Abstract
Eriobotrya japonica (Thunb.) Lindl (loquat) is an evergreen Rosaceae fruit tree widely distributed in subtropical regions. Its leaves are considered as traditional Chinese medicine and are of high medical value especially for cough and emesis. Thus, we sequenced the complete plastid genome of E. japonica to better utilize this important species. The complete plastid genome of E. japonica is 159,137 bp in length, which contains a typical quadripartite structure with a pair of inverted repeats (IR, 26,326 bp) separated by large (LSC, 89,202 bp) and small (SSC, 19,283 bp) single-copy regions. The E. japonica plastid genome encodes 112 unique genes which consist of 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene structure and content of E. japonica plastid genome are quite conserved and show similarity among Rosaceous species. Five large indels are unique to E. japonica in comparison with Pyrus pyrifolia and Prunus persica, which could be utilized as molecular markers. A total of 72 simple sequence repeats (SSRs) were detected and most of them are mononucleotide repeats composed of A or T, indicating a strong A or T bias for base composition. The Ka and Ks ratios of most genes are lower than 1, which suggests that most genes are under purifying selection. The phylogenetic analysis described the evolutionary relationship within Rosaceae and fully supported a close relationship between E. japonica and P. pyrifolia. Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-3702-3) contains supplementary material, which is available to authorized users.
Highlights
Chloroplast, which is derived from free-living cyanobacteria through endosymbiosis (Keeling 2004), plays an essential role in photosynthesis and many biosynthetic activities such as biosynthesis of certain amino acids and fatty acids
We report the first complete plastid genome of E. japonica using next-generation sequencing method (Illumina Hiseq 2000) and conduct comparative analysis with other Rosaceous species, P. pyrifolia and P. persica in particular, which will help with species identification or germplasm selection and provide insights into phylogenetic evolution of Rosaceae family
Genome features of E. japonica The complete plastid genome of Eriobotrya japonica is 159,137 bp in length with a double-strand circle structure with a pair of IRs of 26,326 bp separated by a small single copy of 19,283 bp and a large single copy of 87,202 bp (Fig. 1)
Summary
Chloroplast (cp), which is derived from free-living cyanobacteria through endosymbiosis (Keeling 2004), plays an essential role in photosynthesis and many biosynthetic activities such as biosynthesis of certain amino acids and fatty acids. Chloroplast contains its own genome which displays a typical quadripartite structure with two copies of inverted repeats separated by large single copy and small single copy (Nguyen et al 2015). Plastomes of angiosperms range from 120 to 170 kb and mostly contain 100–120 different genes. The chloroplast genome is usually recognized as highly conserved in gene structure and content, especially in closely related groups. The plastid genome is good resource to provide sufficient information for phylogenetic analysis and DNA barcoding. Thanks to rapid development of next-generation sequencing, the number of whole plastid genome available is increasing constantly, which makes large-scale phylogenetic research based on plastid genomes possible (Jansen et al 2007).
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