Abstract
Opisthopappus Shih (Asteraceae), an endangered genus endemic to the Taihang Mountains of China, is a high-value ornamental and medicinal plant consisting of two species, Opisthopappus longilobus shih and Opisthopappus taihangensis (Ling) Shih. However, the evolutionary relationships and the taxonomic characteristics between the two species remain unknown. In this study, high-throughput transcriptome sequencing was used to analyze the differential metabolic activity and gene expression and screened special molecular markers for exploring the genetic variation and species differentiation in Opisthopappus Shih. The results showed that 33,974 unigenes with an average size of 801 bp were obtained with optimization of de novo assembly. The comprehensive functional annotation based on Gene Ontology (GO), Cluster of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) revealed that these unigenes were mainly related to many physiological, metabolic, and molecular processes. Furthermore, the comparative transcriptome analysis indicated that 3,410 differentially expressed genes were mainly involved in lipid, carbohydrate and amino acid metabolism, xenobiotics biodegradation and metabolism as well as environment adaptation via KEGG. Such as the CYP710A, GST, HSP90A and so on, could be the potential candidate genes for further investigating the molecular mechanism of physiological variations between O. taihangensis and O. longilobus. In addition, the potential 71,804 high quality single nucleotide polymorphisms (SNPs) and 1,444 simple sequence repeats (SSRs) were estimated. Based on the predicted SNP, we have developed eight SNP markers for population genetic analysis in Opisthopappus Shih. A significantly high level of genetic differentiation between the populations of O. longilobus and O. taihangensis were found, and they were clearly grouped into two distinct genetic clusters. These results conformed to the record of Flora Reipublicae Popularis Sinicae (FRPS) and unsupported the taxonomic status in the Flora of China. The transcriptome analysis of Opisthopappus Shih can contribute to in-depth exploring of internal mechanisms in species variation and differentiation based on molecular evidence. With the rich and valuable data resources, the more novel structural, functional, and comparative genomic studies will provide comprehensive insights into the evolutionary relationships between O. taihangensis and O. longilobus.
Highlights
The genus Opisthopappus Shih belonging to the family Asteraceae, was generally considered as consisting of two species, Opisthopappus longilobus shih and Opisthopappus taihangensis (Ling) Shih (Shih, 1979)
The functions of transcripts in Opisthopappus Shih were successfully annotated by NR and Gene Ontology (GO) analyses, and 33,974 unigenes were assigned to 24 GO categories including three main divisions
Comparative efficiency of SRAP, cpSSR, ITS, and single nucleotide polymorphism (SNP) markers for population differentiation of Opisthopappus Shih, we found that the O. taihangensis populations could be clearly separated from the O. longilobus populations by using SNP markers (Murray and Thompson, 1980; Thomas and Kejariwal, 2004; Han, 2013)
Summary
The genus Opisthopappus Shih belonging to the family Asteraceae, was generally considered as consisting of two species, Opisthopappus longilobus shih and Opisthopappus taihangensis (Ling) Shih (Shih, 1979). This genus is endemically distributed in China and is mainly restricted to the Taihang Mountains across the provinces of Shanxi, Hebei, and Henan. It naturally grows on cliff cracks, rock gaps in open forests below cliffs and infertile soil at an elevation of 1,000 m. The desirable traits of Opisthopappus Shih including drought tolerance and leanness-resistant could provide an extensive reservoir of genetic variation for gene excavation and function. Large white-flowered O. longilobus and O. taihangensis with remarkably high ornamental and medical values are used as potential genetic resource for chrysanthemum improvement and modern breeding (Shih and Fu, 1983; Yang et al, 2010; Zhao et al, 2010; Tang et al, 2012). The distribution range of O. longilobus and O. taihangensis is continuously decreasing due to the changes in their habitats and man-made damage, and they have been listed among the Class II State-Protected Endangered Plant Species, which means that relevant studies are urgently needed to carry out and offer effective strategies and potential candidate genes for the protection and utilization of endangered and endemic species (Wang and Xie, 2009)
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