Five Complete Chloroplast Genome Sequences from Diospyros: Genome Organization and Comparative Analysis

Abstract

Diospyros is the largest genus in Ebenaceae, comprising more than 500 species with remarkable economic value, especially Diospyros kaki Thunb., which has traditionally been an important food resource in China, Korea, and Japan. Complete chloroplast (cp) genomes from D. kaki, D. lotus L., D. oleifera Cheng., D. glaucifolia Metc., and Diospyros ‘Jinzaoshi’ were sequenced using Illumina sequencing technology. This is the first cp genome reported in Ebenaceae. The cp genome sequences of Diospyros ranged from 157,300 to 157,784 bp in length, presenting a typical quadripartite structure with two inverted repeats each separated by one large and one small single-copy region. For each cp genome, 134 genes were annotated, including 80 protein-coding, 31 tRNA, and 4 rRNA unique genes. In all, 179 repeats and 283 single sequence repeats were identified. Four hypervariable regions, namely, intergenic region of trnQ_rps16, trnV_ndhC, and psbD_trnT, and intron of ndhA, were identified in the Diospyros genomes. Phylogenetic analyses based on the whole cp genome, protein-coding, and intergenic and intron sequences indicated that D. oleifera is closely related to D. kaki and could be used as a model plant for future research on D. kaki; to our knowledge, this is proposed for the first time. Further, these analyses together with two large deletions (301 and 140 bp) in the cp genome of D. ‘Jinzaoshi’, support its placement as a new species in Diospyros. Both maximum parsimony and likelihood analyses for 19 taxa indicated the basal position of Ericales in asterids and suggested that Ebenaceae is monophyletic in Ericales.

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships

“…The function, order, and GC-content of these genes were all highly conserved as noted for other angiosperms (Palmer, 1991 ). The cp genomes of all the Gynostemma species contained more AT and had a GC content of 36.9–37.0%, similar to previously published Olea and Diospyro s genomes (Mariotti et al, 2010 ; Fu et al, 2016 ), and possibly caused by the high GC content of the rRNA gene sequences located in IR regions.…”

“…Because no perfect assembler program has been created, de novo assembly always generates misassembled contigs; thus, assembled contigs must be checked and corrected by read-mapping and further scanned for any gaps of lower coverage (Naito et al, 2013 ; Nashima et al, 2015 ). Despite the occurrence of gene loss-and-gain events and the rearrangements in several genomes of land plants (Palmer, 1987 ; Fu et al, 2016 ), the eight cp genomes we studied displayed the typical quadripartite structure with two IRs and two SCs. In terms of gene content, each of the cp genomes encoded 133 genes containing with 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene.…”

The Complete Chloroplast Genome Sequences of the Medicinal Plant Forsythia suspensa (Oleaceae)

“…The IR regions are highly conserved and play an important role in stabilizing the cp genome structure [ 20 , 21 ]. For IR and SC boundary regions, their expansion and contraction are commonly considered as the main mechanism behind the length variation of angiosperm cp genomes [ 22 , 23 ].…”

The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids

“…Plastids have small circular genomes, ranging from 135 to 160 kb [ 2 – 4 ]. Most angiosperm plastid genomes so far annotated have a quadripartite structure containing two copies of Inverted Repeat (IR) regions, separating a Large Single Copy (LSC) and Small Single Copy (SSC) regions [ 5 – 7 ]. Recently, with the extraordinary advances in sequencing platforms, many plastid genomes have been annotated and have provided valuable tools for the understanding of plant phylogenies and genome evolution e.g.…”