DataSheet_1_The chromosome-scale reference genome and transcriptome analysis of Solanum torvum provides insights into resistance to root-knot nematodes.pdf

Solanum torvum (Swartz) (2n = 24) is a wild Solanaceae plant with high economic value that is used as a rootstock in grafting for Solanaceae plants to improve the resistance to a soil-borne disease caused by root-knot nematodes (RKNs). However, the lack of a high-quality reference genome of S. torvum hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for S. torvum combining PacBio long reads (HiFi reads), Illumina short reads and Hi-C scaffolding technology. The assembled genome size is ~1.25 Gb with a contig N50 and scaffold N50 of 38.65 Mb and 103.02 Mb, respectively as well as a BUSCO estimate of 98%. GO enrichment and KEGG pathway analysis of the unique S. torvum genes, including NLR and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 NLR genes were highly expressed in roots and fibrous roots and that three homologous NLR genes (Sto0288260.1, Sto0201960.1 and Sto0265490.1) in S. torvum were significantly upregulated after RKN infection. Two ABC transporters, ABCB9 and ABCB11 were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the S. torvum will provide insights into RKN resistance.

Solanum torvum (Swartz) (2n = 24) 为一种具有重要经济价值的野生茄科植物，常作为嫁接用的砧木，以增强茄科植物对根结线虫（RKNs）引起的土壤传播病害的抵抗力。然而，由于缺乏高质量的S. torvum参考基因组，阻碍了其在疾病抗性遗传基础及园艺应用方面的研究进展。本研究中，我们通过结合PacBio长读长（HiFi reads）、Illumina短读长和Hi-C构建技术，对S. torvum基因组序列进行了染色体水平组装。组装得到的基因组大小约为1.25 Gb，其中连续片段N50和构建片段N50分别为38.65 Mb和103.02 Mb，BUSCO估计值达到98%。对S. torvum中独特的基因，包括NLR和ABC转运蛋白的GO富集和KEGG通路分析显示，它们参与了疾病抗性过程。RNA-seq数据也证实了48个NLR基因在根系和纤维根系中高度表达，且在RKN感染后，S. torvum中的三个同源NLR基因（Sto0288260.1、Sto0201960.1和Sto0265490.1）的表达显著上调。同时，鉴定出ABCB9和ABCB11两种ABC转运蛋白为RKN感染响应的关键基因。S. torvum的染色体尺度参考基因组将为根结线虫抗性研究提供新的见解。