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

Asparagus setaceusis a popular ornamental plant cultivated in tropical and subtropical regions globally. Here, we constructed a chromosome-scale reference genome ofA. setaceusto 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 ofA. setaceuscovering 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 ofA. setaceuswas 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 ofA. setaceusfrom its close relativeA. officinalisof ~9.66 million years ago, andA. setaceusunderwent 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 inA. setaceus. These findings provide new knowledge about the characteristics and evolution of theA. setaceusgenome, and will facilitate comparative genetic and genomic research on the genusAsparagus.