Abstract
Asparagus setaceus is a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome of A. setaceus 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 A. setaceus 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 A. setaceus 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 A. setaceus from its close relative A. officinalis of ~9.66 million years ago, and A. setaceus 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 A. setaceus. These findings provide new knowledge about the characteristics and evolution of the A. setaceus genome, and will facilitate comparative genetic and genomic research on the genus Asparagus.
Highlights
Introduction AsparagusL. is a monocot genus belonging to Asparagaceae (Asparagales) that comprises >200 species distributed widely in regions with an arid–subarid climate in the Old World[1,2,3]
Our results provide a foundation for further genome-wide studies on A. setaceus and will be useful for studying the evolution of the Asparagus genus
As a close relative of the important vegetable A. officinalis, comparative genetic and genomic studies on A. setaceus and A. officinalis are helpful for investigating the mechanisms of disease resistance-related agricultural traits, and the origin and evolution of the sex chromosomes of A. officinalis
Summary
L. is a monocot genus belonging to Asparagaceae (Asparagales) that comprises >200 species distributed widely in regions with an arid–subarid climate in the Old World[1,2,3] This genus includes commercially important vegetable species, most prominently A. officinalis, and some species with great ornamental and/or medicinal value, such as A. setaceus and A. cochinchinensis. Within the Asparagus subgenus, all species are dioecious, whereas the species in the Myrsiphyllum and Protasparagus subgenera are hermaphroditic[2] This genus has important commercial value, only the model dioecious (synonyms: A. plumosus, Protasparagus plumosus, and P. setaceus) is a scrambling perennial herb with needle-like fascicled cladodes[12]. As a wild relative species of the important vegetable A. officinalis, A. setaceus is resistant to purple spot disease caused by infection with Stemphylium vesicarium[14] and rust disease
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