AUTHOR=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 

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

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1210513

DOI=10.3389/fpls.2023.1210513

ISSN=1664-462X

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