Structural, evolutionary and phylogenomic features of the plastid genome of Carya illinoinensis cv. Imperial

Abstract

The economically most important nut tree species in the world belong to family Juglandaceae, tribe Jungladeae. Evolutive investigations concerning species from this tribe are important for understanding the molecular basis driving the evolution and systematics of these species. In this study, we release the complete plastid genome of  C. illinoinensis  cv. Imperial. Using an IonTorrent NGS platform we generated  8.5 ´ 10 8  bp of raw sequences, enabling the assemblage of the complete plastid genome of this species. The plastid genome is 160,818 bp long, having a quadripartite structure with an LSC of 90,041 bp, an SSC of 18,791 bp and two IRs of 25,993 bp. A total of 78 protein-coding, 37 tRNA-coding, and 8 rRNA-coding regions were predicted. Bias in synonymous codon usage was detected in cultivar Imperial and three tRNA-coding regions were identified as hotspots of nucleotide divergence, with high estimations of  dN/dS  ratio. The high fraction of SSR loci prospected in non-coding regions may provide informative genetic markers,  useful to a wide range of genetic researches.  Despite the significant structural differences among plastid genomes, the phylogenetic relationships among species is supported by the whole plastid genome analysis, supporting the monophyly of subtribes Caryinae and Juglandinae within family Juglandaceae.