Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros

Abstract

Background: Persimmon (Diospyros kaki) is the most economically cultivated species belonging to the genus Diospyros. However, little is known about the interspecific diversity and mechanism of domestication, partly due to the lack of genomic information that is available for closely related species of D. kaki (DK). Here, we performed transcriptome sequencing on nine samples, including DK, a variety of DK and seven closely related species, to evaluate the interspecific genetic divergence and to identify candidate genes involved in persimmon domestication.

Results: We obtained a total of 483,421 unigenes with N50 at 1490 bp in the nine Diospyros samples and identified 2603 orthogroups that were shared among all the samples using OrthoMCL analysis. A phylogenetic tree was established based on the tandem 2603 one-to-one single copy gene alignments, showing that DK was closely related to D. kaki var. silvestris (DKV) and that it clustered with the clade of D. deyangnsis (DD) and was farthest from the D. cathayensis (DC) species. The nonsynonymous substitutions (Ka), via synonymous substitution (Ks) ratios, was directly proportional to the genetic relationship of the different species. The higher the Ka/Ks ratios, the longer the distance was. Moreover, 31 positively selected genes (PSGs) involved in carbohydrate metabolism and phenolic metabolism were identified and isolated, and nearly all PSGs except the MATE gene had a high expression in the DK or DKV species. It was hypothesized that these genes might contribute to the domestication of the DK species. Finally, we developed the expressed sequence tag-simple sequence repeat (EST-SSR) and identified 2 unique amplicons DKSSR10 and DKSSR39: the former was absent in the DC species but was present in the other species, the latter had a long amplification product in the DJ species.

Conclusion: This study presents the first transcriptome resources for the closely related species of persimmon and reveals interspecific genetic divergence. It is speculated that DK is derived from the hybridization of DD and DO species. Furthermore, our analysis suggests candidate PSGs that may be crucial for the adaptation, domestication, and speciation of persimmon relatives and suggests that DKSSR10 and DKSSSR39 could potentially serve as species-specific molecular markers.

Keywords: Comparative transcriptome; Diospyros; Domestication genes; Genetic divergence; Species.

Fig. 1

Morphological characteristics of the nine Diospyros samples. Photographs showing the leaves, stems, and fruits sampled on October 31, 2018 in the NFGP. Bar = 5 cm

Fig. 2

PAs, TSS and firmness of fruit in the nine Diospyros samples. Fruit sampled on October 31, 2018 in the NFGP. Error bars indicate standard deviation (n = 10)

Fig. 3

Number of PSGs shared among the species-pairs. A total of 2603 single copy orthogroups shared in the nine Diospyros samples. The black and blue font represent the putative orthogroups and the unigenes, respectively, in the nine Diospyros samples

Fig. 4

Phylogenetic relationships and nonsynonymous to synonymous mutation (Ka/Ks) ratio distributions. a. phylogenetic tree derived from the concatenated 2603 one-to-one single copy gene alignments (861,013 amino acid) of the nine samples, b Boxplots of the Ka/Ks ratios for DK compared with others species (DK-vs-DC, DK-vs-DD, DK-vs- DJ, DK-vs-DG, DK-vs-DKV, DK-vs-DL, DK-vs-DO, and DK-vs-DV)

Fig. 5

The Ka/Ks ratio distribution of the orthologs for DK compared with other species (DK-vs-DC, DK-vs-DD, DK-vs- DJ, DK-vs-DG, DK-vs-DKV, DK-vs-DL, DK-vs-DO, and DK-vs-DV)

Fig. 6

Expression pattern of candidate PSGs in the nine Diospyros samples. Relative mRNA expression was evaluated by qRT-PCR. The heatmap was constructed by R language (v3.0.2) indicating the average mRNA expression from 4 biological repeats. Values are colored from green (down-regulated) to red (up-regulated) according to the colour scale