Hah! Yeah, they are surprisingly hard to source and Google tends to treat simple searches with a firehouse of irrelevant ads. I’m under no pretenses that crossing virginiana and ebenum is destined for success, but then again, it’s fun to try to do things nobody else has done. 
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Dig through the linked articles. That is just the most recent, the previous articles put some time into figuring out how far they are separated. It is NOT definitive, meaning that there is plenty of room for further work to define the timeline. More important, there is no reliable timeline for the ebony family and more specifically for the branch where persimmon resides.
One key to understanding when they diverged is knowing that they were successfully hybridized via embryo rescue. I’m not aware of any plant species crosses via embryo rescue that were successful with much more than 1my of divergence. Persimmon can be very long lived trees. This tends to stretch out the timeline for speciation. Flip side, the older the tree gets before it reproduces, the more mutations it will accumulate. I can point out species that diverged in the 250,000 years ago range that can be successfully crossed with some difficulty. I can point out other species that can be crossed via embryo rescue that diverged in the 500,000 to 1,000,000 years ago range. Then I can point out species that diverged more than 1 Mya that can only be crossed via somatic fusion. Since D. virginiana and D. kaki can be crossed via embryo rescue, this suggests they diverged in the 250,000 to 1,000,000 years ago range. But!!! This has not to my knowledge been spelled out yet by detailed research. I would very much like to see an ebony family divergence timeline with solid research behind it.
It is from 2003. It also refutes the idea of a common ancestor, specifically calling out the prior papers that assumed otherwise. The methods section is very good. I recommend it!
The computation of separation time between two species does not provide a time when one specie or the other was instantiated. Thus a 1Myr separation could have occurred 15kyr ago or 70Myr ago.
As you know, I’m also concerned about genetic distance methods utilized in biology papers. I could perhaps agree with a centimorgan computation somehow extrapolated to years. But if the referenced prior papers are using Nei or another non-metric dissimilarity measure then their conclusions are invalid.
Hi all,
This thread is far too much for me to handle in earnest at this time in the year. I will be in direct contact with some people in this thread to source persimmons and you all can look forward to an update of our work on Persimmon once it is underway next year. In the meantime, we are $5k away from being able to sequence the 90 chromosome persimmon (Hexaploid sequencing is very expensive). This has never been done before and will supply some clarity to many questions you all have asked or opinions you’ve shared in this thread. So if you would like to make a tax-deductable donation to this cause, you can contact me through my work email..
We have a geneticist/plant breeder on staff who will be able to answer technical questions once we begin to present our findings. Hopefully we’ll have the genome sequenced by the end of the year.
Thanks.
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@Elizapples
It is true that D. virginiana has yet to be fully sequenced, but certainly other hexaploid plant DNA has been completed on PacBio hardware. The current cost for such a specimen is about $7,000 including Hi-C analysis. If you are having difficulty raising funds I recommend trying a GoFundMe campaign.
@Richard It actually costs 35k to get 90c Persimmon sequenced through HudsonAlpha, and that’s after several quotes. We have raised $30k so far through grants and private donors. If you’d like to talk more about this, I will certainly connect you with our plant breeder if you’d like to discuss more. Please email me through the link I posted if you’d like to have a conversation that way. But I can’t continue on this thread as it’s far too much for me to handle in addition to everything else.
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@Elizapples
I have the 2022 single specimen pricing, all the way up to icosidiploid 308c Morus! But your costs will vary, based on number of specimens and lab services needed by your geneticist. I wish you success in your project.
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Anyone that wants to stop by and see my operation they are welcome. I have made a lot of mistakes and am about half way through all the possible mistakes. I am in Terre Haute IN. I collect persimmon seed, stratify, germinate, grow in pots, this year about 1000 seed in 28 pots, then graft some , this year about 40, have 120 fruiting hybrids. Some interesting. that is about it. text 812 two two nine nine nine four one. I will fill requests for Claypool orchard seed to a degree for hobbyist not sellers, as I collect there often and am friends with the current owner. I have permission from him to set out some new trees in vacant locations in his orchard and would consider your fruit trees to go there if you contact me. Could meet you there. I don’t sell trees or anything, just a hobby and interest of 30 years. I do a lot or experiments that some advanced growers might find interesting.
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Strong work on the persimmon hybrids and orchard. Keep us updated with the ones with large and tasty fruits most cold tolerance.
Tony
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Hi all,
Wanted to give an update.
1.) I was able to harvest 1500 pounds of persimmons at Don Compton’s orchard this year. All have been processed into seed. We did not use Twin Tykes, nor would I ever recommend doing so if you intend to keep your seed lots sorted.
2.) As of right now, PacBio is unveiling the sequenced 90c American persimmon genome at the PAG conference in San Diego. We (Savanna Institute) had entered a PacBio contest in spring of 2022 to help get the 90c persimmon sequenced and, well, they ultimately chose to help us due to the utter complexity of the job. The work is being done at HudsonAlpha and once published, will be available for anyone to nerd out on.
3.) Contrary to this thread’s thoughts on sequencing: This was very expensive and we could not have cut corners in order to get what we/research needed. The sequencing was made possible thanks to personal donations, a grant from the Illinois dept of Ag, getting at-cost sequencing from HudsonAlpha and PacBio covering the rest. Just the 90 ended up costing over 50k. Any questions about this can be directed to my work email on the Savanna Institute website.
4.) This platform is very overwhelming for me because I have a lot going on. I won’t be responding to anything here, just updating from time to time.
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Dar Sofiyivky hybrid persimmon for grocery stores and families growing food:
The winter of 2005-2006 at Kiev Ukraine where Dar Sofiyivky was created and planted there as well as 2011-2012, the plant was not damaged at -22 F nor -28 F.
http://mchr.sofievka.org/article/view/219810
Results. Advantages of D virginiana L. in hybridization with D. kaki Thunb. to increase the persimmon adaptability to unfavorable wintering factors have been confirmed in the extreme temperature conditions of the winters of 2005–2006 and 2011–2012. In the hybrid progeny from free pollination of the ‘Kolhospnytsia’ cultivar with the American persimmon D. virginiana in the genealogy, a new cultivar ‘Dar Sofiyivky’ has been selected.
Facebook: Danes Farms
'Dar Sofiyivky is grown from the south to the north of all of Ukraine. There’s a Facebook group dedicated to growing ‘Dar Sofiyivky’ all thruought Ukraine, I’ve been told.
I have scions right now that I will graft and I’ve passed them around to others, as-well.
Show Buzz or others in the ilk. This 3-month storage capability changes it all and it’s literally time to put rootstocks/seeds in the ground to establish orchards across the continent.
‘Dar Sofiyivky’ is highly parthenocarpic and produces only female flowers. You grow this outside the range, you always have seedless fruit.
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Reading through the genetic information, a significant additional need will be to sequence at least 2 Diospyros species that have 30 chromosomes (diploid). This should give an outgroup with which to compare 60 and 90 chromosome species. In addition, D. kaki sequence will be needed to determine the level of divergence vs D. virginiana. It would be useful to get D. ebenum sequenced just to determine how much it has diverged from the edible fruit species.
edit: fixed typos
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Diospyros oleifera has been sequenced, although I cannot speak for the quality of the assembly. The authors claim that D. oleifera is the diploid progenitor of D. kaki.
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@GrapeNut
I agree with the authors that 2n = 2x = 30 is a divisor of quadraploid and hexaploid karyotype but nothing further. They have no viable sequences of polyploid Diospyros to compare with.
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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.
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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.
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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 .
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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:
