Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations

Pecan ( Carya illinoinensis ) is the most economically important member of the Carya genus and has been collected and evaluated across its broad geographic range in the process of crop improvement. In this study we obtained complete chloroplast genome sequences from two pecan genotypes, 87MX3-2.11 and the ‘Lakota’ cultivar (160,545 and 160,819 bp in length, respectively). The chloroplast genome of C. illinoinensis maintains the conserved structure typical of Juglandaceae and other land plants and is a circular molecule that includes a large single-copy (LSC) and a small single-copy (SSC) region, separated by a pair of inverted repeats (IRa and IRb). There were 124 genes found on the 87MX3-2.11 chloroplast genome and 123 on ‘Lakota’ (including multiple copies of the same gene), with 108 and 107 unique genes, respectively (counting only one copy of each gene). Different genes are found among C. illinoinensis , C. sinensis , and Juglans chloroplast genomes. C. illinoinensis is missing rps16 gene and has fewer copies of some tRNA genes, with ‘Lakota’ lacking a start codon of rps12 gene, compared with other related species. The nucleotide divergence between the two pecan chloroplast genomes reflects the genetic diversity of geographically separated populations of the species. Genomic divergence was also confirmed by the phylogenetic relationship of 19 whole chloroplast genome sequences representing Juglandaceae taxa. The complete chloroplast genome sequences in this study provide a foundation for understanding the influences of geographical adaptation, gene flow, and horticultural trait inheritance, in order to develop functional genomic tools for regional selection and pecan breeding.