基于流式细胞术和基因组survey分析的地黄基因组研究

目的地黄Rehmannia glutinosa是我国传统中药,具有较高的药用价值和经济价值。利用流式细胞技术和高通量测序技术,分析了地黄基因组大小和特征等信息,为绘制地黄全基因组精细图谱提供依据。方法将已知基因组大小的大豆Glycine max和辣椒Capsicum annuum作为对照,用流式细胞技术估算地黄基因组大小。然后利用高通量测序技术对地黄基因组进行survey分析,通过生物信息学分析获得了地黄全基因组重复序列比例、基因组杂合度以及GC含量等信息。结果根据流式细胞实验结果,地黄基因组大小介于大豆和辣椒之间,估算地黄基因组大小应在2.00~2.12 Gb。通过高通量测序,获得了132.79 Gb高质量的数据,总测序深度约为66.40×,估算地黄基因组大小为2.03 Gb。根据Kmer分布情况,估算地黄基因组重复序列比例为78.48%,杂合度为1.93%,GC含量为37.27%。从基因组基本结构特征上看,地黄基因组属于高重复、高杂合、大基因组的复杂基因组。结论获得了地黄基因组大小和特征等信息,这些信息将为绘制地黄全基因组的精细图谱奠定基础,也为阐明地黄有效成分的生物合成和调控途径提供依据。

Estimation of Rehmannia glutinosa genome size based on flow cytometry and genome survey analysis

Objective Rehmannia glutinosa is a traditional Chinese medicine with high medicinal and economic value. In this study, flow cytometry and high-throughput sequencing technology were used to analyze the size and characteristics of R. glutinosa genome so as to provide a basis for the detailed mapping of the whole genome of R. glutinosa in the future. Methods The genome size of R. glutinosa was estimated by flow cytometry using soybean (Glycine max) and pepper (Capsicum annuum) of known genome size as controls. Then, high-throughput sequencing technology was used to carry out survey analysis on the genome of R. glutinosa, and information such as the proportion of repetitive sequences in the whole genome of R. glutinosa, genomic heterozygosity, and GC content were obtained through bioinformatics analysis. Results According to the results of flow cytometry, the genome size of R. glutinosa was between soybean and pepper, and it was estimated that the genome size of R. glutinosa was between 2.00 and 2.12 Gb. Through high-throughput sequencing, 132.79 Gb high-quality data were obtained, with a total sequencing depth of about 66.40×, and the genome size of R. glutinosa was estimated to be 2.03 Gb. According to the distribution of Kmer, the proportion of repetitive sequences, the heterozygosity and the GC content in the whole genome of R. glutinosa were estimated to be 78.48%, 1.93% and 37.27%, respectively. From the perspective of the basic structural features of the genome, the genome of R. glutinosa was a large and complex genome with high heterozygosity and high repetitiveness. Conclusion In this study, the size and characteristics of R. glutinosa genome were obtained, which will lay an important foundation for detailed mapping of the whole genome of R. glutinosa in the future, and also provide a basis for elucidating the biosynthesis and regulatory pathways of active components in R. glutinosa.