Interspecific chloroplast genome sequence diversity and genomic resources in Diospyros

Abstract

BackgroundFruits 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.ResultsChloroplast 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.ConclusionDiospyros 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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1421-3) contains supplementary material, which is available to authorized users.

Chloroplast Genome Variation and Phylogenetic Relationships of Atractylodes species

“…The chloroplast genome is conserved similar to the majority of plants; no rearrangement events were detected in all species. The mVISTA results and nucleotide diversity tests indicate high similarities between the chloroplast genomes implying that the divergence of the Atractylodes chloroplast genome is lower than that of other species [6,37,38].…”

“…The evolution rate is relatively moderate and is between the nuclear and mitochondrial genome [2]. Due to the lack of recombination, small genome size and high copy number per cell [3,4], complete chloroplast genome sequences have been extensively used in phylogenetics analysis and species identi cation [5,6]. The results showed that the chloroplast genome contains additional information to improve phylogenetic analysis [7][8][9][10][11].…”

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

“…Complete plastomes have been suggested as having the potential to increase species resolution among plant species [18,19], and have been used to discriminate species in a number of taxa that are difficult to resolve (e.g., Ficus [20]; Panax [22]; Taxus [24]; Diospyros [25]). In our study, seven of the nine species (78%, Table 2) in Calligonum that have more than one accession, were correctly identified to species.…”

“…A genetic sequence of the complete plastome can be easily obtained through a genome skimming approach of highcopy genomic targets, where its conserved gene content, organization and, structure makes it easy to assemble and annotate [17]. Notably, the compete plastome, in addition to all the standard plastid barcodes, should provide a wealth of informative and variable sites for the genetic identification and phylogenetic analyses of plant species [18,19]: also see e.g., Ficus [20], Lilium [21], Panax [22], Stipa [23], Taxus [24], and Diospyros [25].…”

The complete chloroplast genome sequence of Gillenia trifoliata (Rosaceae)

“…The plants are often used as ornamental plants and folk herbal medicine. In the present study, we assembled the complete chloroplast genome sequence of G. trifoliata based on the next-generation sequencing method (Dong et al 2017;Li et al 2018). Our aims were to establish and characterize the organization of the complete chloroplast genome of G. trifoliata and to calibrate the phylogenetic position of G. trifoliata based on phylogenomic analysis.…”