De Novo Transcriptome Assembly and Population Genetic Analyses for an Endangered Chinese Endemic Acer miaotaiense (Aceraceae)

Abstract

Acer miaotaiense (P. C. Tsoong) is a rare and highly endangered plant in China. Because of the lack of genomic information and the limited number of available molecular markers, there are insufficient tools to determine the genetic diversity of this species. Here, 93,305 unigenes were obtained by multiple assembled contigs with a transcriptome sequencing program. Furthermore, 12,819 expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were generated, 300 were randomly selected and synthesized, 19 primer pairs were identified as highly polymorphic (average number of alleles (Na) = 8, expected heterozygosity (He) = 0.635, polymorphism information content (PIC) = 0.604) and were further used for population genetic analysis. All 261 samples were grouped into two genetic clusters by UPGMA, a principal component analyses and a STRUCTURE analyses. A moderate level of genetic differentiation (genetic differentiation index (Fst) = 0.059–0.116, gene flow = 1.904–3.993) among the populations and the major genetic variance (81.01%) within populations were revealed by the AMOVA. Based on the results, scientific conservation strategies should be established using in situ and ex situ conservation strategies. The study provides useful genetic information for the protection of precious wild resources and for further research on the origin and evolution of this endangered plant and its related species.

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

“…Which con rmed the study of Um et al [49] on P. ginseng, but tri-nucleotide repeat motif was different in P. vietnamensis than other plants, such as Myricarubra [27], Salix, Populus and Eucalyptus [29]. The CG/CG motif (0.17%) was irregularly detected in P. vietnamensis, as also observed by Wu et al [44], which con rmed that the repeat motif CG/CG is not common in numerous dicotyledon plants [63][64][65][66].…”

“…Genetic diversity has important character in the germplasm improvement and generally used in various medicinal plants [66][67][68][69]. The genetic diversity degree in many plants can be linked with the numbers of loci and populations [31,70], the geographical range size [71] and genetic exchange [72].…”

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

“…A number of reports have been published regarding the interspecific relationships between Opisthopappus species based on molecular markers (Wang, 2013;Wang and Yan, 2013); however, such research has been limited due to the lack of specific genomic information on Opisthopappus. Compared with other EST-SSR markers of plants (Kudapa et al, 2012;Onda et al, 2015;Wei et al, 2016;Li et al, 2018), the developed Opisthopappus transcriptomic SSR markers showed a high level of genetic diversity (Table 2), which indicated that the identified microsatellite loci possessed high allele numbers and heterozygosity, which provided efficient genetic markers for Opisthopappus populations.…”

Single-Molecule Long-Read Sequencing of Avocado Generates Microsatellite Markers for Analyzing the Genetic Diversity in Avocado Germplasm

“…Thus, there has been rapid progress in the development of EST-SSR markers based on transcriptome data produced with second-generation sequencing technology for Lilium brownii var. viridulum Baker [27], crataegus Pinnatifida Bunge [28], Acer miaotaiense P. C. Tsoong [29], and Rosa hybrida hort. ex Lavalle [30].…”