The Chloroplast Genome of Carya illinoinensis: Genome Structure, Adaptive Evolution, and Phylogenetic Analysis

Abstract

Research Highlights: For the first time, the complete chloroplast (cp) genome of Carya illinoinensis cv. ‘Pawnee’ was de novo assembled. Comprehensive analysis the cp genome of C. illinoinensis revealed potential cpDNA markers for intraspecies identification, genes involved in adaptation, and its phylogenetic position. Background and Objectives: C. illinoinensis is an economically important nut tree in the family Juglandaceae. Cp-derived markers are helpful for genetic research, but they still need to be developed in C. illinoinensis. Additionally, the adaptation and phylogenetic relationships of C. illinoinensis have not been revealed based on the complete cp genome. Materials and Methods: Chloroplast genomic DNA of C. illinoinensis cv. ‘Pawnee’ was extracted and subjected to Illumina sequencing. Results: The cp genome is 160,819 bp in size, exhibiting a typical quadripartite structure with a large single copy (LSC) of 90,022 bp, a small single copy (SSC) of 18,791 bp, and a pair of inverted repeats (IRA and IRB) regions of 26,003 bp each. The genome was predicted to encode 112 unique genes, including 79 protein-coding genes, 29 tRNAs, and four rRNAs, with 19 duplicates in the IR regions. In total, 213 SSRs and 44 long repeats were identified in the cp genome. A comparison of two different C. illinoinensis genotypes, ‘Pawnee’ and 87MX3-2.11, obtained 143 SNPs and 74 indels. The highly variable regions such as atpF, clpP, and ndhA genes, and matK-rps16, trnS-trnG, and trnT-psbD intergenic spacers might be helpful for future intraspecific identification. Positive selection was acting on the ccsA and rps12 cp genes based on the Ka/Ks ratios. Phylogenetic analysis indicated that C. illinoinensis forms a sister clade to Asian Carya species, represented by C. kweichowensis and Annamocarya sinensis. Conclusions: The genome information in our study will have significance for further research on the intraspecies identification and genetic improvement of C. illinoinensis.

Characterization of the complete chloroplast genome sequence of Koelreuteria bipinnata

“… 2020 ; Mo et al. 2020 ). Here, we de novo assembled the complete chloroplast genome of K. bipinnata , and analyzed its relationship with closely related species.…”

“…Previously, the studies regarding K. bipinnata were mainly focus on its tissue culture (Feng, Li, et al 2009;Cao et al 2018), few data are currently available about its genomic information. In plants, the chloroplast genome is helpful for population genetics study, species-level identification, and phylogenetic analysis (Liu et al 2020;Mo et al 2020). Here, we de novo assembled the complete chloroplast genome of K. bipinnata, and analyzed its relationship with closely related species.…”

The complete chloroplast genome of Ulmus parvifolia, an important landscaping tree

“… 2020 ; Mo et al. 2020 ). In this study, the complete chloroplast genome of U. parvifolia was de novo assembled, annotated, and analyzed phylogenetically.…”

“…Nevertheless, very limited genomic data is available on this species. Chloroplast genome is characterized by small genome size, maternal transmission, and low mutation rate, which make the chloroplast-derived markers suitable for species identification, phylogenetic analysis, and population genetics studies (Li et al 2019;Cai et al 2020;Mo et al 2020). In this study, the complete chloroplast genome of U. parvifolia was de novo assembled, annotated, and analyzed phylogenetically.…”

Characterization and phylogenetic relationships analysis of the complete chloroplast genome of Carya ovata

“…An application of comparative genomic date to illustrate its phylogenetic relationships is still lacking. Chloroplast genome of angiosperms is maternal inheritance and displays a relatively slow rate of evolution compared to nuclear genomes (Daniell et al 2016;Liu et al 2016;Mo et al 2020). Therefore, the polymorphic regions in chloroplast genomes are commonly used for phylogenetic analysis (Chen et al 2018).…”