基于流式细胞术和K-mer分析的广金钱草基因组大小估测

Genome Size Analysis of Desmodium styracifolium by Flow Cytometry and Genome Survey

目的估测广金钱草的基因组大小,为广金钱草基因组测序提供依据。方法采用流式细胞术和全基因组调查(Genome Survey)相结合的方法预估广金钱草基因组大小和杂合度。以OTTO裂解液提取广金钱草细胞核,碘化丙啶对细胞核染色,以番茄为内参,运用流式细胞术预估广金钱草基因组大小;通过第二代高通量测序技术对广金钱草基因组进行低覆盖度评估,利用生物信息学方法估算GC含量、杂合率、重复序列等。结果流式细胞术估算广金钱草的基因组大小为(654.80±11.88)Mbp,经Genome Survey测定获得广金钱草有效数据99.18 Gb,总测序深度约为153.86×,估计基因组的大小约644.62 Mbp,杂合率约0.07%,重复序列含量约59.71%。结论两种方法测得广金钱草基因组大小基本一致,基因组大小适中,杂合度较低,适合进一步的结构基因组研究。

Objective Desmodium styracifolium(Osb.)Merr.is one common"Daodi"medicinal materials of Lingnanregion,mainly used to treat urinary system diseases such as stone disease.Research on the genome of D.styracifolium is helpful for the germplasm resources and identification of this medicinal material.Methods Flow cytometry andgenome survey were combined to estimate the genome size and heterozygosity of D.styracifolium.The nucleuses wereextracted by OTTO lysate and stained with propidium iodide.The genome size of D.styracifolium was estimated byflow cytometry using tomato as internal standard.Low-coverage sequencing evaluation of the genome size withsecond-generation high-throughput sequencing technology was conducted,and bioinformatics methods were used toobtain GC content,heterozygosity,and repeat sequences et al.Results The genome size of D.styracifolium wasestimated to be(654.80±11.88)Mbp by flow cytometry method.The obtained effective sequencing data were 99.18 Gb by genome survey,and the total sequencing depth is about 153.86×.The estimated genome size of D.styracifolium was about 644.62 Mbp,and the heterozygous rate is about 0.07%,the content of repeats is about59.71%.Conclusion The two methods have similar genome size,and the genome size is moderate with lowheterozygosity,which is suitable for further structural genome research.