Chromosome-scale genome analysis of Apocynum venetum sheds light on Apocynum phylogenetics, bast fiber development, and flavonoid synthesis

Abstract

Apocynum venetum is a natural bast fiber crop and officinal plant belonging to the family Apocynaceae. Here, a chromosome-scale genome sequence was assembled using the single molecule sequencing and Hi-C technology. The genome of A. venetum is 228.80 Mb in length and has an N50 of 3.43 Mb. Up to 99.82 % of the contigs were attached to 11 pseudo-chromosomes. A total of 21,327 protein-coding genes were annotated in A. venetum genome. Phylogenetic analysis revealed the evolutionary relationships among the genera of Apocynum, Calotropis, and Catharanthus. Genes involved in bast fiber synthesis were identified in A. venetum by comparing gene expression between stem barks in different locations on the main stem. Combined metabolomic and transcriptomic analysis revealed the coordinated changes in flavonoids and related genes under methyl jasmonate treatment, as well as the dynamic change patterns of the genes encoding enzymes in the biosynthesis of flavonoids. Co-expression network analysis identified key genes that regulate flavonoid biosynthesis, including CHI (Av02G001490 and Av02G016020), MYB (Av01G029390), and bHLH (Av08G002930). The genome assembly of A. venetum provides a useful data set for understanding the evolution of Apocynum, bast fiber synthesis, and flavonoid biosynthesis in A. venetum.