Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus. (1st April 2020)

• Record Type: Journal Article
• Authors: Li, Shu-Fen; Wang, Jin; Dong, Ran; Zhu, Hong-Wei; Lan, Li-Na; Zhang, Yu-Lan; Li, Ning; Deng, Chuan-Liang; Gao, Wu-Jun
• Is Part Of: Horticulture research. Volume 7(2020)
• Publication Date: 2020-04-01
• Subjects: Plant evolution -- Plant molecular biology -- Horticultural plant genomes; Horticulture -- Research -- Periodicals; 635.072
• DOI: 10.1038/s41438-020-0271-y
• Languages: English
• ISSNs: 2052-7276

Abstract

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 .