دانلود رایگان مقاله تنوع ژنتیکی و روابط فیلوژنتیک لیمپوگراس بر اساس ترکیب DNA کلروپلاست

Abstract

Hemarthria R. Br. is a genus which includes important forage grasses. However, there is currently a lack of data analysis on the chloroplast DNA (cpDNA) of Hemarthria species. This study is to use three cpDNA intergenic spacers (trnL-F, trnC-ycf6 and psbC-trnS) to obtain phylogenetic information in 36 Hemarthria samples including four Hemarthria species: Hemarthria altissima (Poir.) Stapf et C. E. Hubb., Hemarthria compressa (L. f.) R. Br., Hemarthria uncinata R. Br., and Hemarthria japonica (Hack.) Roshev. Data analysis revealed that non-significant genetic diversity existed in our samples, which was implied by nucleotide sequences information and the results of haplotypic and nucleotide diversity. The results of phylogenetic trees based on maximum likelihood (ML) and Bayesian inference (BI) revealed that H. altissima and H. compressa samples were not entirely distinct, suggesting that the two species share an intimate genetic relationship. A haplotype median-joining (MJ) network revealed broadly similar results to those derived from the ML and BI trees and implied that haplotype H3 may represent an ancient haplotype. Analysis of the population statistic FST revealed little genetic differentiation among the seven populations of H. altissima in Africa.

4. Discussion

This is the first report analyzing the genetic diversity of Hemarthria species using cpDNA molecular markers. Although cpDNA non-coding regions are generally hypervariable and rich in variation, the 36 Hemarthria samples exhibited relatively low genetic diversity of the cpDNA intergenic spacers trnL-F, trnC-ycf6, and psbC-trnS (Hd ¼ 0.575, 0.522, and 0.354, respectively; p ¼ 0.00151, 0.00131, and 0.00092, respectively). The combined sequence data also exhibited low haplotype diversity (Hd ¼ 0.851) and nucleotide diversity (p ¼ 0.129). This low level of genetic diversity resulted in low efficiency of the cpDNA markers for resolving Hemarthria genotypes or, in other words, poor detection of variable sites (the highest proportion of variable sites was only 2.0%). The proportion of variable sites is a major index that reflects the level of genetic diversity. Similar findings were reported previously for trnC-ycf6 (proportion of variable sites ¼ 0.23%) in Anemoclema glaucifolium (Guan et al., 2013) and for psbC-trnS (0.13%) in pear germplasm resources (Chang et al., 2014) but stood in contrast to results for trnL-F (44%) in field vittarioid gametophytes (Chen et al., 2013). Moreover, such low genetic diversity in our cpDNA analysis contradicts previous studies based on nuclear DNA molecular markers (SCoT and EST-SSR markers) with higher levels of genetic diversity in Hemarthria samples (Huang et al., 2014). A similar situation e low diversity in cpDNA and higher diversity in nuclear markers e was also found in the Miscanthus sinensis (Yan et al., 2015). Lower genetic diversity in cpDNA non-coding spacers compared to nuclear genes may be due to the influences of random genetic drift and genetic bottlenecks (Gong et al., 2011).