Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

• Published in: BMC plant biology Vol. 18; no. 1; p. 210
• Main Authors: Li, Wenqing, Liu, Yanlei, Yang, Yong, Xie, Xiaoman, Lu, Yizeng, Yang, Zhirong, Jin, Xiaobai, Dong, Wenpan, Suo, Zhili
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 26.09.2018; BioMed Central; BMC
• Subjects: Biogeography; Chloroplast DNA; Chloroplast genome; Chloroplasts; Cultivars; Deoxyribonucleic acid; Diospyros; Diospyros cathayensis; Diospyros deyangensis; Diospyros glaucifolia; Diospyros jinzaoshi; Diospyros kaki; Diospyros lotus; Diospyros oleifera; Diospyros rhombifolia; Diospyros virginiana; DNA; Ebenaceae; Fruits; Gene expression; Gene sequencing; Genetic aspects; Genetic diversity; Genomes; Germplasm; Hyper-variable region; Identification and classification; Industrial development; Markers; Multiculturalism & pluralism; Mutation; Nucleotide sequence; Phylogenetics; Physiological aspects; Plant reproduction; RpoB protein; Beijing China; China; Japan; Diospyros; Genetic diversity; Chloroplast genome; Hyper-variable region
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-018-1421-3

Fruits of persimmon plants are traditional healthy food in China, Korea and Japan. However, due to the shortage of morphological and DNA markers, the development of persimmon industry has been heavily inhibited. Chloroplast genomes of Diospyros cathayensis, D. virginiana, D. rhombifolia and D. deyangensis were newly sequenced. Comparative analyses of ten chloroplast genomes including six previously published chloroplast genomes of Diospyros provided new insights into the genome sequence diversity and genomic resources of the genus. Eight hyper-variable regions, trnH-psbA, rps16-trnQ, rpoB-trnC, rps4-trnT-trnL, ndhF, ndhF-rpl32-trnL, ycf1a, and ycf1b, were discovered and can be used as chloroplast DNA markers at/above species levels. The complete chloroplast genome sequences provided the best resolution at inter-specific level in comparison with different chloroplast DNA sequence datasets. Diospyros oleifera, D. deyangensis, D. virginiana, D. glaucifolia, D. lotus and D. jinzaoshi are important wild species closely related to the cultivated persimmon D. kaki. The hyper-variable regions can be used as DNA markers for global genetic diversity detection of Diospyros. Deeper study on these taxa would be helpful for elucidating the origin of D. kaki.