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

First author: Shu-Fen Li; Affiliations: Henan Normal University (河南师范大学): Xinxiang, China

Corresponding author: Wu-Jun Gao 

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.

文竹（学名：Asparagus setaceus）是一个在全球热带和亚热带地区广受欢迎的观赏植物。本文中，作者构建了一个文竹的染色体级别的参考基因组，以促进对于该植物物种的基因组特征和演化研究。通过结合纳米孔Nanopore长reads、Illumina短reads、10× Genomics linked reads和Hi-C数据，作者构建了一个高质量的文竹参考基因组，大小约为710.15 Mb，占预估基因组的98.63%。通过Hi-C数据，作者将96.85%的基因组锚定到10条superscaffolds上，正好对应于10条染色体。基因预测显示文竹基因组编码28410个基因，其中90.28%的基因能够获得功能注释。文竹基因组上重复序列占了65.59%，其中长末端重复序列LTR占主要部分，占了基因组的42.51%。演化分析显示文竹与其近缘种芦笋（Asparagus officinalis）的分化时间约为966万年前，并且文竹经历了两次全基因组复制事件。另外，作者在文竹基因组中鉴定并注释了762个特异基因家族、96受正选择的基因以及76个抗性R基因。本文的发现揭示了有关文竹基因组的基础特征和演化特征，并有利于天门冬属的比较遗传学和比较基因组学研究。

通讯：高武军 (https://www.htu.edu.cn/smkx/2014/0509/c3094a44100/page.htm)

研究方向：1）植物性别决定及分化分子机制；2）植物性染色体起源及演化的细胞及表观遗传学机制。

doi: https://doi.org/10.1038/s41438-020-0271-y

Journal: Horticulture Research

Published date: April 01, 2020