Estimation of genome sizes of Astragalus membranaceus based on flow cytometry and K-mer analysis / 中草药

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.

Flow cytometry and K-mer analysis estimates of genome size of Sophora alopecuroides / 中草药

Objective: In this study, flow cytometry and K-mer analysis were used to estimate genome size and hybridity percentage of Sophora alopecuroides, so as to provide reference for its genome sequencing. Methods: Glycine max served as an internal reference, the multiple relationship between DNA content in Glycine max and S. alopecuroides cells was detected by flow cytometry, and the genome size of S. alopecuroides was calculated. Genome sequencing of S. alopecuroides was carried out using NGS technology, genome size and hybridity percentage of S. alopec uroides were estimated by K-mer analysis. Results: The genome size of S. alopecuroides was about 1 749 Mb measured by flow cytometry. K-mer analysis showed that the genome size of S. alopecuroides was about 1 648 Mb, the hybridity percentage was 1.12%, and the percentage of repetitive sequence was high. Conclusion: The genome size of S. alopecuroides was about 1.7 Gb with high hybridity percentage. The technology of combining Illumina and PacBio is recommended for future genome sequencing.