The complete chloroplast genome of rabbiteye blueberry (Vaccinium ashei) and comparison with other Vaccinium species

Abstract

In order to clarify the characteristics of the chloroplast (cp) genome of Vaccinium ashei Reade cv. ‘brightwell’ and understand its phylogenetic status, the whole cp genome of this sepcies was sequenced and assembled, and its genome structure, gene composition, and signs of adaptation were analyzed. The cp genome has a quadripartite structure with a size of 176,115 bp and a total GC content of 36.81%. The length of large single copy (LSC) region, small single copy (SSC) region and two inverted repeat (IR) regions was 106,029 bp, 3004 bp, and 33,541 bp, respectively. It has a total of 103 genes, containing 74 protein-coding genes, 25 tRNA genes and 4 rRNA genes. A total of 187 SSR sites were observed, with the largest number of mononucleotides in the repeat type, accounting for 72% of the total. By comparing with related Vaccinium genotypes, 25 single nucleotide polymorphisms (SNPs) and 35 insertion/deletions (Indels) were identified. Highly variable regions such as trnM-psaI, trnD-psbM, psbJ-psbB, psaA-trnQ, clpP-rpoA, rpl36-rps8, rpl16-rps3, and trnM-trnL intergenic spacers may be used as candidate markers for intraspecific differentiation. The Ka/Ks calculations showed that the two genes (psbJ and psbT) were strongly positively selected. Phylogenetic results reflected that the Vaccinium genus was clustered into two clades, and V. ashei was more closely related to V. uliginosum. These results provide a reference for the development of molecular markers, phylogeny, cp genome evolution and variety breeding of Vaccinium.