Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan

Abstract

Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.