Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

Jibran, Rubina; Dzierzon, Helge; Bassil, Nahla V.; Bushakra, Jill M.; Edger, Patrick P.; Sullivan, Shawn; Finn, Chad E.; Dossett, Michael; Vining, Kelly J.; VanBuren, Robert; Mockler, Todd C.; Liachko, Ivan; Davies, Kevin; Foster, Toshi; Chagné, David

doi:10.1038/s41438-017-0013-y

Cited by 48 publications

(48 citation statements)

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“…The PacBio-based contigs were assembled into scaffolds and then into pseudomolecules using Hi-C and Proximity-Guided Assembly. This approach was previously used by Jibran et al [ 11 ] to cluster and order 9,650 of the 11,936 V1 black raspberry contigs into seven pseudomolecules spanning 223.8 Mb (97.3% of the assembly). The Illumina-based Hi-C data from Jibran et al [ 11 ] was remapped to the PacBio assembly and clustered into seven pseudomolecules using the Proximo Hi-C scaffolding pipeline (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The black raspberry genome was sequenced using an NGS-based approach, yielding a fragmented but much needed draft assembly [ 10 ]. This draft was anchored into a chromosome-scale assembly using a high-throughput chromatin conformation capture (Hi-C)-based scaffolding approach [ 11 ]. However, the reference used for scaffolding is ∼50 Mb smaller than the estimated genome size and is likely missing important genomic features.…”

Section: Introductionmentioning

confidence: 99%

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A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

et al. 2018

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BackgroundThe fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies.FindingsHere, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis.ConclusionsThe improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

et al. 2018

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“…Additionally, Hi-C technology captures chromatin interactions within the nucleus, which can be used to infer the location of unanchored contigs and, thus, help to reconstruct haplotypes at the chromosomal level. Recently, several high-quality plant genomes have been obtained by using PacBio sequencing and Hi-C technologies [11][12][13] .…”

Section: Introductionmentioning

confidence: 99%

The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution

2020

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Salix suchowensis is an early-flowering shrub willow that provides a desirable system for studies on the basic biology of woody plants. The current reference genome of S. suchowensis was assembled with 454 sequencing reads. Here, we report a chromosome-scale assembly of S. suchowensis generated by combining PacBio sequencing with Hi-C technologies. The obtained genome assemblies covered a total length of 356 Mb. The contig N50 of these assemblies was 263,908 bp, which was~65-fold higher than that reported previously. The contiguity and completeness of the genome were significantly improved. By applying Hi-C data, 339.67 Mb (95.29%) of the assembled sequences were allocated to the 19 chromosomes of haploid willow. With the chromosome-scale assembly, we revealed a series of major chromosomal fissions and fusions that explain the genome divergence between the sister genera of Salix and Populus. The more complete and accurate willow reference genome obtained in this study provides a fundamental resource for studying many genetic and genomic characteristics of woody plants.

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“…The approaches generally taken nowadays combines long read sequencing technologies together with technologies providing medium to long range distance information, such as optical and chromatin interaction mapping [35,36]. In most of the cases however, with some notable exceptions [37][38][39], chromosome scale contiguity is not achieved without the help of other mapping information such as genetic mapping [7,40,41]. The challenge lies in the large spectrum of the contiguity information needed, from reads to chromosomes.…”

Section: Discussionmentioning

confidence: 99%

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

Rao

Vignal

Morisson

et al. 2019

Preprint

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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.

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Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

Cited by 48 publications

References 36 publications

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome

The chromosome-scale assembly of the willow genome provides insight into Salicaceae genome evolution

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

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