Improvement of the assembly of heterozygous genomes
of non-model organisms, a case study of the genomes of
two Spodoptera frugiperda host strains
Anaı̈s Gouin, Anthony Bretaudeau, K Labadie, Jean-Marc Aury, Emmanuelle
D’Alençon, Claire Lemaitre, Fabrice Legeai
To cite this version:
Anaı̈s Gouin, Anthony Bretaudeau, K Labadie, Jean-Marc Aury, Emmanuelle D’Alençon, et
al.. Improvement of the assembly of heterozygous genomes of non-model organisms, a case
study of the genomes of two Spodoptera frugiperda host strains. Arthropod Genomics 2015,
Jun 2015, Manhattan (Kansas), United States. 2015.
HAL Id: hal-01240443
https://hal.inria.fr/hal-01240443
Submitted on 9 Dec 2015
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Improvement of the assembly of heterozygous genomes of non-model organisms,
a case study of the genomes of two Spodoptera frugiperda host strains
Anaïs GOUIN1, Anthony BRETAUDEAU2, Karine Labadie3,Jean-Marc Aury3, Emmanuelle d'Alençon4, Claire LEMAITRE1 and Fabrice LEGEAI11,2
1
INRIA/IRISA/GenScale, Rennes, France
2
INRA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Rennes, France
3
CEA Genoscope, Evry, France
4
INRA, Diversité, Génomes et Interaction Micro-organismes (DGIMI), Montpellier France
Motivation
:
Some heterozygous
regions have a signif icant divergence
between the two haplotypes and the
assembly process can lead to the
construction of two different contigs,
instead of one consensus sequence.
Number of scaffolds
Objective
Expected
coverage
:
Set up a strategy to detect
and correct false duplications in alreadybuilt assemblies.
Expected read-depth /2
Read-depth
scaffold_a
Potential
erroneous
duplications
scaffold_b
Potential
duplications
superscaffold_c
Coverage of scaffolds
RE-ASSEMBLY
Pre-selection of
“similar” scaffolds
Re-alignment of
selected pairs
Chaining
Lastz
Plast
< 1kb &
< 80% of query
AxtChain
dist1 ≤ Abp
reference
query
Genome
correction
Identif ication of
mis-assemblies
lim1 ≤
sum(cov)
dist2 ≤ Abp
“end”
≤ lim2
Includeds : the smallest scaffold is
deleted
“border”
Analysis of chains
matching known
false duplications
Filter over
chain size
Set up
thresholds :
A, B, lim1, lim2
Pairs of
Alleles
Seqs
Filtering duplications
by checking
uniqueness of matches
“included”
“inner”
lim1 ≤
sum(cov)
reference
query
Borders : the scaffolds are linked by their
extremities, keeping the allele present on
the longest scaffold of the pair
≤ lim2
≥ B% of query
RE-ANNOTATION
Alignments of
impacted genes
onto scaffolds
Exonerate
Case A
Gene cannot be aligned
New gene
predictions
Intersection of
the annotation
Bedtools
Case B
Gene is aligned
on a segment w/o
a gene prediction
Case C
Gene is aligned, and
includes in a
prediction on the other
scaffold
Case D
Gene is aligned, and
overlapping a
prediction on the other
scaffold
Case E
Gene is aligned, and
overlapping 2 gene
predictions
new segment
deleted segment
Before
After
Augustus
APPLICATION : Spodoptera frugiperda genomes
Annotation stats
Assembly stats
283 208 scaffoldspairs with significant similarity
Previous release : 25,041 genes
Initial assembly
Allpaths
22.5 million chains
ENDs
652K
INNERs
1.4M
A: 500
B: 90
5020 “INCLUDEDs”
62.5Mb
1675 “BORDERs”
BUSCO* stats
Unicity
Corrected
assembly
Total size (Mb)
526.0
470.1
437.9
Nb. scaffolds
48 272
41 633
41 577
N50 (bp)
39 593
75 578
52 781
13.6 Mb
56.1 Mb
11.4 Mb
No hit
14
9
15
Single hit
1497
2047
1885
Multi hit
782
237
393
Total Gap length
Lim1: 120, lim2 : 220
Platanus assembly
3 746 genes to remap
# genes % success
Case A
34
0
Case B
747
45.4%
Case C
643
100.0%
Case D/E
2322
86.3%
New release : 21,578 genes
25.7Mb
Comparison of 2 Spodoptera strains: the genome of the Spodoptera frugiperda “rice variant” has been sequenced and assembled with Platanus, and
annotated with the help of Maker. The comparison of the two draft sequences leads to the identification of about 16,000 pairs of orthologous genes, and
thousands of segmental rearrangements (deletions, duplications or inversions).
www.inra.fr/bipaa
DGIMI