Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers

Abstract

Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.

Demographic history and local adaptation of Myripnois dioica (Asteraceae) provide insight on plant evolution in northern China flora

“…promoted population divergence of plants in northern China flora, which has been indicated in previous results (Chai et al, 2020;Hou et al, 2014;Zhao et al, 2011). As phylogeographic information is useful in characterizing potential phylogeoregions, current genetic pattern of M. dioica and phylogeographical result in Opisthopappus suggests Taihang Mountains may be a potential phytogeographical boundary in Northern China (Chai et al, 2020). It is worth mentioning that we should be careful to estimate expansion and divergence time and population size changes from ABC model, as our data could not provide reliable distributions parameters and only provide a reference.…”

Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers

“…However, traditional SSR development methods are labour intensive [ 13 ]. At present, SSR markers developed by high-throughput sequencing are reliable and effective [ 19 , 38 – 41 ]. Genomic SSRs have not been developed thus far in V. amoena , and a new set of highly polymorphic SSR markers was successfully developed in the present study.…”

“…The results indicated that the trinucleotide SSRs in the V. amoena genome are mainly located in exon regions. The frequent distribution of trinucleotide repeats in coding regions indicates the effects of selection and evolution [ 41 ].…”

Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species

“…The markers used in the previous researches might reveal less genetic information than the markers used in this study that obtained across the whole genome of Opisthopappus . The EST-SSR markers developed from the transcriptome data also divided Opisthopappus populations into two clusters [ 43 ].…”