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

• Published in: Frontiers in plant science 2023-07, Vol.14, p.1210513-1210513
• Main Authors: Zhang, Hongyuan, Chen, Hao, Tan, Jie, Huang, Shuping, Chen, Xia, Dong, Hongxia, Zhang, Ru, Wang, Yikui, Wang, Benqi, Xiao, Xueqiong, Hong, Zonglie, Zhang, Junhong, Hu, Jihong, Zhang, Min
• Format: Article
• Language: English
• Subjects: ABC transporter; genome; Plant Science; root-knot nematode; Solanum torvum; transcriptome
• ISSN: 1664-462X; 1664-462X
• DOI: 10.3389/fpls.2023.1210513

(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 . hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for . 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 . genes, including and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 genes were highly expressed in roots and fibrous roots and that three homologous genes ( , and ) in were significantly upregulated after RKN infection. Two ABC transporters, and were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the . will provide insights into RKN resistance.