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From: "Rieseberg, Loren" <loren.rieseberg@botany.ubc.ca>
To: "RIVIERE, Nathalie" <nathalie.riviere@biogemma.com>
CC: "COQUE, Marie" <marie.coque@biogemma.com>, Jerome Gouzy
	<jerome.gouzy@toulouse.inra.fr>, nicolas langlade
	<Nicolas.Langlade@toulouse.inra.fr>, "John M. Burke" <jmburke@uga.edu>
Subject: Re: sunflower genome
Thread-Topic: sunflower genome
Thread-Index: AQHP2s5dkG9z6Qs1QUaBZUpQvcXyog==
Date: Sun, 28 Sep 2014 03:43:28 +0000
Message-ID: <173469EE-3C0E-410A-B222-A81A0BA0B4F2@mail.ubc.ca>
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Dear Nathalie,

I had hoped to be able to provide a final set of pseudomolecules to you in =
late spring, but the sunflower genome has not cooperated (as usual).  We di=
d annotate the Celera assembly and developed numerous tools linking the ass=
embly (in JBrowse)  to various genetic maps, QTLs, SNPs, expression data, B=
last capability, and so forth. I hope these have been useful to the group a=
t Biogemma.

We have posted a set of =E2=80=9Cbronze pseudomolecules,=E2=80=9D which rep=
resent a merger of the Allpaths and Celera assembly, and which have been or=
dered and oriented as far as possible using the physical map and six geneti=
c maps.  This semi-final genome covers 3.64 Gb and is contained in 31,392 s=
uper-scaffolds, with an N50 of 226 Kb.  It has been error-corrected and the=
 final gap-filling step starts next week.  We have been trying out various =
gap-filling tools, but they were not very good at dealing with both 454 and=
 Illumina data, so we developed our own tool, which works better.  We are u=
sing SAP=E2=80=99s Cloud server for the gap-filling, so we can do many iter=
ations rather quickly.

We are not entirely pleased with the bronze pseudomolecules because the mer=
ger created some erroneous duplicate genes and chimeric scaffolds.  While t=
hese problems have been largely corrected via masking or splitting, we have=
 developed a second merged assembly in parallel, in which much more aggress=
ive filtering and repeat masking was employed prior to the merger.  It also=
 included the new BAC-end sequences from INRA in the linkage group-specific=
 scaffolding step.  This =E2=80=9Cgold" version of the genome has reduced m=
erger artifacts and gives us a much higher N50, but it also has reduced the=
 total number of called base pairs in the genome by about 20%.  

Going forward, we planning to offer two fully annotated genomes - the bronz=
e and gold version, which we think will be useful for different purposes.  =
The bronze genome should  be ready for annotation soon, possibly by the end=
 of next week if the gap-filling goes well.  It will be at least a month be=
fore the gold version is ready.

In terms of the future, we have submitted a proposal to NSF (John Burke is =
the PI) and are in the process of submitting a proposal to Genome Canada fo=
r funding in the $6.5 million range.  The focus of both proposals is on the=
 genomics of abiotic stress resistance.  As before, these will be collabora=
tive projects between UBC, INRA, UGA, and several companies (including Biog=
emma - we have been in communication with Marie about this), as well as the=
 USDA.  Although the focus is on abiotic stress, we are intending to use so=
me of the money for PacBio sequencing (or other long-read sequencing) and p=
ossibly optical mapping to improve the genome.

Over the next three months our hope is to complete and annotate (with Jerom=
e) the bronze and gold versions of the genome.  2015 will be devoted in par=
t to linking the tools/resources we have developed to these new assemblies.=
  We also have circa 550 WGS sequences for wild and cultivated sunflower ge=
nomes that we plan to align to the new assemblies and call variants.  This =
will mainly be done using some alignment and variant calling approaches we =
have developed with SAP that outperform current approaches. We will also de=
velop a sunflower pan-genome based on all of this sequence (i.e., we will a=
ssemble the unaligned genomic fraction for each genotype) and provide ances=
try / pedigree information for the 290 or so cultivated genotypes we have s=
equenced.  Lastly, we will provide GBS-based genotypes of pre-bred material=
 created by the USDA and by our lab (the latter is being done in collaborat=
ion with SOLTIS).  I have cc:ed Jerome, Nicolas, and John, so they can add =
details about their plans as well.

We have not yet discussed whether the consortium will continue in its curre=
nt form beyond 2016.  We have been in discussions with Nicolas about having=
 INRA take on greater responsibility for the databasing in the next project=
 phase, since they have annual base support for this effort.  Likewise, sim=
ilar discussions are underway with the USDA about whether they could contri=
bute permanent resources for databasing of sunflower genomic resources.  Fi=
nally, we are developing the DivSeek Initiative with the Global Crop Divers=
ity Trust, which is a broader effort to provide such a database for 25 prio=
rity food security crops (sunflower is the only oilseed on this list).  Thu=
s, it is possible that we might find alternative support for the long term =
support of a website/database for sunflower genomic resources.  However, if=
 we cannot come up with permanent public funding, then we might continue to=
 rely in part on contributions from interested companies.  We will discuss =
this in greater detail at the PAG meetings in January.

Best Wishes, Loren










On Sep 25, 2014, at 6:27 AM, RIVIERE, Nathalie <nathalie.riviere@biogemma.c=
om> wrote:

> Hi Loren,
> I hope you had a great summer, and that things are running well. As you k=
now we discussed with Jerome and team a couple of weeks ago about a new rel=
ease on your website, but it seems that it does not correspond to the final=
 one. I guess you will send an e-mail when the final version is available.
> I also wanted to discuss further about what you have in mind for the futu=
re. It seems that there is still work to do on the current data, for assemb=
ly and annotation, which will probably be done in the coming months in the =
frame of 2014 workplan. But for 2015, do you plan to maintain the current c=
onsortium, and if so, what would be the workplan? Are you considering apply=
ing for funding a new project?
> It is important for us to understand what can to be done , and I would gr=
eatly appreciate that you give me more information on that.
> Regards
> Nathalie
> 
> PS: I won=E2=80=99t attend the PAG this time, but some of my colleagues w=
ill certainly do so.
> 
> _________________________________
> Nathalie Rivi=C3=A8re
> Upstream Genomics Coordinator
> Bioinformatics Manager
> 
> BIOGEMMA
> Route d'Ennezat
> SITE DE LA GARENNE 
> CS 90126
> 63720 CHAPPES
> 
> Tel  : +33 (0)4-73-67-88-05
> Mobile: +33(0)6-47 24 63 58
> Fax: + 33 (0)4-73-67-88-99
> _________________________________
> 
> BIOGEMMA S.A.S. au capital social de 48.335.652,00 =E2=82=AC
> 1, Rue Edouard Colonne - 75001 PARIS
> RCS PARIS 412 514 366
> 
> 
> This message and any attachments are confidential and intended solely for=
 the use of the addressee(s) named above. The information contained in this=
 email may also be legally privileged. If you have received this email in e=
rror, please notify us immediately by reply email or by fax and then delete=
 it. Any use, distribution or reproduction of this message is strictly proh=
ibited. The integrity or authenticity of this message cannot be guaranteed.=
 We therefore shall not be liable for the message if altered, changed or fa=
lsified. Thank you.
> 
> Cet email et ses pi=C3=A8ces jointes sont strictement confidentiels et de=
stin=C3=A9s uniquement =C3=A0 l'usage du (des) destinataire(s) sus-indiqu=
=C3=A9(s). Les informations contenues dans cet email sont l=C3=A9galement p=
rot=C3=A9g=C3=A9es. Si vous avez re=C3=A7u cet email par erreur, merci de n=
ous le retourner imm=C3=A9diatement par courrier =C3=A9lectronique ou t=C3=
=A9l=C3=A9copie avant de le supprimer. Toute utilisation ou reproduction de=
 cet email est strictement interdite. La v=C3=A9racit=C3=A9 et l'authentici=
t=C3=A9 de cet email et de son contenu ne peuvent =C3=AAtre garanties et no=
us ne pouvons =C3=AAtre tenus responsables de leur alt=C3=A9ration, modific=
ation ou falsification. Merci.

Loren Rieseberg
Botany Department
University of British Columbia
3529-6270 University Blvd
Vancouver, B.C. V6T 1Z4
Phone: 604-827-4540
Fax: 604-822-6089

Loren Rieseberg
Botany Department
University of British Columbia
3529-6270 University Blvd
Vancouver, B.C. V6T 1Z4
Phone: 604-827-4540
Fax: 604-822-6089


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{\rtf1\ansi\ansicpg1252\fromtext \fbidis \deff0{\fonttbl=0A=0D{\f0\fswiss\f=
charset0 Arial;}=0A=0D{\f1\fmodern Courier New;}=0A=0D{\f2\fnil\fcharset2 S=
ymbol;}=0A=0D{\f3\fmodern\fcharset0 Courier New;}}=0A=0D{\colortbl\red0\gre=
en0\blue0;\red0\green0\blue255;}=0A=0D\uc1\pard\plain\deftab360 \f0\fs20 De=
ar Nathalie,\par=0A=0D\par=0A=0DI had hoped to be able to provide a final s=
et of pseudomolecules to you in late spring, but the sunflower genome has n=
ot cooperated (as usual).  We did annotate the Celera assembly and develope=
d numerous tools linking the assembly (in JBrowse)  to various genetic maps=
, QTLs, SNPs, expression data, Blast capability, and so forth. I hope these=
 have been useful to the group at Biogemma.\par=0A=0D\par=0A=0DWe have post=
ed a set of \'93bronze pseudomolecules,\'94 which represent a merger of the=
 Allpaths and Celera assembly, and which have been ordered and oriented as =
far as possible using the physical map and six genetic maps.  This semi-fin=
al genome covers 3.64 Gb and is contained in 31,392 super-scaffolds, with a=
n N50 of 226 Kb.  It has been error-corrected and the final gap-filling ste=
p starts next week.  We have been trying out various gap-filling tools, but=
 they were not very good at dealing with both 454 and Illumina data, so we =
developed our own tool, which works better.  We are using SAP\'92s Cloud se=
rver for the gap-filling, so we can do many iterations rather quickly.\par=
=0A=0D\par=0A=0DWe are not entirely pleased with the bronze pseudomolecules=
 because the merger created some erroneous duplicate genes and chimeric sca=
ffolds.  While these problems have been largely corrected via masking or sp=
litting, we have developed a second merged assembly in parallel, in which m=
uch more aggressive filtering and repeat masking was employed prior to the =
merger.  It also included the new BAC-end sequences from INRA in the linkag=
e group-specific scaffolding step.  This \'93gold" version of the genome ha=
s reduced merger artifacts and gives us a much higher N50, but it also has =
reduced the total number of called base pairs in the genome by about 20%.  =
\par=0A=0D\par=0A=0DGoing forward, we planning to offer two fully annotated=
 genomes - the bronze and gold version, which we think will be useful for d=
ifferent purposes.  The bronze genome should  be ready for annotation soon,=
 possibly by the end of next week if the gap-filling goes well.  It will be=
 at least a month before the gold version is ready.\par=0A=0D\par=0A=0DIn t=
erms of the future, we have submitted a proposal to NSF (John Burke is the =
PI) and are in the process of submitting a proposal to Genome Canada for fu=
nding in the $6.5 million range.  The focus of both proposals is on the gen=
omics of abiotic stress resistance.  As before, these will be collaborative=
 projects between UBC, INRA, UGA, and several companies (including Biogemma=
 - we have been in communication with Marie about this), as well as the USD=
A.  Although the focus is on abiotic stress, we are intending to use some o=
f the money for PacBio sequencing (or other long-read sequencing) and possi=
bly optical mapping to improve the genome.\par=0A=0D\par=0A=0DOver the next=
 three months our hope is to complete and annotate (with Jerome) the bronze=
 and gold versions of the genome.  2015 will be devoted in part to linking =
the tools/resources we have developed to these new assemblies.  We also hav=
e circa 550 WGS sequences for wild and cultivated sunflower genomes that we=
 plan to align to the new assemblies and call variants.  This will mainly b=
e done using some alignment and variant calling approaches we have develope=
d with SAP that outperform current approaches. We will also develop a sunfl=
ower pan-genome based on all of this sequence (i.e., we will assemble the u=
naligned genomic fraction for each genotype) and provide ancestry / pedigre=
e information for the 290 or so cultivated genotypes we have sequenced.  La=
stly, we will provide GBS-based genotypes of pre-bred material created by t=
he USDA and by our lab (the latter is being done in collaboration with SOLT=
IS).  I have cc:ed Jerome, Nicolas, and John, so they can add details about=
 their plans as well.\par=0A=0D\par=0A=0DWe have not yet discussed whether =
the consortium will continue in its current form beyond 2016.  We have been=
 in discussions with Nicolas about having INRA take on greater responsibili=
ty for the databasing in the next project phase, since they have annual bas=
e support for this effort.  Likewise, similar discussions are underway with=
 the USDA about whether they could contribute permanent resources for datab=
asing of sunflower genomic resources.  Finally, we are developing the DivSe=
ek Initiative with the Global Crop Diversity Trust, which is a broader effo=
rt to provide such a database for 25 priority food security crops (sunflowe=
r is the only oilseed on this list).  Thus, it is possible that we might fi=
nd alternative support for the long term support of a website/database for =
sunflower genomic resources.  However, if we cannot come up with permanent =
public funding, then we might continue to rely in part on contributions fro=
m interested companies.  We will discuss this in greater detail at the PAG =
meetings in January.\par=0A=0D\par=0A=0DBest Wishes, Loren\par=0A=0D\par=0A=
=0D\par=0A=0D\par=0A=0D\par=0A=0D\par=0A=0D\par=0A=0D\par=0A=0D\par=0A=0D\p=
ar=0A=0D\par=0A=0DOn Sep 25, 2014, at 6:27 AM, RIVIERE, Nathalie <nathalie.=
riviere@biogemma.com> wrote:\par=0A=0D\par=0A=0D> Hi Loren,\par=0A=0D> I ho=
pe you had a great summer, and that things are running well. As you know we=
 discussed with Jerome and team a couple of weeks ago about a new release o=
n your website, but it seems that it does not correspond to the final one. =
I guess you will send an e-mail when the final version is available.\par=0A=
=0D> I also wanted to discuss further about what you have in mind for the f=
uture. It seems that there is still work to do on the current data, for ass=
embly and annotation, which will probably be done in the coming months in t=
he frame of 2014 workplan. But for 2015, do you plan to maintain the curren=
t consortium, and if so, what would be the workplan? Are you considering ap=
plying for funding a new project?\par=0A=0D> It is important for us to unde=
rstand what can to be done , and I would greatly appreciate that you give m=
e more information on that.\par=0A=0D> Regards\par=0A=0D> Nathalie\par=0A=
=0D> \par=0A=0D> PS: I won\'92t attend the PAG this time, but some of my co=
lleagues will certainly do so.\par=0A=0D> \par=0A=0D> _____________________=
____________\par=0A=0D> Nathalie Rivi\'e8re\par=0A=0D> Upstream Genomics Co=
ordinator\par=0A=0D> Bioinformatics Manager\par=0A=0D> \par=0A=0D> BIOGEMMA=
\par=0A=0D> Route d'Ennezat\par=0A=0D> SITE DE LA GARENNE \par=0A=0D> CS 90=
126\par=0A=0D> 63720 CHAPPES\par=0A=0D> \par=0A=0D> Tel  : +33 (0)4-73-67-8=
8-05\par=0A=0D> Mobile: +33(0)6-47 24 63 58\par=0A=0D> Fax: + 33 (0)4-73-67=
-88-99\par=0A=0D> _________________________________\par=0A=0D> \par=0A=0D> =
BIOGEMMA S.A.S. au capital social de 48.335.652,00 \'80\par=0A=0D> 1, Rue E=
douard Colonne - 75001 PARIS\par=0A=0D> RCS PARIS 412 514 366\par=0A=0D> \p=
ar=0A=0D> \par=0A=0D> This message and any attachments are confidential and=
 intended solely for the use of the addressee(s) named above. The informati=
on contained in this email may also be legally privileged. If you have rece=
ived this email in error, please notify us immediately by reply email or by=
 fax and then delete it. Any use, distribution or reproduction of this mess=
age is strictly prohibited. The integrity or authenticity of this message c=
annot be guaranteed. We therefore shall not be liable for the message if al=
tered, changed or falsified. Thank you.\par=0A=0D> \par=0A=0D> Cet email et=
 ses pi\'e8ces jointes sont strictement confidentiels et destin\'e9s unique=
ment \'e0 l'usage du (des) destinataire(s) sus-indiqu\'e9(s). Les informati=
ons contenues dans cet email sont l\'e9galement prot\'e9g\'e9es. Si vous av=
ez re\'e7u cet email par erreur, merci de nous le retourner imm\'e9diatemen=
t par courrier \'e9lectronique ou t\'e9l\'e9copie avant de le supprimer. To=
ute utilisation ou reproduction de cet email est strictement interdite. La =
v\'e9racit\'e9 et l'authenticit\'e9 de cet email et de son contenu ne peuve=
nt \'eatre garanties et nous ne pouvons \'eatre tenus responsables de leur =
alt\'e9ration, modification ou falsification. Merci.\par=0A=0D\par=0A=0DLor=
en Rieseberg\par=0A=0DBotany Department\par=0A=0DUniversity of British Colu=
mbia\par=0A=0D3529-6270 University Blvd\par=0A=0DVancouver, B.C. V6T 1Z4\pa=
r=0A=0DPhone: 604-827-4540\par=0A=0DFax: 604-822-6089\par=0A=0D\par=0A=0DLo=
ren Rieseberg\par=0A=0DBotany Department\par=0A=0DUniversity of British Col=
umbia\par=0A=0D3529-6270 University Blvd\par=0A=0DVancouver, B.C. V6T 1Z4\p=
ar=0A=0DPhone: 604-827-4540\par=0A=0DFax: 604-822-6089\par=0A=0D\par=0A=0D}
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