Analysis of the complete chloroplast genome of Castanea pumila var. pumila, the Allegheny chinkapin
Tree Genetics & Genomes, 11(1), pp 14, 2015-2
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.
Castanea pumila var. pumila; Castanea dentata; Castanea mollissima; American chestnut; Chinese chestnut; Allegheny chinkapin; cp genome