Comparing diploid vs hexaploid is still the optimum path forward in figuring out how the genome works. if the few online articles currently available are correct, there is now a full hexaploid genome that has not yet been published.
One of the more intriguing aspects of persimmon genetics is the proclivity to produce polyploids. There seems to be a survival advantage to hexaploid as compared with diploid.
I agree. The quoted paper had no hexaploid to compare to, nor any basis for claiming D. oleifera is the progenitor of D. kaki.
Their sequence is a notable accomplishment. There was no need to embellish it.
I mischaracterized their claim in my previous post. They don’t claim D. oleifera to be the only progenitor, just one possible progenitor.
Their claim is based on the correlation between a D. kaki genetic linkage map and the physical map from the D. oleifera genomes. Some D. kaki linkage groups show clear collinearity with D. oleifera chromosomes, while others do not. So I think there is definitely a possibility for D. oleifera to have contributed to D. kaki ancestry. It would also suggest that D. kaki isn’t an autopolyploid.
As the genome of hexaploid cultivated persimmon remains unpublished, the availability of the D. oleifera genome provides an alternative comparable reference for D. kaki . Based on the D. oleifera genome, 26.86% of the 11,204 markers (n = 3009) in the D. kaki genetic linkage map were assigned to and showed high colinearity with the newly completed D. oleifera genome sequences. Thus, it can be proposed that D. oleifera was one of the diploid ancestors of hexaploid D. kaki , and this evidence supports the previous hypothesis of Kanzaki4 and the preliminary predictions resulting from genomic in situ hybridization (GISH) studies60 and the comparison of chloroplast genome sequences22,61. The relationship between chromosomes and LGs suggested that D. oleifera may also be closely related to other ancestors of D. kaki , and chromosome breakage and rearrangement may have occurred during the evolution of D. kaki from D. oleifera .
At the bottom of page 2:
Fu et al. sequenced the complete chloroplast genomes from D. kaki, D. lotus, D. oleifera, D. glaucifolia and D. ‘Jinzaoshi’
Here is the citation for Fu’s paper:
Fu, J. M. et al. Five complete chloroplast genome sequences from Diospyros: genome organization and comparative analysis. PLoS ONE 11, e0159566 (2016).
The manufacturer of their sequencer has been stating for years – most recently last month – that significant subsequences and complete sequences of D. kaki are not currently not possible.
Looking further at Zhu’s paper: their “analysis” was performed by biostatistics packages whose buzzwords (and text from the documentation!) are included in the article. This is standard practice in the plant genomics literature. The methodologies shown in several figures are known to be erroneous as reported here:
http://wireilla.com/papers/ijcsa/V12N4/12422ijcsa01.pdf.
A genome sequence isn’t necessary to construct a linkage map. For maps using SSR markers you don’t need a reference genome at all. For SNP markers, a sequence is helpful for identifying the SNPs, but the map construction is independent of the reference genome. The authors of this paper didn’t use a reference genome to create their linkage map.
The main problem I have with their linkage map is that 77 progeny isn’t really a big enough mapping population for an outcrossing species like persimmons.
This is good food for thought. I’m not really qualified to discuss this, however.
I agree. But they claim to have a complete sequence!
Their linkage map (and most that I’ve seen) is based on a singular matrix – something their software doesn’t check for.
It turns out that SSR markers are uncorrelated with what is in high quality reference genomes, and often the SSR annealing process returns a few hundred counts when the marker is not present in the specimen. Here is an example using generalized discrete correlation that accounts for errors in the sequencing process:
