De novo assembly and Transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics

• DOI: 10.1186/s12870-020-02571-5
• Publication Date: 2020-07-29T17:02:53Z
• Authors: Dinh Duy Vu; Syed Noor Muhamma...; Mai Phuong Pham; Van Thang Bui; Minh Tam Nguyen; Thi Phuong Trang ...
• Keywords: 0301 basic medicine; Population genetics; Evolutionary biology; Plant Science; Gene; Genetic diversity; Agricultural and Biological Sciences; Conservation, EST-SSRs; Sociology; Expressed Sequence Tags; Elicitor Signal Transduction for Metabolite Production; Allele; 0303 health sciences; Ecology; Loss of heterozygosity; High-Throughput Nucleotide Sequencing; Molecular Mechanisms and Medical Applications of Ginseng; Life Sciences; FOS: Sociology; Habitat; Vietnam; Pharmacological Effects of Licorice Roots; Conservation genetics; Research Article; Gene Flow; Genetic Markers; Pharmacology, Toxicology and Pharmaceutics; Population; Panax; Endangered species; Molecular Mechanisms of Plant Development and Regulation; Meta-analysis in Ecology and Agriculture Research; 03 medical and health sciences; Panax vietnamensis; Biochemistry, Genetics and Molecular Biology; Genetics; Molecular Biology; Biology; Ecology, Evolution, Behavior and Systematics; Genome-wide Analysis; Demography; Pharmacology; Gene Expression Profiling; Endangered Species; Botany; Genetic Variation; Microsatellite; Molecular Sequence Annotation; 15. Life on land; Genetics, Population; QK1-989; FOS: Biological sciences; Transcriptome; Microsatellite Repeats; Panax Ginseng

AbstractBackgroundUnderstanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management.Panax vietnamensisHa et Grushv. is medicinally important, endemic and endangered species of Vietnam. However, genetic diversity and structure of population are unknown due to lack of efficient molecular markers.ResultsIn this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes ofP. vietnamensis(roots, leaves and stems). Raw reads total of 23,741,783 was obtained and then assembled, from which the generated unigenes were 89,271 (average length = 598.3191 nt). The 31,686 unigenes were annotated in different databases i.e. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Nucleotide Collection (NR/NT) and Swiss-Prot for functional annotation. Further, 11,343 EST-SSRs were detected. From 7774 primer pairs, 101 were selected for polymorphism validation, in which; 20 primer pairs were successfully amplified to DNA fragments and significant amounts of polymorphism was observed within population. The nine polymorphic microsatellite loci were used for population structure and diversity analyses. The obtained results revealed high levels of genetic diversity in populations, the average observed and expected heterozygosity were HO = 0.422 and HE = 0.479, respectively. During the Bottleneck analysis using TPM and SMM models (p < 0.01) shows that targeted population is significantly heterozygote deficient. This suggests sign of the bottleneck in all populations. Genetic differentiation between populations was moderate (FST = 0.133) and indicating slightly high level of gene flow (Nm = 1.63). Analysis of molecular variance (AMOVA) showed 63.17% of variation within individuals and 12.45% among populations. Our results shows two genetic clusters related to geographical distances.ConclusionOur study will assist conservators in future conservation management, breeding, production and habitats restoration of the species.