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

Abstract

Background: Understanding the genetic diversity in endangered species that occur inforest remnants is necessary to establish efficient strategies for the species conservation, restoration and management. Panax vietnamensis Ha 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. Results: In this study, we employed Illumina HiSeq™ 4000 sequencing to analyze the transcriptomes of P. 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 H O = 0.422 and H E = 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 (F ST = 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.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

“…Recently, 123 SSRs were identified in the A. tsaoko chloroplast genome; the mean density of SSR loci is up to 1/1.33 kb; however, they have not been validated for A. tsaoko [ 48 ]. In recent years, the use of transcriptome data to obtain sequences containing microsatellites, and the study of their genetic diversity has been successfully reported [ 52 – 54 ]. Excluding mononucleotide repeats, trinucleotides were found to be the most abundant repeats in the present study.…”

Target Capture Reveals the Complex Origin of Vietnamese Ginseng

“…Furthermore, there is no difference between cultivated individuals and those found in the wild. High genetic diversity and gene flow between P. vietnamensis populations have recently been attributed to insect dispersal (Vu et al, 2020 ). Strong gene flow and insufficient splitting time between cultivated populations has also been observed for P. notoginseng (Pan et al, 2016 ), and was attributed to non-random mating among the individuals of the population.…”

“…Other studies have investigated the differentiation between P. vietnamensis and P. ginseng (Vasyutkina et al, 2018 ). Studies on P. vietnamensis continue to shed new light on intra- and interspecific evolutionary relationships (Nguyen et al, 2020 ; Vu et al, 2020 ).…”

Research Progress and Future Development Trends in Medicinal Plant Transcriptomics

“…This study provided a basis for further research on S. oleoides. Dinh et al (2020) used the Illumina HiSeq 4000 sequencing platform to analyze the transcripts (from roots, leaves, and stems) of Populus alba. A total of 11,343 EST-SSRs were detected, and 101 primer pairs were screened from 7,774 pairs for polymorphism verification.…”