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

Abstract

<i>Solanum torvum</i> (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 <i>S</i>. <i>torvum</i> hinders research on the genetic basis for disease resistance and application in horticulture. Herein, we present a chromosome-level assembly of genomic sequences for <i>S</i>. <i>torvum</i> 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 <i>S</i>. <i>torvum</i> genes, including <i>NLR</i> and ABC transporters, revealed that they were involved in disease resistance processes. RNA-seq data also confirmed that 48 <i>NLR</i> genes were highly expressed in roots and fibrous roots and that three homologous <i>NLR</i> genes (<i>Sto0288260.1</i>, <i>Sto0201960.1</i> and <i>Sto0265490.1</i>) in <i>S. torvum</i> were significantly upregulated after RKN infection. Two ABC transporters, <i>ABCB9</i> and <i>ABCB11</i> were identified as the hub genes in response to RKN infection. The chromosome-scale reference genome of the <i>S</i>. <i>torvum</i> will provide insights into RKN resistance.