Estimation of genome sizes of Astragalus membranaceus based on flow cytometry and K-mer analysis
10.7501/j.issn.0253-2670.2019.06.029
- Author:
Hui-Gai SUN
1
Author Information
1. College of Life and Environmental Sciences, Minzu University of China
- Publication Type:Journal Article
- Keywords:
Astragalus membranaceus (Fisch.) Bunge;
Flow cytometry;
Genome size;
Hybridity percentage;
K-mer analysis
- From:
Chinese Traditional and Herbal Drugs
2019;50(6):1448-1452
- CountryChina
- Language:Chinese
-
Abstract:
Objective: To determinate the genome size and complexity of Astragalus membranaceus by using flow cytometry (FCM) and K-mer analysis, which can lay the foundation for the screening of functional genes of A. membranaceus. Methods Lycopersicon esculentum was served as an internal reference in this study. The mixed sample of A. membranaceus cell nucleus and L. esculentum cell nucleus was stained using propidium iodide (PI). The PI fluorescence intensities of the sample were measured by FCM. The genome size of A. membranaceus was calculated by comparing the multiple relationship between the peak of DNA content in the cells of A. membranaceus and L. esculentum. The genome of A. membranaceus was sequenced by using high-throughput sequencing technologies. The genome size of A. membranaceus was calculated by K-mer analysis. The hybridity percentage, repetitive sequence, and GC of A. membranaceus were estimated by bioinformatics analysis. Results The genome size of A. membranaceus was about 1 426 Mb. For K-mer analysis, more than 95 Gb high quality data from the genome was generated. The average genome size and sequencing coverage depth of A. membranaceus was about 1 456 Mb and 39 times respectively. The genome of A. membranaceus had obvious hybridity peak by K-mer method, and the hybridity percentage as high as 2.1%. Conclusion The genome size of A. membranaceus was about 1.45 Gb and the heterozygosity is high. These data would provide a reference for the genomic research in A. membranaceus.
