Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations

Authors: Wang, Xinwang; RHEIN, HORMAT - New Mexico State University; JENKINS, JERRY - Hudsonalpha Institute For Biotechnology; SCHMUTZ, JEREMY - Hudsonalpha Institute For Biotechnology; GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology; Grauke, Larry; RANDALL, JENNIFER - New Mexico State University

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/7/2020
Publication Date: 6/5/2020
Citation: Wang, X., Rhein, H., Jenkins, J., Schmutz, J., Grimwood, J., Grauke, L.J., Randall, J. 2020. Chloroplast genome sequences of Carya illinoinensis from two distinct geographic populations. Tree Genetics and Genomes. 16:48. https://doi.org/10.1007/s11295-020-01436-0.
DOI: https://doi.org/10.1007/s11295-020-01436-0

Interpretive Summary: Pecan (Carya illinoinensis) is the most economically important member of the Carya genus (hickories). Pecan trees have been collected and evaluated across their broad geographic range in the process of crop improvement. Like many trees, pecans inherit their chloroplasts from their female parent. Chloroplasts are important little organs (organelles) in the cell that use chlorophyll to capture light and conduct photosynthesis, help with fatty acid synthesis, and are involved in the plant's immune response. We knew that the chloroplasts of pecan trees are very different in different geographic populations. We developed the full chloroplast genome sequence for a seedling tree (87MX3-2.11) that represents the southern-most population of pecans, from Oaxaca, Mexico. We also developed the full chloroplast genome sequence for a commercial pecan cultivar developed by breeding ('Lakota'). We compared these sequences to each other, and to other members of the walnut family, Juglandaceae. This report explains the differences found in those comparisons. This information will help us develop even better tools to study differences between our trees so we can do a better job in breeding.

Technical 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 to 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.