Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

Abstract

<i>Asparagus setaceus</i> is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of <i>A. setaceus</i> to facilitate the investigation of its genome characteristics and evolution. Using a combination of Nanopore long reads, Illumina short reads, 10× Genomics linked reads, and Hi-C data, we generated a high-quality genome assembly of <i>A. setaceus</i> covering 710.15 Mb, accounting for 98.63% of the estimated genome size. A total of 96.85% of the sequences were anchored to ten superscaffolds corresponding to the ten chromosomes. The genome of <i>A. setaceus</i> was predicted to contain 28,410 genes, 25,649 (90.28%) of which were functionally annotated. A total of 65.59% of the genome was occupied by repetitive sequences, among which long terminal repeats were predominant (42.51% of the whole genome). Evolutionary analysis revealed an estimated divergence time of <i>A. setaceus</i> from its close relative <i>A. officinalis</i> of ~9.66 million years ago, and <i>A. setaceus</i> underwent two rounds of whole-genome duplication. In addition, 762 specific gene families, 96 positively selected genes, and 76 resistance (R) genes were detected and functionally predicted in <i>A. setaceus</i>. These findings provide new knowledge about the characteristics and evolution of the <i>A. setaceus</i> genome, and will facilitate comparative genetic and genomic research on the genus <i>Asparagus</i>.