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.

山核桃（山核桃illinoinensis）是的经济上最重要部件山核桃属和已被收集并在作物改良的过程在其广阔的地域范围进行评价。在这项研究中，我们从两种山核桃基因型87MX3-2.11和'Lakota'品种获得了完整的叶绿体基因组序列（分别长160,545和160,819 bp）。illinoinensis的叶绿体基因组保持菊科和其他陆地植物典型的保守结构，是一个圆形分子，包括一个大的单拷贝（LSC）和一个小的单拷贝（SSC）区域，由一对反向重复序列（IRa和IRb）隔开。在87MX3-2.11叶绿体基因组上发现了124个基因，在“ Lakota”上发现了123个基因（包括同一基因的多个副本），分别具有108个和107个独特基因（每个基因仅占一个副本）。不同的基因中发现C. illinoinensis，山茶，以及核桃叶绿体基因组。伊利诺伊杯与其他相关物种相比，它缺少rps16基因并且缺少一些tRNA基因的拷贝，其中“ Lakota”缺少rps12基因的起始密码子。两个山核桃叶绿体基因组之间的核苷酸差异反映了该物种在地理上分离的种群的遗传多样性。基因组差异还通过代表胡桃科分类单元的19个完整叶绿体基因组序列的系统发育关系得到证实。本研究中完整的叶绿体基因组序列为了解地理适应，基因流和园艺性状遗传的影响提供了基础，以便开发用于区域选择和山核桃育种的功能基因组工具。