INRA GDEC ClermontFerrand France 3B Sequenced physical map MTP BACs 8452 3B MTPBAC sequencing BAC pools 922 Roche 8 kb MP lib 922 bp coverage ID: 931004
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Slide1
Frédéric
CHOULET
A pseudomolecule of 774 Mb: the 3B experience
INRA GDEC – Clermont-Ferrand, France
Slide23B
Sequenced physical map
#
MTP
BACs
8452
3B MTP-BAC sequencing
#
BAC pools
922
#
Roche 8 kb MP lib.
922
bp
coverage
(Roche/454)
36x
BAC-ends
(Sanger)
42,551
Whole Genome Prof. tags
327,282
Whole 3B shotgun
(Illumina)
82x
Slide3
#
BACs
#BAC-
contigs
Physical map
132,000 (19x)
1282
#
MTP-BACs
8452
3B
900 Mb
3B physical map
Slide4ACGTAGACTACA
3B
Assembly and scaffolding
3B-v1
16,136
scaff
1,040
Mb
Slide5Curation of the scaffolding
V. Barbe, S.
Mangenot (Genoscope)
Assembly and scaffolding
Integration of
BAC-end
match positions
Parsing of MP read positions
scaff00001
scaff00013
scaff00024
scaff00008
scaff00011
scaff00007
scaff00005
3B-v1
16,136
scaff
1,040
Mb
18% Ns
3B-v3
4,999
scaff
992
Mb
13% Ns
Slide6Curation of the scaffolding
V.
Barbe, S. Mangenot
(
Genoscope
)
Assembly and scaffolding
3B-v3
4,999
scaff
992
Mb
1
3% Ns
3B-v1
16,136
scaff
1,040 Mb
Gap filling
Seq. error corrections
JM.
Aury
, A.
Couloux
(
Genoscope
)
Illumina
reads
Whole
3B Shotgun
109,914 gaps filled
126,290 bases corrected
(error rate: 0.1%)
18% Ns
3B-v4
-
-
8
% Ns
Slide7Curation of the scaffolding
V.
Barbe, S. Mangenot
(
Genoscope
)
Assembly and scaffolding
3B-v1
16,136
scaff
1,040
Mb
Gap filling
Seq. error corrections
JM.
Aury
, A.
Couloux
(
Genoscope)
Redundancy removal and scaffold merging
S.
Theil (INRA GDEC)
Pool_A
Pool_B
ctg1
ctg2
2,808
scaff
833 Mb
3B-v443
scaffAssembler.pl
3B-v4
4,999
scaff
992
Mb
redundancy:
160 Mb
Slide8Search for shared TE-junctions
Slide9Ordering scaffolds
2,808
scaff
833 Mb
3B-v443
SNP discovery
Bait
TE
DNA captured from 10 genotypes
gene
52,265 baits
isbpProbeDesign.pl
39,077 SNPs
SureSelect
®
seq. capture
(
E.
Paux
, N.
Cubizolles
, E. Rey
)
Slide10Ordering scaffolds
SNP discovery
Genetic mapping
(
P.
Sourdille
)
+ Neighbor map: 3865 markers
LD mapping
(
F.
Balfourier
)Anchor map: 384 indiv
Cs x Renan Genotyping mapping pop
3,075 SNPs367 lines from a core-
collection
Slide113B
Ordering scaffolds
genetic map
4
4.8
cM
152 scaffolds
LD map
19
LD blocks
366 bins
0
cM
133
cM
554 bins
Slide1264 markers
at
the same genetic position
Linkage Disequilibrium
Slide13Ordering scaffolds
pseudomolBuilder
.pl
1358
scaff
774 Mb
pseudomolecule
unlocalized
1450
scaff
59 Mb
93%
7%
N
N
N
N
N
N
N
N
SNP discovery
Genotyping mapping pop
Integration of phys. map info
Slide143
cM
0
1
2
3
3
4
5
6
A
B
C
D
E
orientation unknown:
48%
of the seq.
micro-order unknown:
554 bins / 1358
scaff
?
?
RH map
Optical map
Long reads
Future Improvements
?
Slide157264
protein
coding genes
TRIANNOT
234,606
TEs
CLARI-TE
774 Mb
Annotation
Slide16Bioinformatics
Scaffolding/pseudomolecule construction
scaffAssembler.pl
Annotation
gapCloser
ssrFinishing
triAnnot
(new modules: filtering, pseudogenes, transfer annotation)
clari
-TE &
clari
-TE-lib
Data management
gowDB
(Bio::DB::
seqFeatureStore
)
Gbrowse
@ URGI
pseudomolBuilder
.pl
isbpProbeDesign.pl
Assembly
Newbler
Slide173B-MTP
3B-CSS
Pseudomolecule
vs
GenomeZipper
Slide18Sébastien
Theil
Natasha Glover
Josquin Daron
Lise
Pingault
Pierre Sourdille
Etienne Paux
Philippe Leroy
Jacques Le
Gouis
Nicolas Guilhot
Aurélien
Bernard
Nelly Cubizolles
Catherine Feuillet
François
Balfourier
M.
Alaux
L.
Couderc
V.
Jamilloux
H.
Quenesville
URGI
H. Berges
A. Bellec
CNRGV
BIA
A.
AlbertiV.
BarbeJ. Poulain
C. DurandS.
Mangenot
JM. Aury
A. Couloux
P. Wincker
Genoscope
J.
Dolezel
J. Safar
IEB
K.
Vandepoele
K. Mayer et al.
P.
Schnable
S.
Rounsley
D. Ware
C.
Gaspin
SAB
VIB
MIPS
Acknowledgments
Hélène
Rimbert
TGAC
J.
Rogers, M.
Caccamo
et al.
J. Rogers
K.
Eversole