Characterization of the Complete Chloroplast Genome and Phylogenetic Implications of Euonymus microcarpus (Oliv.) Sprague

Abstract

Euonymus microcarpus (Oliv.) Sprague, is a species of evergreen shrub of the genus Euonymus, family Celastraceae. Here, we extracted the genomic DNA from the leaves of E. microcarpus and constructed a paired-end library. The chloroplast genome of E. microcarpus was generated with the high-throughput sequencing by the illumina Hiseq X Ten platform and de novo assembly. The chloroplast genome had a quadripartite structure, containing a long single copy region with a size of 85,386 bp and a short single copy region with a size of 18,456 bp, separated by two inverted repeat regions of 26,850 bp. The chloroplast genome contained 133 genes identified in total, including 87 potential protein-coding genes, 38 transfer RNA genes, and eight ribosomal RNA genes. A total of 282 simple sequence repeats and 63 long repeats were found. Furthermore, the phylogenetic relationships inferred that E. microcarpus is sister to E. japonicus and E. schensianus. A comparison of the structure of the chloroplast genomes of eight Euonymus species suggests a nucleotide variability of the junction sites and a higher divergence of non-coding regions, compared to the coding regions. The original findings of the study serves as a good reference for chloroplast genome assembly and a valuable foundation for the genetic diversity and evolution of E. microcarpus.

Complete chloroplast genome sequences of the ornamental plant Prunus Cistena and comparative and phylogenetic analyses with its closely related species

“…The fragment length of ycf1 was between 4.561bp to 4, 614bp in IRa region, and ranged from 1, 036bp to 1, 051bp in IRb region. These overlapping segments of ycf1 were pseudogenized and observed at the junction of JSB in all of the six selected Prunus species, which was consistent with the ndings of earlier reports [22,31].…”

“…2). Similar to the previous results for other study, most of the codons ending with A or T have RSCU values greater than 1, while, most of those ending with C or G have RSCU values of less than 1 [21][22][23].…”

“…Therefore, the attendance of the ycf3 gene might result in an extra study of Prunus chloroplast. The rps12 genes were located at the 5' end on the LSC region and meanwhile the duplicated 3' ends was set in the IRs regions due to the phenomenon it has been called trans-spliced gene [22,26,35]. The ycf1 gene expected a basic part in the chloroplast genome.…”

“…There were some related studies exposed ycf1 as a paramount pseudogene in plants, leading to incomplete duplication of the gene within IRs [31,36]. The ycf1 gene repeated twice in the chloroplast genome of P. Cistena, which was similar to other Prunus plants [22,37]. It has been testi ed that the introns play a signi cant role in regulating the expression of genes, which might control the gene expression level in different spatiotemporal [19,31,38].…”

“…The repeat sequences may raise the genetic diversity of the species and advance the cpDNA rearrangements [22,39]. Generally, the cpSSRs are valuable genetic tools for population genetics and evolution studies, because of their codominant nature, high polymorphism and low substitution rate [40][41].…”