Genome survey study of Alpinia katsumadai based on Illumina high throughput sequencing / 中草药

ABSTRACT

Objective: To analyze the genome survey of medicinal and edible plant Alpinia katsumadai and complete its genome genetic information. Methods: This study was based on high throughput sequencing platform Illumina, and K-mer analysis was applied to estimate the genome size and heterozygosity rate of A. katsumadai. Meanwhile, simple sequence repeat (SSR) loci that were suitable as markers were identified by MISA software. Results: The estimated genome size of A. katsumadai was 1.60 Gb, with a 0.44% heterozygosity rate and 72.72% repeats; In the genome sequence, 364 395 simple sequence repeats (SSRs) were detected by SSR molecular marker analysis, among which mono-nucleotide, di-nucleotide and tri-nucleotide repetitive motifs ranked the higher percentages of 64.25%, 24.05% and 10.31%, summed up to 98.61%; From the 350 bp library obtained by sequencing, 10 000 single-end reads were randomly selected and blasted with NT bank, the results showed that its genetically close species Alpinia zerumbet and Elettaria cardamomum were blasted with the reads of 12.89% and 12.36% in NT bank. Conclusion: The genome size, heterozygosity rate and SSR molecular marker analysis' genome survey study on A. katsumadai indicated that the genome of A. katsumadai species was a complex, highly repetitive and large genome, which provided genetic information support for the resource protection, genetic diversity analysis and variety breeding of A. katsumadai.