A duck RH panel and its potential for assisting NGS genome assembly

Rao, Man; Morisson, Mireille; Faraut, Thomas; Bardes, Suzanne; Fève, Katia; Labarthe, Emmanuelle; Fillon, Valérie; Huang, Yin; Li, Ning; Vignal, Alain

doi:10.1186/1471-2164-13-513

Cited by 31 publications

(37 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Another linkage group (how many scaffolds) is homologous to the region 9.9Mb to 19Mb of human chromosome 19 (HSA19) and should therefore correspond 7/22 to chicken chromosome 30 (Morisson et al, 2007). This result is consistent with our previous result by PCR-based genotyping [20].…”

Section: The Smallest Microchromosomessupporting

confidence: 94%

“…These scaffolds may be considered as putative chimeric scaffolds and the remaining 1,625 scaffolds as non-chimeric scaffolds. Chimeric scaffolds in the duck genome assembly had been already detected in [20]. The resulting maps were used to construct a pseudomolecule for each of the 29 chromosomes (see Materials and Methods).…”

Section: Map Construction and Pseudomoleculesmentioning

confidence: 99%

“…By taking advantage of rapid progress in NGS, we propose here an effective and high throughput method for assigning and ordering contigs/scaffolds onto chromosomes. A duck whole genome RH panel was previously developed [20], in the meantime, duck genome was sequenced using the Illumina Genome Analyzer II technology, providing a de novo genome assembly of 78,487 scaffolds with a N50 scaffold of 1.2Mb [21]. In order to bring this highly fragmented assembly to chromosome-scale contiguity we performed a survey sequencing (0.3X of duck specific sequences) of the 100 clones of the duck RH panel enabling to perform RH mapping using the scaffolds as markers.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

RH mapping by sequencing: chromosome-scale assembly of the duck genome

Rao

Vignal

Morisson

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

Like many other species, the duck genome has been sequenced thanks to the technological breakthrough provided by the emergence of Next Generation Sequencing (NGS). The resulting de novo assemblies are however made of thousands of scattered scaffolds. To achieve chromosome-scale contiguity, long-range intermediate genome maps remain indispensable. Radiation Hybrid (RH) maps have been used to assist the generation of chromosome-scale genome assemblies by taking advantage of the high density SNP chips that provide a large number of markers that can be efficiently genotyped on the panel.In the absence of such a resource in duck, we sequenced 100 hybrid clones of a duck RH panel enabling direct genotyping of the assembly scaffolds on the panel. The rationale is to use scaffolds as markers and to genotype the scaffolds by sequencing the clones: the presence/absence of a scaffold in a particular sequenced hybrid is attested by the presence/absence of reads mapping specifically to this scaffold. The detection of scaffolds exhibiting a chromosomal breakage resulting from the irradiation process revealed itself to be a critical issue of this genotyping by sequencing process. This process resulted in the construction of RH vectors for 2,027 scaffolds, representing a total of about 1 Gb of sequences (95% of the current Duck genome assembly). The subsequent linkage analysis enabled the construction of RH maps and therefore to organize, i.e. order and orient, the scaffolds into pseudomolecules associated to the corresponding duck chromosomes. We describe here the whole mapping process, from sequence-based genotyping to the construction of comparative maps, as well as few examples of intrachromosomal rearrangements that have been identified by the comparison with the chicken, turkey and zebra finch genomes and subsequently confirmed by FISH.We describe a method to order and orient sequence scaffolds into super-scaffolds spanning entire chromosomes. The method, which requires a pre-existing RH panel and sequence scaffolds from an NGS assembly, relies on a shallow sequencing of the RH clones. This approach was applied to the duck genome and produced chromosome-scale scaffolds for 29 out of the 41 duck chromosomes.

show abstract

Section: The Smallest Microchromosomessupporting

confidence: 94%

Section: Map Construction and Pseudomoleculesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

RH mapping by sequencing: chromosome-scale assembly of the duck genome

Rao

Vignal

Morisson

et al. 2019

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Pour le principe de la cartographie d'hybrides irradiés* (RH*), voir encadré 1. Plusieurs réarrangements intra-chromosomiques inédits entre les chromosomes de poule et de canard ont pu ainsi être mis en évidence (Rao et al 2012). Le principe de l'ordonnancement et de l'orientation des scaffolds*, basé sur la séquence de la poule, puis revu par cartographie RH* chez le canard est présenté dans la figure 4.…”

Section: / Assemblage En Chromosomesunclassified

“…Le principe de l'ordonnancement et de l'orientation des scaffolds*, basé sur la séquence de la poule, puis revu par cartographie RH* chez le canard est présenté dans la figure 4. Des cartes pour deux premiers chromosomes ont été réalisées par test classique de présence ou absence de fragments d'ADN courts (marqueurs) en PCR, tel que décrit dans l'encadré 1B (Rao et al 2012). Afin de réaliser des cartes pour l'ensemble du génome, la présence ou l'absence de fragments chromosomiques de canard est maintenant testée par séquençage des hybrides et alignement des séquences obtenues sur les scaffolds* de la séquence du génome.…”

Section: / Assemblage En Chromosomesunclassified

Génomique des canards

Vignal

Diot

Molette³

et al. 2013

INRA Prod. Anim.

View full text Add to dashboard Cite

Duck genomicsAs DNA sequencing throughputs increase and genomics becomes commonplace, more and more animal species are studied. Thus, the duck genome sequence was published recently. However, although this is an important step and will drastically increase our knowledge on the biology of this species, complementary projects are needed. Some have been initiated, amongst which SNP (Single Nucleotide Polymorphism) detection for population studies and management, radiation hybrid maps for ordering the sequence along chromosomes, genetic maps for QTL (Quantitative Trait Locus) detection and transcript sequencing for structural and functional annotation. The first QTL detection for traits influencing the performances of the mule duck, performed using microsatellite markers in the common duck, will be completed by a second study using specifically designed SNP, allowing for an improved coverage of the genome. Transcript and protein models constructed from the sequences will facilitate proteomics and transcriptomics studies. Génomique des canards / 401INRA Productions Animales, 2013, numéro 5The mule duck, the product of a cross between the common duck and the Muscovy duck, has an important agronomic interest for the foie gras industry and will also have to be studied. VIGNAL A., DIOT C., MOLETTE C., MORISSON M., FARAUT T., RAO M., PITEL F., FILLON V., MARIE-ETANCELIN C., 2013. Génomique des canards. In : Palmipèdes à foie gras. Fortun-Lamothe L. (Ed). Dossier, INRA Prod. Anim., 26,[391][392][393][394][395][396][397][398][399][400][401][402]

show abstract