Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)

@article{Linsmith2019PseudochromosomelengthGA,
  title={Pseudo-chromosome–length genome assembly of a double haploid “Bartlett” pear (Pyrus communis L.)},
  author={Gareth Linsmith and Stephane Rombauts and Sara Montanari and Cecilia Hong Deng and Jean Marc Celton and Philippe Gu{\'e}rif and Chang Liu and Rolf Lohaus and Jason D. Zurn and Alessandro Cestaro and Nahla V. Bassil and Linda V. Bakker and Elio G. W. M. Schijlen and Susan E Gardiner and Yves Lespinasse and C. E. Durel and Riccardo Velasco and David B. Neale and David Chagn{\'e} and Yves van de Peer and Michela Troggio and Luca Di Bianco},
  journal={GigaScience},
  year={2019},
  volume={8}
}
We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87… 

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

This is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

Chromosome-level draft genome of a diploid plum (Prunus salicina)

This work constructed the first high-quality chromosome-level plum genome using Pacific Biosciences, Illumina, and Hi-C technologies, which provides a valuable resource for facilitating plum breeding programs and studying the genetic diversity mechanisms of plums and Prunus species.

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

Haplotype-resolved genome assembly of the tetraploid potato cultivar ‘Otava’ sheds light on functional organization of the Tetraploids genome and provides the potential for genomics-assisted breeding.

High-quality genome assembly of 'Cuiguan' pear (Pyrus pyrifolia) as a reference genome for identifying regulatory genes and epigenetic modifications responsible for bud dormancy

The repressive effects of DAM genes on bud break are determined using a virus-induced gene silencing system and provide a foundation for the practical regulation of dormancy release in fruit trees as an adaptation to climate change.

Chromosome Level Assembly of Homozygous Inbred Line ‘Wongyo 3115’ Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria × ananassa)

The chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line is generated and a linkage map constructed to identify QTLs associated with fruit firmness.

Phased diploid genome assemblies and pan-genomes provide insights into the genetic history of apple domestication

The haplotype-resolved genomes of the cultivated apple and its two major wild progenitors are reported and it is revealed that introgression of new genes/alleles is a hallmark of apple domestication through hybridization.

High quality genome sequence reveals the 12 pseudo-chromosomes of Ganoderma boninense

This work reports the first report of chromosomal-scale genome assembly for the most important fungal pathogen on oil palm, Ganoderma boninense.

Genetic mapping of a locus controlling the intergeneric hybridization barrier between apple and pear

A hybridization barrier between apple and pear belonging to different genera in the subtribe Malinae of the family Rosaceae is detected, implying there is a distinct cross-(in)compatibility reaction occurring in Pyrus species.

Transposon insertions regulate genome‐wide allele‐specific expression and underpin flower colour variations in apple (Malus spp.)

The importance of TEs in regulating ASE on a genome‐wide scale is demonstrated and a novel method for rapid identification of ASE genes and their regulatory elements in plants is presented.

References

SHOWING 1-10 OF 65 REFERENCES

The Draft Genome Sequence of European Pear (Pyrus communis L. ‘Bartlett’)

Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple.

The genome of the pear (Pyrus bretschneideri Rehd.)

The draft genome of the pear using a combination of BAC-by-BAC and next-generation sequencing is reported, and size differences between the apple and pear genomes are confirmed mainly due to the presence of repetitive sequences predominantly contributed by transposable elements (TEs), while genic regions are similar in both species.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity

A near-complete genome of diploid woodland strawberry (Fragaria vesca) is reported using single-molecule real-time sequencing from Pacific Biosciences and how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions is demonstrated.

The genome of the domesticated apple (Malus × domestica Borkh.)

It is shown that a relatively recent (>50 million years ago) genome-wide duplication has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae, which partly support the monophyly of the ancestral paleohexaploidy of eudicots.

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

Comparisons showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.

Phased diploid genome assembly with single-molecule real-time sequencing

The open-source FALCON and FALcon-Unzip algorithms are introduced to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes.

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

High-quality de novo assembly of the apple genome is produced and genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

The Rosa genome provides new insights into the domestication of modern roses

The rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication and a model of interconnected regulation of scent and flower color are proposed, providing a foundation for understanding the mechanisms governing rose traits.

Genome sequence and analysis of the tuber crop potato

The potato genome sequence provides a platform for genetic improvement of this vital crop and predicts 39,031 protein-coding genes and presents evidence for at least two genome duplication events indicative of a palaeopolyploid origin.

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla

A high-quality draft of the genome sequence of grapevine is obtained from a highly homozygous genotype, revealing the contribution of three ancestral genomes to the grapevine haploid content and explaining the chronology of previously described whole-genome duplication events in the evolution of flowering plants.
...