崖壁植物太行菊与长裂太行菊全基因组大小及特征分析

Genome sizes and characteristics of cliff plants Opisthopappus taihangensis and O. longilobus on Taihang Mountains

关键词:  太行菊, 长裂太行菊, 基因组调查, 基因组大小, 高通量测序

Key words:  Opisthopappus taihangensis, O. longilobus, genome survey, genome size, high-throughput sequencing

摘要:

太行菊(Opisthopappus taihangensis)、长裂太行菊(O. longilobus),为太行山特有多年生崖壁草本植物,菊科(Compositae)重要野生资源,具有较高的经济与生态价值。为确定适合两物种的全基因组测序策略,该研究利用流式细胞法和高通量测序技术,分析两物种基因组大小、杂合率、重复序列及GC含量等信息。结果表明:(1)流式细胞法估算太行菊基因组大小约为2.1 Gb,长裂太行菊基因组大小约为2.4 Gb。(2)高通量测序修正后太行菊基因组大小为3.13 Gb,重复序列比例为84.35%,杂合度为0.99%,GC含量为36.56%; 长裂太行菊基因组为3.18 Gb,重复序列比例为83.83%,杂合度为1.17%,GC含量为36.62%。(3)初步组装后GC含量分布及平均深度存在异常,出现分层现象,可能是两物种基因组杂合率较高所致。综上结果表明,太行菊、长裂太行菊均属于高重复、高杂合、大基因组的复杂基因组,建议使用Illumina + PacBio测序组装策略,进行全基因组测序分析。

Abstract:

Opisthopappus taihangensis and O. longilobus, being perennial cliff herbs and endemic to Taihang Mountains, are important wild germplasm resources of Compositae, and have high economic and ecological values. To determine the appropriate sequencing strategy for the whole genome of O. taihangensis and O. longilobus, in this study, the genome sizes, heterozygosity, GC content, and repeatability were analyzed through the flow cytometry and high-throughput sequencing methods. The results were as follows:(1)Using maize of known genome size as controls, the genome size of O. taihangensis was approximately 2.1 Gb, while that of O. longilobus was approximately 2.4 Gb.(2)For O. taihangensis, the revised genome size was 3.13 Gb, and the repetitive sequences proportion, heterozygosity and GC content in the whole genome were estimated to be 84.35%, 0.99% and 36.56% respectively. Within O. longilobus, the revised genome size, the repetitive sequences proportion, heterozygosity and GC content were 3.18 Gb, 83.83%, 1.17% and 36.62% respectively.(3)The initial depth and content distribution of GC appeared abnormal after initial assembly, which might be related to the relatively high heterozygous rate of the two species. Above all, the whole genomes of O. taihangensis and O. longilobus were both large and complex genomes with high heterozygosity and repetitiveness. Therefore, it suggests that the use of Illumina + PacBio sequencing assembly strategy for the whole genome sequencing analysis of two Opisthopappus species in the future.