Genome survey and characteristic analysis of SSR in Callicarpa nudiflora.
10.19540/j.cnki.cjcmm.20190730.104
- Author:
Fu-Lai YU
1
;
Mei HUANG
1
;
Ying-Bo ZHANG
1
;
Zhen-Xia CHEN
1
;
Yu-Xin PANG
2
;
Zhi-Xin GU
3
;
Wei LI
4
;
You-Gen WU
5
Author Information
1. Tropical Crops Genetic Resources Institute,Chinese Academy of Tropical Agricultural Sciences Haikou 571101,China.
2. School of Chinese Materia Medica Resources,Guangdong Pharmaceutical University Yunfu 527500,China.
3. Key Laboratory of Phytochemical R&D of Hunan Province and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research,Ministry of Education,Hunan Normal University Changsha 410081,China.
4. Hainan Jiuzhitang Pharmaceutical Co.,Ltd. Haikou 570311,China.
5. College of Horticulture,Hainan University Haikou 570228,China.
- Publication Type:Journal Article
- Keywords:
Callicarpa nudiflora;
genome size;
heterozygosity rate;
simple-sequence repeat(SSR)
- MeSH:
Callicarpa/genetics*;
Genetic Markers;
Genome, Plant;
Microsatellite Repeats;
Polymorphism, Genetic
- From:
China Journal of Chinese Materia Medica
2019;44(18):3974-3978
- CountryChina
- Language:Chinese
-
Abstract:
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.
