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

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.

Genome survey and characteristic analysis of SSR in Callicarpa nudiflora / 中国中药杂志

Callicarpa nudiflora,which is a big brand of Li nationality medicine with Hainan characteristics,has the effects of dissolving stasis,hemostasis,anti-inflammatory and antibacterial. At present,there is a lack of information about the reference genome of C. nudiflora. The study of the genome size,heterozygosity rate and characteristics of SSR of C. nudiflora,can provide an effective basis for the formulation of the whole genome de novo sequencing strategy and development of SSR molecular markers of C. nudiflora. To realize this purpose,high throughput sequencing platform Illumina Hiseq was used to sequence the genome structure of C. nudiflora and K-mer analysis was applied to estimate genome size,repeat sequences and heterozygosity rate. Simple-sequence repeat( SSR) loci that are suitable as markers were identified by MISA software. The results showed the estimated genome size of C. nudiflora was 822. 43 Mb,with a 0. 85% heterozygosity rate and 71. 67% repeats,and the GC content of genome was about 49. 20%. Therefore,C. nudiflora belongs to a complex genome with high heterozygosity and repetition. SSR molecular genetic markers were analyzed in the genome sequence,and a total of 206 049 SSRs were identified,among which mono-nucleotide,di-nucleotide and tri-nucleotide repetitive motifs summed up to 198 993,accounting for 96. 57% of the total SSRs. Among the 2-6 nucleotide repeats,AT/AT,AAT/ATT,AGCC/CTGG,AAAAT/ATTTT and AGATAT/ATATCT have the largest number,respectively. This report represents the first genome-wide characterization of C. nudiflora,and provides a reference for the construction of the library for the fine sequencing of the genome,and a molecular basis for the development of SSR molecular markers as well as for the protection and utilization of gene resources.