Transcriptome

Reference-based genotyping of 168 sunflower transcriptomes

ESTs from a variety of cultivated and wild sunflowers were produced via Sanger, 454, and Illumina sequencing. Each sample's ID, species, subspecies or ecotype, and technology used for sequencing is presented in the table of metadata below. Reads were aligned to the TranscriptomeRef_mar30.fa reference assembly using BWA and individuals were genotyped with SAMtools. Indels were excluded. Genotypes are presented in a tab-delimited table with reference sites in rows, and individuals in columns. See the bottom of this page for a descriptive table of the accessions used in genotyping.

Accessions

IDSpeciesSSP/EcotypeRead Technology
HA412annuuselite454
HA369annuuseliteillumina
HA384annuuseliteillumina
HA412coldannuuseliteillumina
HA412droughtannuuseliteillumina
HA412-flowersannuuseliteillumina
HA412-roots_stemsannuuseliteillumina
HA89-5annuuseliteillumina
HA89-9annuuseliteillumina
KOSIannuuseliteillumina
MAIannuuseliteillumina
RHA274annuuseliteillumina
Sunriseannuuseliteillumina
VNIIMK8931annuuseliteillumina
ha89annuuselitesanger
psc8annuuselitesanger
rha280annuuselitesanger
rha801annuuselitesanger
CANannuusinvasive454
EUW1annuusinvasive454
EUW2annuusinvasive454
ISIannuusinvasive454
QLDannuusinvasive454
WANannuusinvasive454
SAW3annuusinvasiveillumina
HODLannuuslandrace454
SELannuuslandrace454
ARLannuuslandraceillumina
HAannuuslandraceillumina
HALannuuslandraceillumina
HAW59annuuslandraceillumina
HILannuuslandraceillumina
HOPLannuuslandraceillumina
MALannuuslandraceillumina
MELannuuslandraceillumina
MENannuuslandraceillumina
ZULannuuslandraceillumina
HTAIannuustexanus454
14TB-2annuustexanusillumina
2OTB-7annuustexanusillumina
arg14B-14annuustexanusillumina
btm11-1annuustexanusillumina
btm3-2annuustexanusillumina
btm35-4annuustexanusillumina
btm6-1annuustexanusillumina
K111annuustexanusillumina
TEXannuustexanusillumina
CAWannuusweedy454
INWannuusweedy454
KAWannuusweedy454
UTWannuusweedy454
ALBannuusweedyillumina
Canal2annuusweedyillumina
Canal5annuusweedyillumina
Manteca4annuusweedyillumina
Manteca8annuusweedyillumina
CON2annuuswild454
IOWannuuswild454
KSNannuuswild454
MOWannuuswild454
NDWannuuswild454
NMNannuuswild454
OKWannuuswild454
UTN1annuuswild454
Academy2annuuswildillumina
Academy7annuuswildillumina
ALBannuuswildillumina
LEW1annuuswildillumina
MENannuuswildillumina
NEWannuuswildillumina
TEWannuuswildillumina
ann1312annuuswildsanger
HW10annuuswinteriiillumina
HW1annuuswinteriiillumina
HW3annuuswinteriiillumina
HWE13annuuswinteriiillumina
HWE2annuuswinteriiillumina
HWE5annuuswinteriiillumina
F1-14annuus X petiolarisF1illumina
F1-17annuus X petiolarisF1illumina
F1-1annuus X petiolarisF1illumina
F1-3annuus X petiolarisF1illumina
F1-4annuus X petiolarisF1illumina
F1-7annuus X petiolarisF1illumina
F1-TAannuus X petiolarisF1illumina
F1-TBannuus X petiolarisF1illumina
Ano1495anomalus illumina
arg1820argophyllus 454
Ames449argophyllus illumina
Ames695argophyllus illumina
arg11B-11argophyllus illumina
arg14B-7argophyllus illumina
ARG1805argophyllus illumina
ARG1820argophyllus illumina
ARG1834argophyllus illumina
arg2B-4argophyllus illumina
arg4B-8argophyllus illumina
arg6B-1argophyllus illumina
btm10-5argophyllus illumina
btm13-4argophyllus illumina
btm17-4argophyllus illumina
btm19-1argophyllus illumina
btm19-2argophyllus illumina
btm20-8argophyllus illumina
btm21-4argophyllus illumina
btm22-8argophyllus illumina
btm25-2argophyllus illumina
btm26-4argophyllus illumina
btm27-3argophyllus illumina
btm30-6argophyllus illumina
btm31-6argophyllus illumina
btm32-3argophyllus illumina
btm34-6argophyllus illumina
btm5-1argophyllus illumina
btm7B-14argophyllus illumina
btm9-4argophyllus illumina
argophyllus.chwlmsargophyllus sanger
argophyllus.chwxyzargophyllus sanger
argophyllus.qhargophyllus sanger
ciliaris.chclmsciliaris sanger
Dahlia-buds_flowers_leavesDahlia sp. illumina
HDWdeblis 454
K105deblis illumina
RAR43deblis illumina
RAR46deblis illumina
RAR50deblis illumina
RAR55deblis illumina
RAR57deblis illumina
arg4B-14debliscucumerifoliusillumina
btm30-4debliscucumerifoliusillumina
btm33-4debliscucumerifoliusillumina
Des1484deserticola illumina
des2458deserticola illumina
exilis.chelmsexilis sanger
exilis.chelmsexilis sanger
king141Bparadoxus illumina
king145Bparadoxus illumina
king147Aparadoxus illumina
King151paradoxus illumina
king152paradoxus illumina
King156Bparadoxus illumina
paradoxus.chulmsparadoxus sanger
paradoxus.chuxyzparadoxus sanger
paradoxus.qhparadoxus sanger
PL109petiolaris 454
GSD1439petiolaris illumina
GSD975petiolaris illumina
ISS01petiolaris illumina
ISS19petiolaris illumina
KSG54petiolaris illumina
pet2119petiolaris illumina
Pet2152petiolaris illumina
PET-2petiolaris illumina
PET2341petiolaris illumina
PET2342petiolaris illumina
PET2343petiolaris illumina
PET2344petiolaris illumina
PET-3petiolaris illumina
pet489petiolaris illumina
Pet489petiolaris illumina
Pi468805petiolaris illumina
PI468812petiolaris illumina
PI468815petiolaris illumina
PI503232petiolaris illumina
PI531058petiolaris illumina
PI547210petiolaris illumina
PI586932b_1petiolaris illumina
PI613767petiolaris illumina
PI649907petiolaris illumina
PL109petiolaris illumina
petiolaris.chpxyzpetiolaris sanger
btm13-6praecoxrunyoniiillumina
btm14-4praecoxrunyoniiillumina
btm15-2praecoxrunyoniiillumina
btm16-2praecoxrunyoniiillumina
tuberosus.chtlmstuberosus sanger
tuberosus.chtxyztuberosus sanger