Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644007, Sichuan, China.
BMC Genomics. 2023 Apr 5;24(1):174. doi: 10.1186/s12864-023-09256-x.
Eutrema salsugineum (2n = 14), a halophyte in the family Brassicaceae, is an attractive model to study abiotic stress tolerance in plants. Two versions of E. salsugineum genomes that previously reported were based on relatively short reads; thus, the repetitive regions were difficult to characterize.
We report the sequencing and assembly of the E. salsugineum (Shandong accession) genome using long-read sequencing and chromosome conformation capture data. We generated Oxford Nanopore long reads at high depth (> 60X) of genome coverage with additional short reads for error correction. The new assembly has a total size of 295.5 Mb with 52.8% repetitive sequences, and the karyotype of E. salsugineum is consistent with the ancestral translocation Proto-Calepineae Karyotype structure in both order and orientation. Compared with previous assemblies, this assembly has higher contiguity, especially in the centromere region. Based on this new assembly, we predicted 25,399 protein-coding genes and identified the positively selected genes associated with salt and drought stress responses.
The new genome assembly will provide a valuable resource for future genomic studies and facilitate comparative genomic analysis with other plants.
盐芥（2n = 14），十字花科的一种盐生植物，是研究植物非生物胁迫耐受性的理想模式植物。此前报道的两种盐芥基因组版本都是基于相对较短的reads，因此重复区域难以进行特征描述。
我们利用长读测序和染色体构象捕获数据，报告了盐芥（山东品系）基因组的测序和组装。我们生成了牛津纳米孔长reads，深度>60X，覆盖了基因组，同时还使用了额外的短reads 进行纠错。新的组装基因组大小为 295.5 Mb，其中 52.8%为重复序列，盐芥的染色体核型与祖先的转座体 Proto-Calepineae 染色体核型结构在顺序和方向上一致。与之前的组装相比，这个组装具有更高的连续性，尤其是在着丝粒区域。基于这个新的组装，我们预测了 25399 个编码蛋白的基因，并鉴定了与盐和干旱胁迫反应相关的正选择基因。
这个新的基因组组装将为未来的基因组研究提供有价值的资源，并促进与其他植物的比较基因组分析。
