Maximum likelihood (ML), BI, and MP phylogenetic results obviously revealed that subgenus Cyathophora composed brand new four developed variety: An excellent
DNA base mutations can be divided into two categories based on their effects to the encoded amino acids: synonymous mutations (Ks) and nonsynonymous mutations (Ka). Synonymous mutations do not result in amino acid changes, the frequency of which is represented by Ks; nonsynonymous mutations resulted in a change of amino acid, the frequency of which is indicated by Ka . Interestingly, the synonymous nucleotide substitutions occurred at a higher frequency than nonsynonymous substitutions, and thus Ka/Ks ratios are constantly <1 in most genes [9, 74], and our study is similar with this. Between different regions and genes, the Ka/Ks ratios were usually specific (Figure 8). Most conserved genes (56 of 65 genes) had an average Ka/Ks value ranging from 0 to 0.49 for the fifteen comparison groups, indicating that most genes were under purifying selection. On the contrary, the average Ka/Ks values of the ycf1 and ycf2 genes were >1 in the fifteen comparison groups, revealing that some selective pressure may execute on them in six Allium species. Previous studies have shown that ycf1 and ycf2 genes were two large open reading frames; they were important to tobacco, and the gene knockout experiments showed that ycf1 and ycf2 played important role in a healthy cell . Hu et al. suggested that plants have a variety of adaptation strategies in response to unforeseen environmental conditions. Recent studies about Allium species also suggested that the selective pressure in chloroplast genomes play an important role in Allium species adaptation and evolution [17, 71]. In our field investigations, the species of subgenus Cyathophora grows in slopes or grasslands with altitude ranging from 2700 m to 4800 m. The elevated Ka/Ks ratios observed about some genes in the six Allium species may suggest that it is relate to their specific living environment. What is more, there were four genes (matK, rpoB, petA, and rpoA) with Ka/Ks > 1 in at one or more pairwise comparisons (Figure 8, Table S3), and among these genes, rpoA was also undergone positive selection in species of Annonaceae . Previous study demonstrated that rpoA encodes the ? subunit of plastid RNA polymerase (PEP), which is in charge of the expression of most photosynthesis-related genes . It is generally believed that low temperature and strong ultraviolet radiation are not conducive to effective photosynthesis of plants; therefore, plants that survive and reproduce at high altitudes need a special photosynthetic protection strategy [79, 80]. In this study, the population of subgenus Cyathophora is mainly distributed in the Qinghai-Tibet Plateau and its adjacent high-altitude regions . Therefore, we speculated that the positive selection of these genes may be related to the difference between their optimal growth environment.
5. Results
Here, i sequenced, put together, and annotated half dozen chloroplast genomes off Allium with high-throughput sequencing tech. The fresh gene material and you may orders of the cp genomes was indeed most traditional, in addition to their cp genomes are also quadripartite structure. Frequent sequence and SSRs are helpful source to possess development new molecular ino acids of your own six species exhibited line of codon incorporate choices, and in addition we should understand codon utilize prejudice knowing development processes. We also discover 7 extremely variable common genetics that’s accustomed write helpful markers to own phylogenetic data and you may distinguish types when you look at the Allium. The brand new Ka/Ks analysis revealed that some choosy pressure may guardian soulmates use for the multiple family genes from the chloroplast genomes out of half dozen Allium L. kinds. cyathophorum, A great. cyathophorum var. farreri, A. spicatum, and you can A beneficial. mairei, and Good. cyathophorum var. farreri keeps a closer relationship with Good. spicatum. This research doesn’t only provide skills on cp genome services out of kinds in the subgenus Cyathophora as well as also provide of use genetic info to own phylogenetic analysis away from genus Allium.
