Abstract
Objectives: To broaden the genetic information base of Juniperus and resolve phylogeny of Juniperus polycarpos through sequencing and characterization of its chloroplast genome. Methods: The chloroplast (cp) genome of J. polycarpos was sequenced and assembled using the Next-Generation Sequencing pairedend reads platform of BGISEQ-500 and annotated using CpGAVAS. The phylogenetic analysis was performed in MEGA7. Findings: Here, we report the complete cp genome sequence of J. polycarpos. The cp genome size is 127,825 bp with a typical circular structure and lack canonical inverted repeats having a total of 119 genes comprised of 82 protein-coding genes, 33 tRNA genes and four rRNA genes. The cp genome encodes 105 single copy genes and five duplicated genes (ndhK, ccsA, rps12, trnE-TTC and trnQ-TTG), and one tetraplicated gene(trnM-CAT). In these genes, 9 genes (rpl2, ycf2, trnA-TGC, trnETTC,rpoC, rpoB, ndhB, ndhA and atpF) harboring a single intron, three genes (accD, rrn23s and ycf3) having two introns and one gene (ycf1) harboring three introns. The overall GC content of J. polycarpos chloroplast DNA was 35%. Phylogenetic analysis among 14 species of order Coniferales based on cp genomes indicated a close relationship between J. polycarpos, J. cedrus and J. communis. Novelty and application: This is the first report on the cp genome of J. polycarpos. The current study is expected to add to the already available genomic resources needed for more comprehensive population genetics studies and resolving phylogenetic relationships of order Coniferales. Besides, it will provide baseline data for future research on Juniperus of Pakistan in particular. Keywords: BGISeq-500; Cloroplast Genome; Persian Juniper; Phylogeny
Highlights
The genus Juniperus (Cupressaceae), commonly known as “cedar”, is among the most diverse genera of conifers: lacking consensus, on number of species
The complete cp genome of Juniperus polycarpos was assembled in the present work, using BGISEQ-500 (BGI, Shenzhen) paired-end reads derived from the whole genome
A single group of land plants consisting of several allied tribes in the subfamily Papilonoideae of the legume family (Fabaceae) lack major inverted repeat of roughly 10-76 kb that contains the rRNA genes and adjacent DNA which results in extensive genome sequence rearrangements[40,41]
Summary
The genus Juniperus (Cupressaceae), commonly known as “cedar”, is among the most diverse genera of conifers: lacking consensus, on number of species. Farjon [1], for example, reported 52 species of Juniperus while Adams[2] documented 67 species. In Pakistan, five species of Juniperus are reported. The Juniper forest (Juniperus polycarpos) of Ziarat area in the province of Balochistan, Pakistan, are stretched on an area of 110 000 ha and is said to be the second largest of its kind in the world. The trees of juniper here are believed to be among the oldest living trees in the world and are, referred to as “living fossils”(7) making the species of immense importance for climate change and ecological studies
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