Draft genome sequencing of Diospyros

Initially, we assembled a draft genome from ca 65X PacBio long read coverage of the expected haploid genome size (907Mb from flow cytometry [18], 877.7Mb from kmer analysis) using Falcon (S1 Fig, S1 Table). This resulted in 3,073 primary contigs totaling 746.1Mb, which covers ca 85% of the genome, and 5,901 “secondary” contigs, which are putative allelic contigs to the primary contigs. Next, we built three genetic maps, created from two segregating F1 populations (N = 314 and 119, see Materials and Methods and S2 Table). These maps were created from a total of 5,959 markers derived from GBS/ddRAD sequencing and allowed for the anchoring of the ca 61.8% scaffolds into 15 pseudomolecules (Fig 1, S1 Fig, S2 and S3 Tables).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 1. Characterization of the draft persimmon genome.

a, Fifteen pseudomolecules with the genetically anchored contigs. Black, white and gray bars indicate the positions of the original contigs that were assembled in forward, reverse, or unknown direction respectively. b, Relative SNP density in the KK population. c, Relative density of repetitive sequences d, Relative gene density. e, Syntenic relationships within the persimmon genome.

https://doi.org/10.1371/journal.pgen.1008566.g001

To start characterizing this newly assembled genome, we documented sequence variation between female and male individuals of D. lotus and content and type of repeat sequences of the draft sequence compared to other sequences eudicots (Fig 1B and 1C, S3 and S4 Tables). Mapping of transcriptome data to this draft genome resulted in 40,532 predicted gene locations (Fig 1D, S1 Dataset). These numbers are similar to results from other asterid plant species, such as tomato (N = 34,879) [12] or kiwifruit (N = 39,040) [19] (S2 and S3 Figs). Of these primary genes, we selected 12,058 which were determined to be either unique or low copy number within the genome (see Materials and Methods).

Identification of a whole-genome duplication event specific to the Diospyros genus

To investigate gene duplication patterns, we analyzed the distribution of silent divergence rate (dS) between homologous gene pairs. We compared the distribution of silent divergence rate of homologous gene pairs within the persimmon genome, with those within the kiwifruit (Actinidia), tomato (Solanum) and grape (Vitis) genomes. A subset of persimmon genes formed a clear peak of silent divergence rate (Fig 2A, dS = ca 0.5–0.9, mode dS = 0.69), suggesting that a whole-genome duplication (WGD) event, named Dd-α, occurred in this clade. Next, we performed a genome-wide synteny analysis, based on the location of the gene pairs with dS values ranging from 0.5 and 0.9, using SynMap in CoGe [20] (https://genomevolution.org/coge/). The results indicated long syntenic blocks throughout the persimmon genome (S4A and S4B Fig). The genomic regions including the gene pairs in this peak exhibited long regions of synteny (S5 Fig). The distribution of four-fold synonymous (degenerative) third-codon transversion (4DTv) supported this lineage-specific WGD (Fig 2B). Comparison of intraspecific dS between homologous gene pairs in the Diospyros genome and interspecific dS between the orthologs from Diospyros and Actinidia, or from Diospyros and Vitis, indicated that the Dd-α event postdated the divergence of Diospyros and Actinidia, and might coincide with the divergence of the Ebenaceae family (Fig 2C and 2D). Two other events, Ad-α and Ad-β, have been inferred by a similar analysis in the Actinidia genome [19] (S6 Fig) but are not detectable in the Diospyros genome. Thus, Actinidia and Diospyros differ by at least three lineage-specific ancestral WGD events. These occurred at a time similar to previously reported whole-genome duplication events in the asterids [19, 21, 22], as well as across the angiosperms [11, 23], concentrated around the K-Pg (Cretaceous-Paleogen) boundary (Fig 2E).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 2. Characterization of lineage-specific whole-genome duplication events.

a, Distribution of silent divergence rates between homologous gene pairs within the Diospyros, Actinidia, Solanum, and Vitis genomes. Diospyros shows a peak, indicated by an asterisk, at the same dS value as the Solanum triplication (T-tri), indicating the concurrent whole-genome duplication events. b, Comparison of the 4-fold degenerative transversion rates (4DTv) between the putative paralogous gene pairs, in the Diospyros, Actinidia, and Vitis genomes. Consistent with the distribution of dS values, a peak, which corresponds to Dd-α, was detected specifically in the persimmon genome, as indicated by an asterisk (*). In the Actinidia and Vitis genomes, peaks putatively corresponding the Ad-α/β and the hexaploidization-γ, were detected, as shown by the green and gray bands, respectively. c, Comparison of the dS values between the paralogous pairs in the Diospyros genome (orange), and the dS values between the orthologs in Diospyros and Actinidia (green), and in Diospyros and Vitis (purple). d, Estimated divergence time between Diospyros, Actinidia, and Vitis, with Arabidopsis as the outgroup. The concatenated sequences of 175 conserved genes across these species were used to determine divergence time, based on the previous estimated divergence of Actinidia and Vitis at 117MYA in the TIMETREE database (http://www.timetree.org). e, Summary of the lineage-specific WGD events in the asterids. The time scale is estimated from dS values and previous reports [21–23]. K-Pg, Cretaceous-Paleogene boundary.

https://doi.org/10.1371/journal.pgen.1008566.g002

Only a few gene, including MeGI, exhibit signs of positive selection but divergent expression patterns are common following the WGD event

To explore the evolutionary significance of lineage-specific duplications, and particularly of the Dd-α WGD event, dN/dS values between the duplicated gene pairs putatively derived from the Dd-α WGD events (N = 2,619) were calculated. The dN/dS values averaged over the coding regions indicated that most of the duplicates experienced either purifying or neutral selection (dN/dS ≤ 1.0, Fig 3A). In contrast, site- and evolutionary branch-specific tests for positive selection (dN/dS >> 1.0), using PAML, suggested that at least 9 genes experienced strong positive selection (posterior probability > 0.99 in Bayes Empirical Bayes analysis) following the Dd-α WGD event (Fig 3B and 3C). Importantly, MeGI and its paralog, named Sister of MeGI (SiMeGI), were one of these 9 gene pairs. Consistently, MeGI and SiMeGI were included in the same gene family after OrthoMCL analysis. They are located on Chr 13 (Dlo_pri0799F.1) and Chr 4 (Dlo_pri0025F.1), respectively, and these regions showed syntenic collinearity around these genes based on sequence similarity (Fig 3D–3F, S7 Fig). Syntenic blocks derived from gene order (with genes with dS values between 0.5 and 0.9) were observed with SynMap in CoGe as well (Fig 3E). These findings are consistent with the hypothesis that they were derived from the Dd-α WGD event, although we cannot exclude the possibility that they were generated from a simple segmental duplication concurrent with the Dd-α.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 3. Fate of paleoduplicated genes in Diospyros.

a, Distribution of the pairwise dN/dS values in the Dd-α-derived paralogous gene pairs, from the alignment of the full ORF sequences. Most gene pairs are under purifying selection (dN/dS < 1.0), while only approximately 0.3% of the gene pairs (shown in red) exhibited neutral selection (N.S.) or weak positive selection (dN/dS ~ 1.0). b, model for the detection of the genes that underwent significant site-branch specific positive selection (posterior probability > 0.99 in Bayes Empirical Bayes method) after Dd-α, using Actinidia, Solanum, and Vitis as outgroups. c, Functional annotation of the 9 genes that underwent significant site-branch specific positive selection after Dd-α. MeGI is highlighted in gray. d, Inter-chromosomal collinearity between Chr. 4 and Chr. 13. Genes pairs showing significant similarity (<e^-100 in blastp) are linked (green lines). The segments surrounding SiMeGI and MeGI exhibit syntenic collinearity. e, Synteny analysis of chromosomes 4 and 13, based on gene order using SynMap (CoGe). The dotted rectangle highlights blocks of gene pairs with dS values ranging between approximately 0.5 and 0.9, including the MeGI-SiMeGI pair. The MeGI-SiMeGI syntenic region is indicated by a red circle, a more detailed figure is available in Supplementary S7 Fig. f, Microsynteny analysis of the genomic fragments including SiMeGI and MeGI, using promer in MUMmer. g-h, Comparison of the expression patterns of paralog pairs derived from the Dd-α event, focusing on the sex differentiation stages. The ratio of expression levels in male versus female developing flowers (g) and mature flowers (h) were compared in the paralogs putatively derived from the Dd-α WGD event. The ratios were expressed in log₁₀ scale. Approximately 10% of the gene pairs exhibited a statistically significant (P < 0.01, 2x2 Fisher’s exact test, orange circles) expression bias between the two paralogs (S3 Dataset), and 18.5% of the gene pairs (N = 242) showed >5-fold differences between the two paralogs.

https://doi.org/10.1371/journal.pgen.1008566.g003

In contrast to very small number of genes exhibiting positive selection, a larger proportion of the gene pairs derived from the Dd-α WGD events exhibited significant differences in expression patterns. We described expression patterns in male and female buds/flowers using transcriptome data from 8 time points throughout the annual cycle (see Materials and Methods for details). Our results suggest that 45.5% of the gene pairs (597/1,311 pairs) showed significant differentiation (Pearson product-moment correlation test r² < 0.3, S2 Dataset). To investigate differences in expression pattern between male and female flowers throughout development, we conducted 2x2 Fisher’s exact test on the Dd-α-derived gene pairs (see Materials and Methods) and identified 36 and 65 gene pairs (of 1,311 pairs) exhibiting significant differentiation (p < 0.01) in expression patterns between male and female flowers at developing and maturing stages, respectively (Fig 3G and 3H, S3 Dataset). These might have potentially contributed to the establishment of Diospyros-specific sex determining mechanisms. Such frequent variation in expression patterns is consistent with previous results in soybean [24] and could have originated from rapid evolution in cis-motifs after WGD.

Adaptive evolution of MeGI to act specifically for repression of androecium development

Genome-wide survey of the HD-Zip1 family, to which MeGI belongs, found 34 genes in the D. lotus genome. Phylogenetic analysis of MeGI/Vrs1 orthologs from representative angiosperm species indicated that only MeGI and SiMeGI belong in the MeGI/Vrs1 clade (bootstrap = 100/100, Fig 4A, S8 Fig). Finer evolutionary analysis on the MeGI/SiMeGI orthologs, to detect site-branch specific evolutionary rates using PAML, indicated that specific regions of MeGI experienced strong positive selection soon after the Dd-α event (Fig 4B, p = 0.0027 for dN/dS > 1.0, post. prob. > 0.99 for P23-V40-S152, and Fig 4C and 4D, dN/dS > 2.0 for the region between 45 and 165 bp in the sliding window test).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 4. Lineage-specific adaptive evolution of MeGI.

a, Phylogeny of the HD-Zip1 type homeodomain genes in the D. lotus genome. Only MeGI and SiMeGI were nested within the MeGI/Vrs1-clade with statistically significant support (100/100 and 74/100 for the divergence of MeGI/Vrs1 clade and MeGI/SiMeGI subclade in D. lotus, respectively). b, Divergence of the MeGI/SiMeGI-like orthologs in the asterids and evidence of strong positive selection immediately after the Dd-α WGD event in Diospyros species (colored in red). No significant positive selection was detected elsewhere in this tree. Pairwise dN/dS values within the current MeGI (0.095) and SiMeGI (0.22) sequences suggest that both genes have been functionally fixed. c, Branch-specific dN/dS rates sliding window analysis of MeGI/SiMeGI-like genes from various asterid species. MeGI specifically exhibits positive selection in the 5’ region (~0-170bp). The three asterisks indicate the positions of the positively selected sites according to the site-branch specific detection analysis performed using PAML. The position of the homeobox domain (HB) is indicated by the thick black line. d, Sliding window assessment of the pairwise dN/dS values in the current MeGI and SiMeGI alleles. All three of the positions positively selected in MeGI sites after the Dd-α WGD event (asterisks) are under stronger purifying selection in MeGI than in SiMeGI, consistent with a situation of an adaptive evolution utilizing the mutations positively selected after WGD.

https://doi.org/10.1371/journal.pgen.1008566.g004

On the other hand, MeGI experienced strong purifying selection overall (average dN/dS = 0.095) since the establishment of the Ebenaceae (Euclea and Diospyros) (Fig 4B). Furthermore, the regions that experienced positive selection early are currently under stronger purifying selection in MeGI than in SiMeGI (Fig 4E). This is also consistent with the idea that MeGI first underwent neofunctionalization following the whole-genome duplication event, and that these changes were later fixed by positive selection. On the other hand, stronger purifying selection in MeGI than in SiMeGI could reflect lesser functional importance of SiMeGI (or possibly that it is degenerating since the whole-genome duplication occurred). Alternatively, it could reflect the need to conserve high sequence homology between OGI and MeGI in order to maintain the regulatory role of OGI via smRNA targeting MeGI.

Consistent with the evolutionary analysis presented above, ectopic expression of MeGI or SiMeGI in Nicotiana tabacum indicate differentiation of their protein functions. Constitutive induction of MeGI under the control of the CaMV35S promoter resulted in severely dwarfed plants and repressed androecium development (Fig 5A–5C, 5G and 5H, S9 Fig, S5 Table), consistent with previous results using the same construct in A. thaliana [5]. On the other hand, constitutive induction of SiMeGI under the control of the same promoter resulted in plants of only slightly reduced stature and normal androecium development in N. tabacum (Fig 5D–5H, S9 Fig, S6 Table). The function of MeGI as repressor of androecium in persimmon is due to the ability to regulate PISTILLATA (PI) in young developing androecium [25]. The expression level of PI in N. tabacum was significantly down-regulated in the transgenic lines with MeGI, while the lines transformed with SiMeGI showed no changes in PI expression (Fig 5I and 5J). In Arabidopsis, which is a very far lineage from Diospyros, high expression of SiMeGI typically did not result in altered flower morphology although it occasionally resulted in inhibited androecium development (S10 Fig, S7 and S8 Tables).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 5. Functional differentiation between MeGI and SiMeGI.

a-h, N. tabacum transgenic lines expressing either of MeGI or SiMeGI under the control of the 35S promoter. The lines expressing MeGI (a-c) showed rudimental anthers (a) which did not produce functional pollen grains (b), and severe dwarfism with chlorophyll starvation and narrow leaves (c, see S7 Fig for the detail). The lines expressing SiMeGI (d-f) developed regular anthers (d) which produced fertile pollen (e), and showed moderate dwarfism (f). pis: pistil, ra: rudimental anthers, an: anthers. g-h, Both MeGI- and SiMeGI-overexpressing lines were phenotypically different from the control plants transformed with empty vectors (cont), but the MeGI-expressing lines exhibited more severe departure from the WT controls for specific traits, such as leaves width (see S9 Fig). Bars indicate 5mm for a and d, 50mm for c, f, g, and h. i-j, expression patterns of MeGI, SiMeGI, and PI, with actin as a positive control, in the transgenic lines transformed with CaMV35S-MeGI (i) and CaMV35S-SiMeGI (j). k, DNA motifs identified as preferentially bound to following transcription factors all nested within the MeGI/SiMeGI clade: MeGI [25], SiMeGI (our experiments), and three Arabidopsis HD-ZIP1 genes [29], using DAP-Seq analyses (see Methods). l-n, expression patterns of MeGI and SiMeGI in buds and flower primordia were highly correlated (Pearson’s r > 0.7). Expression levels in female (l) and male (m) are expressed as RPKM values. n, Developmental stages.

https://doi.org/10.1371/journal.pgen.1008566.g005

Taken together, our results are consistent with the hypothesis that a role in androecium development is specific to MeGI. This is further supported by the fact that mutants of the MeGI/SiMeGI orthologs which are normally expressed in flower primordia in other angiosperm species, do not affect androecia development [15–17]. Our evolutionary analyses revealed that the positive selection that affected MeGI specifically did not occur on the region binding to the target cis-motifs, called homeobox-domain (HB) (Fig 4D and 4E), but rather on the 5’ undefined region and on the leucine zipper region putatively forming heterodimers [26, 27]. This was supported by the results of DNA affinity purification sequencing (DAP-Seq) [28] using MeGI [25] or SiMeGI fused to a Halo-tag. This allowed us to identify which genes and/or motifs is preferentially targeted by each of these transcription factors. The DAP-Seq reads were mapped to the D. lotus genome to characterize the accumulated recognition motifs (see Materials and Methods). We identified the motifs using the top 1,000 high-confidence peaks, and determined that the AATWATT sequence was enriched when using MeGI [25] and SiMeGI as the probes (Fig 5K). This motif is commonly recognized by the Arabidopsis HD-ZIP1 genes as well [25, 29]. Thus, it is possible that the feminization role of MeGI could have resulted from either increased efficiency or novel affinity to interact with other factors. Finally, the native expression patterns of MeGI and SiMeGI in persimmon are also slightly different in developing buds and flower primordia (Fig 5L–5N, S11 and S12 Figs). Specifically, MeGI exhibits higher expression than SiMeGI during the flower maturing stages (Fig 5L–5N). This expression differentiation might also contribute to MeGI-specific feminizing function.

Formation of a lineage-specific, and slowly evolving Y-chromosome in Diospyros

To investigate the sequence and structure of the sex chromosomes, we undertook the following steps. First, we anchored some pseudo-autosomal scaffolds to chromosome 15, using sex-linked SNPs markers, previously derived from the F1 population described above (S9 Table). On the other hand, the male-specific region of the Y-chromosome, including OGI, could not be anchored using SNPs, presumably due to large structural variation between the X and Y chromosome at these locations. Therefore, we anchored 7 Y-chromosomal scaffolds surrounding OGI using the end-sequences of BAC clones selected for sequencing based on successive walking starting from OGI itself [5]. We then assessed their genomic context by mapping short sequencing reads from male and female individuals of the KK population (Fig 5A) to these scaffolds. The regions flanking OGI were male-specific or hyper-repetitive, often including palindrome-like structures (S13 Fig), that are consistent with the sequence context of sex chromosomes in animal [30]. Putative pseudo-autosomal region (PAR)-like sequences, which include both X- and Y-allelic genes, were observed only 200–300 kb from OGI (Fig 6A). Such a short Y-specific region is consistent with our previous results [5].

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 6. Genomic context of the Y-chromosomal region surrounding OGI.

a, Read coverage from male (blue) and female (pink) samples and male/female coverage ratio across the scaffolds covering the male-specific region of the Y-chromosome. For both the male and female reads, expected coverage a single-copy sites is approximately 20 (grey lines across). This male-specific region was assembled via anchoring of the scaffolds with BAC sequences. Approximately 1.3Mb region was covered by Y-allelic scaffolds. More than 400kb of long repetitive sequences (dotted lines), flank OGI. Outer regions of these hyper repetitive sequences contain male-specific sequences (blue bands in M/F rate) and pseudo autosomal region (PAR)-like sequences (orange lines), where M/F rate was less than 70%, and the percentage of repetitive sequences was much lower. b, The silent divergence rate (dS) between X and Y alleles of the genes located in the PAR-like sequences (orange circles) decreases with distance to OGI. Stil, for most of these genes, the dS value between the X and Y alleles was larger than the average interspecific dS between the X alleles of D. lotus and D. mespiliformis (green square and dotted line), D. lotus and D. virginiana (blue square and dotted line), and D. lotus and D. kaki (red square dotted line). These results suggest that, in these PAR-like sequences, recombination between the X and Y alleles was suppressed before the divergence of Diospyros species, or at least predates the divergence between D. lotus and D. kaki. dS values for genes located in the regions closest to OGI are comparable to dS values between OGI and MeGI (gray circle, dS = 0.205), which suggest that little or no recombination occurred between these sequences after the establishment of OGI. In comparison, dS values between the X and Y alleles of genes located in the recombining region of chromosomes 15 are much lower (while circles on the right).

https://doi.org/10.1371/journal.pgen.1008566.g006

The silent divergence rate (dS) between the X and Y alleles of the genes located within the PAR-like sequences decreased with increasing distance from OGI, but was always higher than the interspecific dS rate between D. lotus and other Diospyros species (Fig 6B), suggesting that recombination was suppressed in the regions flanking OGI before the divergence of some Diospyros species. Large structural variation specific to male (or large male-specific region) were frequently observed within the PAR-like sequences (Fig 6A). Contrary to the observation of synteny around MeGI and SiMeGI, sequence similarity between the regions surrounding OGI (Chr. 15) and MeGI (Chr. 13), was only observed in the transcriptional regions of MeGI and OGI (S14 Fig). No significant gene order synteny was observed using SynMap (CoGe). Finally, the phylogenetic relationship between SiMeGI, MeGI, and the inverted and forward repeats of OGI (S15 Fig) suggested that the inverted structure of OGI was derived from local inversion after segmental duplication of MeGI and (proto)OGI. Altogether, these results suggest that OGI was not derived from a whole-genome duplication event but from a local segmental duplication event.

Transitions towards dioecy are associated with duplication events

Our results suggest the following working hypothesis for the evolutionary path into dioecy in Diospyros. The Diospyros-specific WGD event, Dd-α resulted in the appearance of MeGI and promoted the neofunctionalization of this gene into a dominant suppressor of androecium, as a feminization factor. This was followed by a second, segmental duplication of MeGI to derive a Y-encoded OGI, which is a dominant repressor of MeGI (Fig 7). Interestingly, the information available so far from other dioecious species hints at the possibility that this type of pattern may have played a role in the evolution of dioecy in other species. For example, in the establishment of dioecy in garden asparagus, the Y-encoded putative sex determinant, SOFF, is thought to have originated from an Asparagus-specific gene duplication event, which was followed by the acquisition of its function as a dominant suppressor of feminization (SuF) [6]. Furthermore, the Y-encoded putative sex determinant in kiwifruit (Actinidia spp.), Shy Girl, which acts as a dominant suppressor of feminization, also arose via an Actinidia-specific duplication event [7], probably one of the Actinidia-specific WGD events, Ad-α [19]. These parallel paths towards the independent evolution of all three of these sex determinants is probably not coincidental, but consistent with the theoretical framework described above. In flowering plants, transition into separated sexuality requires the appearance and selection of a gain-of-function event in order to acquire a dominant suppressor(s), such as MeGI. Whole-genome duplication events provide good opportunities for such a scenario. The concentration of independent paleoplodization events in the K-Pg boundary is consistent with the adaptive evolution of plants against the substantial environmental changes, including mass extinction of their pollinators that took place at the time [11, 31]. A selfing habit engendered by polyploidy would be advantageous, but protracted evolutionary success would be favored by an eventual return to outcrossing. The neofunctionalization of MeGI resulting in the acquisition of a lineage-specific new sexual system could be one of these adaptive strategies. This hypothesis is also consistent with the observed wide diversity of sex determination system within plants.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Fig 7. Hypothetical model for the role of duplication events in the evolution sexual systems in Diospyros.

The Dd-α event triggered positive selection on the 5-end and bZIP motifs, resulting in the acquisition of a new role for MeGI as repressor of male organs. This was potentially associated with the first switch in sexual system, from hermaprhodistism to monoeocy. The following duplication event, a segmental event, resulted in formation of OGI, containing an inverted repeat, which acquired the function of repression of MeGI expression via small-RNA production. This potentially triggered the establishment of the XY (heterogametic male) sexual system [5]. On the right, the dS scale, corresponds to the evolution of the MeGI/SiMeGI families and the observed sexual systems in each era. Based on the study of fossil records, unisexual (male) flowers were present during the Eocene era, which occurred significantly later than the Dd-α event (or the K-Pg boundary) [65]. The OGI/MeGI divergence and the establishment of the current function of OGI is ancestral to diversification within Diospyros and consistently, the Y-encoded OGI regulates dioecy in the whole Diospyros genus [5].

https://doi.org/10.1371/journal.pgen.1008566.g007

Initial genome sequence assembly

Dormant buds of D. lotus cv. Kunsenshi-male were burst in the dark for 2-weeks to harvest chlorophyll-starved young leaves (S10 Table). High molecular weight DNA were extracted using the Genome-tip 100/G kit (QIAGEN, Tokyo, Japan), followed by purification using phenol/chloroform extraction. Libraries were size-selected using the Blue Pippin and the following size minimums: 12 kb (14 SMRT cells), 15 kb (34 SMRT cells) and 16 kb (12 SMRT cells). A total of 60 SMRT cells and 54 Gb of PacBio raw data were obtained using the PacBio RSII. Filtered sub-reads were pooled and the longest were retained for assembly, by removing all filtered subreads shorter than 12 kb. This resulted in approximately 32x coverage of the estimated 1 Gb haploid genome size. PacBio reads were assembled using Falcon, producing 3,417 primary contigs and 6,318 alternate contigs. Next, all contigs were assessed for the presence of contaminating sequences by aligning each contig to a custom database using BLASTN+ version 2.2.31+. The custom database contained Kiwifruit psuedomolecule (http://bioinfo.bti.cornell.edu/pub/kiwifruit/Kiwifruit_pseudomolecule.fa.gz), the A. thaliana chromosomes (http://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/), as well as the human draft genome and representative bacterial / archaeal genome databases (pre-formatted blast+ database http://ftp.ncbi.nlm.nih.gov/blast/documents/blastdb.html). Hits to the two contaminant databases were identified and used to remove sequences that were largely contaminant, or to trim those with non-contaminant sequences at least 10kb long. After this step, 3,252 primary and 5,939 alternative contigs were retained. This set of contaminant-free contigs were next polished using quiver (version 2.3.0–140936) and default parameters. After this last step, 3,073 primary and 5,901 alternative contigs remained.

Illumina library construction and sequencing

Gene prediction and genome/genes annotation

The RNA-Seq data for gene prediction was obtained from developing buds and flowers from D. lotus Kunsenshi-male at the following eight time points in 2013 to 2015 (June, July, August, October, January, March, early April, and late April) to cover the annual cycle of leaves/flower development. The RNA-Seq reads were trimmed according to previous reports [5]. The cleaned reads were mapped onto the scaffolds of DLO_r1.1 using TopHat 2.0.14 [36], and the BAM files obtained were used for BRAKER1 1.9 pipeline [37]. In the pipeline, GeneMark-ET 4.32 [38] and Augustus 3.1 [39] were used to construct the training set, and Augustus 3.1 was used for the gene prediction, using the training set. Genes were compared to the UniProtKB (http://www.uniprot.org/uniprot/) and of Araport11 [40] peptide sequences using BLASTP with E-value cutoff of 1E-10. Genes that were similar to those in the databases were categorized as “highly confident” (HC). Analysis of the conservation of the single-copy genes was conducted using BUSCO v1 [41]. Repeat sequences were detected using RepeatScout 1.0.5 [42] and RepeatMasker 4.0.6 (http://www.repeatmasker.org) against the Repbase database [43], according to the method used previously [44]. The HC genes on the primary scaffolds (DLO_r1.1 primary) were compared to the genes of Actinidia chinensis (kiwifruit; 39,040 genes [19]), Vitis vinifera (grape; 29,927 genes (IGGP 12x.31) [45]), Solanum lycopersicum (tomato; 34,789 genes (ITAG 3.10) [12]) and Arabidopsis thaliana (27,655 genes (Araport11)) using OrthoMCL 2.0.9. To estimate the divergence time between D. lotus, A. chinensis, V. vinifera, and A. thaliana, the single copy genes conserved amongst all four species were aligned by MUSCLE 3.8.31 [46]. InDels in the alignment were eliminated using Gblocks 0.91b [47], and the sequences were concatenated by species and used to construct the phylogenetic tree using the Maximum Likelihood method using MEGA 7.0.26 [48] with the Jones-Taylor-Thornton (JTT) model as the substitution model. The divergence time was estimated based on that between A. chinensis and V. vinifera (117 MYA) published in TIMETREE (http://www.timetree.org).

Construction of the persimmon database

The sequence data obtained was released in the form of the PersimmonDB (http://persimmon.kazusa.or.jp). In the database, BLAST searches can be conducted against the scaffolds (DLO_r1.0) and pseudomolecules (DLO_r1.0_pseudomolecules), cds (DLO_r1.1_cds), and pep (DLO_r1.1_pep). Keyword searches are available against the results of the similarity searches against TrEMBL and peptide sequences in Araport11. The genomic and genic sequences, GFF files of the scaffolds and pseudomolecules, and BED files can be downloaded from the database. The scaffolds are also available under accession numbers BEWH01000001-BEWH01008975 (8,975 entries) in DDBJ. The raw sequence data is also available from under accession numbers DRA006168 (Illumina WGS for D. lotus Kunsenshi-male and female), DRA006169-DRA006176 (ddRAD-Seq/GBS for KK and VM populations), DRA006177 (RNA-Seq for D. lotus Kunsenshi-male), and DRA006182-DRA006184 (PacBio WGS for D. lotus Kunsenshi-male) in DDBJ.

Genetic anchoring of the scaffold using two mapping populations

The sequence reads from the ddRAD-Seq and GBS libraries were mapped onto the primary contigs of the DLO_r1.0 reference sequence using Bowtie 2 (version 2.2.3) [49]. SNP calling was performed using the mpileup command of SAMtools (version 0.1.19) [50] and the view command of BCFtools [50]. High-confidence SNPs were selected using VCFtools (version 0.1.12b) [51] using the following parameters: ≥10× coverage of each sample (—minDP 10); >999 SNP quality value (—minQ 999); ≥0.2 minor allele frequency (—maf 0.2), and <0.5 missing data rate (—max-missing 0.5). Totals of 3,535 and 4,027 high-confident SNPs were obtained in the KK and VM populations, respectively. Genotype information for all lines were prepared for the CP mode of JoinMap (version 4) and classified into groups using the Grouping Module of JoinMap with LOD scores of 4 to 7. Marker order and relative map distances were calculated using its regression-mapping algorithm with the following parameters: Haldane’s mapping function ≤0.35 recombination frequency, and  ≥2.0 LOD score. LPmerge (version 1.5) [52] was used to integrate the linkage maps into a single consensus map. To construct pseudomolecule sequences, scaffolds assigned to the genetic map for the Kunsenshi-male, the cultivar used for the genome sequencing analysis, were ordered and oriented in accordance with marker order if at least two marker loci were mapped on a single scaffold. Otherwise, in the cases of a single marker on a scaffold, the orientation of the sequence was determined as “unknown”.

Genomic characterization of the male-specific region of the Y-chromosome

For the male-specific regions of the Y-chromosome (MSY), including OGI, which was not anchored into Chr. 15 with SNPs markers, we aligned the candidate scaffolds using BAC-end sequences walking from the seed BAC clone that including OGI [5]. BAC library construction and screening were described previously [5]. A total of 14 BAC clones were isolated to connect each other, and anchor 7 scaffolds surrounding OGI. The genomic reads of 10 male and 10 female individuals from the KK population [5] were mapped to these sequences using BWA with the default mismatch allowance to determine reads coverage, and with no mismatch allowed to define the allele type (X or Y). In this study, >3kb sequences were defined as pseudo-autosomal region (PAR)-like sequences, based on the fact that > 30% of mapped reads were female (excluding repetitive sequences).

To investigate the timing of divergence (or suppression of recombination) between the X and Y alleles of the genes located within the MSY and within the seven anchored scaffolds, X-allelic sequences were reconstructed by mapping the Illumina reads from female individuals from the KK population, to the Y-allelic reference sequences. The X- and Y-allelic sequences were aligned with MAFFT ver. 7 and analyzed with DnaSP 5.1 [53] to detect dS values between X-Y alleles. To standardize the estimated timing of divergence, the interspecific dS values between the X-alleles in D. lotus and three Diospyros species (D. kaki, D. virginiana, and D. mespiliformis; [5]) were assessed using DnaSP 5.1. The X-Y allelic dS were also measured in the recombining regions of the sex chromosomes (Dlo_pri0017F.1 and Dlo_pri0114F.1).

Comparative genomics

Whole genome-resequencing analysis on the Kunsenshi-male and female individuals were performed as described in Shirasawa et al. (2017) [54]. Paired-end sequences reads were obtained from the male and female lines with Illumina NextSeq, and trimmed and filtered based on quality score using Prinseq [55] and base similarity to adapter sequences, AGATCGGAAGAGC, using fastx_clipper in the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). The resulting reads were mapped on the primary contigs of DLO_r1.0 reference sequence with Bowtie2, and single nucleotide polymorphisms were detected with SAMtools mpileup [50] and filtered with the conditions of sequence depth of ≥10 in each line (—minDP 10) and mapping quality of >200 in each SNP locus (—minQ 200) using VCFtools [51]. The effect of SNPs on gene function were predicted with SnpEff [56] to assign the SNPs to four impact categories, high, moderate, modifier, and low, predifined by SnpEff. Synteny relationship of the genome structures were predicted with PROmer program of Mummer package [57] between Diospyros (this study) and Actinidia [19], as well as within the Diospyros lotus genomic fragments. The results were filtered using delta-filter and default parameters, and options of -i 20 -u 20. The results were visualized using Mummerplot or Circos [58]. Collinearity of homologous genes (<e^-100 in blastp analysis) was visualized using Strudel [59]. Collinearity of gene order was analyzed and visualized using SynMap and GEvo in CoGe [20] (https://genomevolution.org/coge/).

Detection of genetic diversity within paralogs

Genes annotated as potential transposable elements by blastn/blastp using the TAIR/nr databases, and potentially repetitive genes which produced >5 homologous genes in the D. lotus genome (<e^-20 in blastp), were discarded. D. lotus gene pairs showing significant sequence similarity (<e^-20 in blastp), and their orthologs from three species, Actinidia, Solanum and Vitis, which were nested into the same gene family according to OrthoMCL results [60], were subjected to in-codon frame alignment using their protein and nucleotide sequences with Pal2Nal and MAFFT ver. 7 under the L-INS-i model. The resulting alignments were subjected to Mega v.6 to estimate the Jukes and Cantor corrected values of synonymous (dS) and non-synonymous (dN) substitutions and the index of evolutionary rate (dN/dS). The four-fold degenerative sites were extracted from the alignments with PAML (icode = 11), and their pairwise transversion rates (4DTv) were calculated according to previous reports [61]. To estimate the divergence time between the gene pairs, we adopted an estimated rate of 2.81 × 10⁻⁹ substitutions per synonymous site per year, according to the report in Actinidia [62].

Evolutionary analysis on the paralogs derived from Dd-α WGD event

To search for signs of positive selection, aligned nucleotide sequences of each gene pair and an outgroup ortholog, from either the Actinidia, Solunum or Vitis genomes, were subjected to codon-based detection of positive selection test using PAML [63]. The statistical significance of positive selection on branches was evaluated using the likelihood ratio test of the null hypothesis that dN/dS = 1. Site-specific positive selection was assessed by Bayes Empirical Bayes analysis. To examine the positively selected sites common across the all three outgroups, in-frame alignments of the D. lotus gene pairs with the orthologs from all of the Actinidia, Solanum or Vitis genomes were used for the construction of evolutionary topologies using ML method by Mega v. 6, using the general time reversible (+I+G) model. Based on these alignments and topology, the branch- and site-specific positive selection test was performed using PAML, as well.

To define the phylogenetic relationship between the MeGI/SiMeGI-like orthologs/paralogs in angiosperms, genes showing significant homology (<1e^-10 in blastp analysis) to a HD-ZIP1 OsHOX4 from Oryza sativa, which was previously used as the outgroup gene for the MeGI clade [5], were collected from the Diospyros lotus, Solanum lycopersicum, Arabidopsis thaliana, Oryza sativa, and Zea mays genomes. A total of 174 protein sequences from these genomes, and that of Vrs1 from barley [15] were aligned using MAFFT ver. 7, followed by manual pruning with SeaView. The pruned alignment was subjected to the NJ approach using Mega v. 6, with the JTT model, to construct phylogenetic tree (S6 Fig).

To assess selective pressure on MeGI and SiMeGI, their alleles from other members of the Ebenaceae family (Diospyros and Euclea genera), and their orthologs in the Actinidia, Solunum or Vitis genomes were subjected to in-codon frame alignment by MAFFT ver. 7, followed by a ML approach using Mega v. 6, with HKY+G model, to construct an evolutionary topology. The putative ancestral sequences of the MeGI and SiMeGI origins in the Ebenaceae family, and the sequences in the most recent common ancestor (MRCA) of the order Ericale and of the Asterids, were estimated using Mega. Informative SNPs in the aligned sequences were analyzed by DnaSP 5.1 [53] and used to calculate a series of window-average dN/dS values, from the start codon (ATG) in a 150-bp window with a 30-bp step size, until the walking window reached the stop codon.To assess differentiation of expression patterns between the Dd-α-derived paralog pairs, we conducted Pearson’s product moment correlation analysis and Fisher’s exact test. Differentiation between the developmental stages of the buds/flowers throughout the annual cycle was examined by the “cor.test” function in R (with “pearson” method), using mRNA-Seq transcriptome data from datapoints (S3 Dataset). Differentiation of expression pattern between male and female flowers was examined for each paralog pair using a 2x2 Fisher’s exact test (“fisher.test” function in R), and using mRNA-Seq transcriptome data from early developing stage and maturing stage, respectively (S3 Dataset).

Transformation of MeGI and SiMeGI

Full length sequences of the MeGI and SiMeGI transcripts were amplified by PCR using PrimeSTAR Max (TaKaRa) from cDNA synthesized from RNA, itself derived from developing flower buds of D. lotus cv. Kunsenshi-male. The amplicons were cloned into the pGWB2 vector to place the genes under the control of CaMV35S promoter. We constructed pGWB2-MeGI and pGWB2-SiMeGI using the Gateway system (Invitrogen) and the pENTR/D-TOPO cloning kit and LR clonase. Tobacco plants (N. tabacum) cv. Petit Havana SR1 were grown in vitro under white light with 16-h-light and 8-h-dark cycles at 22°C until transformation. The binary construct was introduced into the A. tumefaciens strain EHA101. Young petioles and leaves of tobacco plants were transformed by the leaf disk method as previously described [5]. Transgenic plants were selected on Murashige and Skoog medium supplemented with 100 μg/mL kanamycin. Pollen tube germination was assessed 6 h after placing the pollen grains on 15% sucrose/0.005% boric acid/1.0% agarose media at 25°C. The pollen germination ratio was counted as average percentages in batches of 200 pollen grains from the first three flowers.

RNA in situ hybridization

RNA in situ hybridization was performed as previously described [64], but with minor modifications. Briefly, bud samples were fixed in FAA (1.8% formaldehyde, 5% acetic acid, 50% ethanol), dehydrated using an ethanol: t-butanol series, and then embedded in paraffin. The embedded tissues were sliced into ca 10-μm sections, and the sections were mounted on FRONTIER coated glass slide (Matsunami Glass Ind., Japan). Paraffin was removed with xylene, and the tissue sections were rehydrated in an ethanol series. The tissue sections were then incubated in a Proteinase K solution (700U/mL Proteinase K, 50mM EDTA, 0.1M Tris-HCl pH 7.5) for 30 min at 37°C, followed by acetylation with acetic anhydride (0.25% acetic anhydride in 0.1 M triethanolamine solution) for 10 min. Full length MeGI and SiMeGI cDNA sequences were cloned into the pGEM-T Easy vector (Promega, WI, USA) to synthesize the DIG-labelled probes, respectively. Antisense RNA probes were synthesized using the DIG-labeling RNA synthesis kit (Roche, Switzerland), according to the manufacturer’s instruction. The probe solution including RNaseOUT (Thermo Fisher Scientific, Waltham, USA) was applied to the slides and covered with parafilm. Hybridization was performed at 48°C for >16 h. For detection, 0.1% Anti-Digoxigenin-AP Fab fragments (Sigma-Aldrich, St. Louis, USA) was used as the secondary antibody to stain with NBT/BCIP solutions.