Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations
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ORIGINAL ARTICLE
Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations Xinwang Wang 1 & Hormat Shadgou Rhein 2 L. J. Grauke 1 & Jennifer J. Randall 2
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Jerry Jenkins 3
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Jeremy Schmutz 3
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Jane Grimwood 3
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Received: 2 October 2019 / Revised: 12 March 2020 / Accepted: 7 April 2020 # This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020
Abstract 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. Keywords Pecan . Carya . Chloroplast . Phylogeny . Adaptation . Breeding
Introduction Xinwang Wang and Hormat Shadgou Rhein contributed equally to this work. Communicated by M. Wirthensohn Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11295-020-01436-0) contains supplementary material, which is available to authorized users. * Xinwang Wang [email protected] * L. J. Grauke [email protected] * Jennifer J. Randall [email protected] 1
USDA ARS Pecan Breeding and Genetics, Somerville, TX 77879, USA
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New Mexico State University, Las Cruces, NM 88003, USA
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HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
The genus Carya constitutes subtribe Caryinae of tribe Juglandeae in the walnut family, Juglandaceae (Manos and Stone 2001; Manos et al. 2007). Carya is phylogenetically interesting due to its representation in As
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