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

• Published in: PloS one Vol. 11; no. 7; p. e0159566
• Main Authors: Fu, Jianmin, Liu, Huimin, Hu, Jingjing, Liang, Yuqin, Liang, Jinjun, Wuyun, Tana, Tan, Xiaofeng
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 21.07.2016; Public Library of Science (PLoS)
• Subjects: Base Sequence; Biogeography; Biology and Life Sciences; Chloroplasts; Chromosome Mapping; Comparative analysis; Dacus lotus; Deoxyribonucleic acid; Diospyros; Diospyros - genetics; Diospyros kaki; DNA; DNA sequencing; Ebenaceae; Ebony (Plant); Ericales; Evolution; Food resources; Forestry; Gene sequencing; Genes; Genes, Plant; Genetic aspects; Genetic testing; Genome, Chloroplast; Genome, Plant; Genomes; INDEL Mutation - genetics; Inverted Repeat Sequences - genetics; Laboratories; Leaves; Molecular biology; Morphology; New species; Phylogenetics; Phylogeny; Physiological aspects; Plant sciences; Prunus; R&D; Reproducibility of Results; Research & development; Research and Analysis Methods; rRNA; Sequence Alignment; Sequence Analysis, DNA; Studies; Taxa; Timber; tRNA; China; Alps; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0159566

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.