半夏倍性调查及全基因组Survey分析

Ploidy and whole genome Survey of Pinellia ternata

半夏Pinellia ternata在我国分布广泛,以块茎入药,有燥湿化痰等功效。其倍性复杂,且目前未获得全基因组图谱,限制了分子辅助育种及多组学的深入研究。该研究首先基于流式细胞术对来自我国16个省市的144株不同表型半夏进行基因组大小评估,发现其均值为(7.97±0.43)Gb,最高及最低值分别为7.06、9.21 Gb。此外,云南半夏基因组大小相对偏低[(7.24±0.09)Gb],而采自湖北仙桃的紫皮半夏个体间基因组大小较为一致[(8.07±0.04)Gb]。进一步通过根尖染色体计数发现,流式细胞测定结果为8.18 Gb的半夏(2n=8x=104)为八倍体,其余均为非整倍体植株。采用Illumina技术完成该八倍体的75×深度,使用3种方法完成测序结果的K-mer分析。该八倍体半夏基因组大小为7367.082~7541.213 Mb,重复序列比率为91.3%±1.7%,杂合率为1.68%,是一种复杂基因组。该研究开展半夏群体的倍性调查及特定倍性株系的全基因组Survey分析,可为其全基因组测序和组装奠定基础,同时为倍性复杂、纯系缺乏、植株矮小的草药提供可参考的全基因组调查分析策略。

Pinellia ternata,a widely distributed species in China,has been used as a herbal medicine for centuries,with the effects of drying dampness and resolving phlegm.However,its complex ploidy and lack of whole-genome map limit in-depth research on molecular-assisted breeding and multi-omics.In this study,flow cytometry was employed to evaluate the genome sizes of 144 P.ternata plants with different phenotypes collected from 16 geographical locations in China,which revealed the average,maximum,and minimum genome sizes of(7.97±0.43)Gb,7.06 Gb,and 9.21 Gb,respectively.In addition,the plants from Yunnan province had small genomes(7.24±0.09)Gb,while those with purple skin from Xiantao,Hubei presented similar genome sizes(8.07±0.04)Gb.The plant with a flow cytometry result of 8.18 Gb(2n=8x=104)was identified as an octoploid by the root tip chromosome counting method.Illumina was employed to sequence the octoploid P.ternata at a depth of 75×,and three mainstream methods were used for K-mer analysis.The estimated genome size range of this plant was 7367.082-7541.213 Mb,and the heterozygosity rate and repeated sequence ratio were 1.68%and 91.3%±1.7%,respectively.A ploidy Survey of P.ternata populations and a whole-genome survey of specific ploidy strains were carried out,which laid a foundation for whole-genome sequencing and assembly.Meanwhile,this study provided a reference strategy of whole genome Survey for herbal species with complex ploidy,lack of pure lines,and dwarf plants.