Abstract
Carya cathayensis, an important economic nut tree, is narrowly endemic to eastern China in the wild. The complete cp genome of C. cathayensis was sequenced with NGS using an Illumina HiSeq2500, analyzed, and compared to its closely related species. The cp genome is 160,825 bp in length with an overall GC content of 36.13%, presenting a quadripartite structure comprising a large single copy (LSC; 90,115 bp), a small single copy (SSC; 18,760 bp), and a pair of inverted repeats (IRs; 25,975 bp). The genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. A total of 252 simple sequence repeats (SSRs) and 55 long repeats were identified. Gene selective pressure analysis showed that seven genes (rps15, rpoA, rpoB, petD, ccsA, atpI, and ycf1-2) were possibly under positive selection compared with the other Juglandaceae species. Phylogenetic relationships of 46 species inferred that Juglandaceae is monophyletic, and that C. cathayensis is sister to Carya kweichowensis and Carya illinoinensis. The genome comparison revealed that there is a wide variability of the junction sites, and there is higher divergence in the noncoding regions than in coding regions. These results suggest a great potential in phylogenetic research. The newly characterized cp genome of C. cathayensis provides valuable information for further studies of this economically important species.
Highlights
The genus Carya, belonging to the family Juglandaceae, comprises ~18 species and4 varieties, which are distributed in the temperate and tropical regions of East Asia and eastern North America [1,2]
The noncoding regions of cp genomes can be harnessed for phylogenetic analysis due to a relatively high level of genetic variation resulting from the low selective pressure [5]
The synteny was identified by comparing the C. cathayensis cp genome to the reference (Table S1), which showed that most of the sequences of the genomes were conserved
Summary
4 varieties, which are distributed in the temperate and tropical regions of East Asia and eastern North America [1,2]. Carya species from East Asia and eastern North America are phylogenetically separated [2], while the relationships among some taxa within the genus have not been resolved yet. Several plastid (matK, rbcL-atpB, rpoC1, rps, trnH-psbA, and trnL-F) and nuclear (ITS and phyA) DNA markers have been used for the phylogenetic study of the genus Carya. These nuclear genes were identified by ortholog screening, cloning, and sequencing; these methods can be costly and time-consuming. The cp genomes of C kweichowensis [12], C. cathayensis [13], and C. illinoinensis (NBCI accession number: NC_041449.1) have been published, and the publication of more cp genomes of Carya species will facilitate the identification of genetic variations via sequence comparison, providing new insights into the evolutionary history and interspecific relationships among Carya species
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
