Complete plastid genome sequence ofPrimula sinensis(Primulaceae): structure comparison, sequence variation and evidence foraccDtransfer to nucleus
Species-rich genusPrimulaL. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence ofPrimula sinensisand compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. TheaccDandinfAgenes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome ofPrimula sinensis, comparing with another available plastome ofP. poissonii. The four most variable regions,rpl36–rps8,rps16–trnQ,trnH–psbAandndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found fromP. sinensistranscriptome showed a high similarity to plastidaccDfunctional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastidaccDhas been functionally transferred to the nucleus inP. sinensis.