Analysis of the complete chloroplast genome of Castanea pumila var. pumila, the Allegheny chinkapin

Abstract

The complete plastid genome of Castanea pumila L. Mill. var. pumila, the Allegheny chinkapin, was generated using next-generation sequencing of the leaf transcriptome of the species and fill-ins of missing regions via Sanger sequencing. The chloroplast (cp) genome of C. pumila showed high homology (99.8 %) to the genome of Castanea mollissima (the Chinese chestnut, 600,799 bp) in overall gene organization and size (160, 603 bp). Castanea dentata 454 sequence data ( www.fagaceae.org ) were used to generate a partial chloroplast genome of the American chestnut (93 % coverage). Comparisons of the cp genomes of the American and Chinese Castanea species indicated that the species shared 68.0 % of the mutations at coding and intronic regions, while 18.0 % of the mutations were specific to C. pumila and 13.9 % to C. dentata. The loss and nuclear localization of the rpl22 gene was similarly a feature of the genome of the American Castanea species. Since a higher number of mutational events separated C. pumila from C. mollissima, a more recent divergence of C. dentata from a common ancestor was hypothesized.