RNA-seq 数据和通过 MAKER 注释管道进行的精选序列进行基因注释，生成了 24255 个基因模型。结果表明，EL10.1 基因组组装是一个与已发表的甜菜参考基因组高度一致的连续基因组组装。EL10.1 的大规模重复基因分析表明，基因组内很少发生大规模的重复。与其他核心真双子叶植物相比，注释良好的基因家族的基因拷贝数减少，尤其是转录因子。通过对 50 个个体进行流式细胞术研究，发现 B. vulgaris 的基因组大小存在差异，估计范围为 633 到 875Mb/1C。来自其他甜菜种质资源的短读全基因组序列的读深度映射表明，甜菜基因组中相对较少的区域与高拷贝数变异相关。
