The genome of black raspberry ( Rubus occidentalis ), Plant J, vol.87, pp.535-547, 2016. ,
Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity, Gigascience, vol.7, pp.1-7, 2018. ,
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development, Nat. Genet, vol.49, pp.1099-1106, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01602554
Size does matter, Nat. Plants, vol.4, pp.859-860, 2018. ,
Genetic diversity of the genus Malus and implications for linkage mapping with SNPs, Tree Genet. Genomes, vol.7, pp.857-868, 2011. ,
Genome sequence and analysis of the tuber crop potato, Nature, vol.475, pp.189-195, 2011. ,
Sequencing the rice genome, Plant Cell, vol.12, 2000. ,
Structure and Architecture of the Maize Genome, PLANT Physiol, vol.139, pp.1612-1624, 2005. ,
The genome of the domesticated apple (Malus × domestica Borkh, Nat. Genet, vol.42, pp.833-839, 2010. ,
The genome of the pear (Pyrus bretschneideri Rehd ,
, Genome Res, vol.23, pp.396-408, 2013.
The Draft Genome Sequence of European Pear (Pyrus communis L, PLoS One, vol.9, p.92644, 2014. ,
Chromosome doubling of pear haploid plants and homozygosity Version postprint Comment citer ce document ,
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus assessment using isozyme and microsatellite markers, Euphytica, vol.123, pp.255-262, 2002. ,
A graphical representation of genetic and physical maps: the Marey map, Genomics, vol.11, pp.219-241, 1991. ,
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation, Genome Res, vol.27, pp.722-736, 2017. ,
Phased diploid genome assembly with single-molecule real-time sequencing, Nat. Methods, vol.13, pp.1050-1054, 2016. ,
The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution, Nat. Genet, vol.45, pp.487-494, 2013. ,
The Rosa genome provides new insights into the domestication of modern roses, Nat. Genet, vol.50, pp.772-777, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01798003
The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature, vol.449, pp.463-467, 2007. ,
, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana, Nature, vol.408, pp.796-815, 2000.
Engineering a software tool for gene structure prediction in higher organisms, Inf. Softw. Technol, vol.47, pp.965-978, 2005. ,
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants, BMC Genomics, vol.19, p.257, 2018. ,
ORCAE: online resource for community annotation of eukaryotes, Nat. Methods, vol.9, pp.1041-1041, 2012. ,
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes, Genome Biol, vol.14, p.134, 2013. ,
Apple whole genome sequences: recent advances and new prospects, Hortic. Res, vol.6, p.59, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02348055
Two methods of haploidization in pear, Pyrus communis L.: greenhouse seedling selection and in situ parthenogenesis induced by irradiated pollen, Theor. Appl. Genet, vol.87, pp.229-232, 1993. ,
Oryzalin as an Efficient Agent for Chromosome Doubling of Haploid Apple Shoots in vitro, Plant Breed, vol.113, pp.343-346, 1994. ,
Detection of Histone Modifications in Plant Leaves, J. Vis. Exp, 2011. ,
Prominent topologically associated domains differentiate global chromatin packing in rice from Arabidopsis, Nat. Plants, vol.3, pp.742-748, 2017. ,
KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies, Bioinformatics, vol.33, pp.574-576, 2017. ,
HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, vol.12, pp.357-360, 2015. ,
, EvidentialGene: mRNA Transcript Assembly Software. Available at, p.16, 2019.
BLAT---The BLAST-Like Alignment Tool, Genome Res, vol.12, pp.656-664, 2002. ,
Development of a highly efficient Axiom TM 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization ,
JoinMap® 4.0: software for the calculation of genetic linkage maps Version postprint Comment citer ce document ,
Pseudo-chromosome-length genome assembly of a double haploid, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-02563877
Fast gapped-read alignment with Bowtie 2, Nat. Methods, vol.9, pp.357-359, 2012. ,
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions, Nat. Biotechnol, vol.31, pp.1119-1125, 2013. ,
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler, Gigascience, vol.1, p.18, 2012. ,
Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome Biol, vol.15, p.46, 2014. ,
Repbase Update, a database of repetitive elements in eukaryotic genomes, Mob. DNA, vol.6, p.11, 2015. ,
,
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc, vol.8, pp.1494-1512, 2013. ,
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nat. Protoc, vol.7, pp.562-578, 2012. ,
Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol, vol.29, pp.644-652, 2011. ,
,
Using native and syntenically mapped cDNA alignments to improve de novo gene finding, Bioinformatics, vol.24, pp.637-644, 2008. ,
Genome Annotation in Plants and Fungi: EuGène as a Model Platform, Current Bioinformatics, vol.3, 2008. ,
SpliceMachine: predicting splice sites from high-dimensional local context representations, Bioinformatics, vol.21, pp.1332-1338, 2005. ,
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Res, vol.31, pp.5654-66, 2003. ,
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments, Genome Biol, vol.9, p.7, 2008. ,
Inference of Genome Duplications from Age Distributions Revisited, Mol. Biol. Evol, vol.30, pp.177-190, 2013. ,
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Syst. Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
An efficient algorithm for large-scale detection of protein families, Nucleic Acids Res, vol.30, pp.1575-84, 2002. ,
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1797, 2004. ,
A codon-based model of nucleotide substitution for proteincoding DNA sequences, Mol. Biol. Evol, vol.11, pp.725-761, 1994. ,
Phylogenetic Analysis by Maximum Likelihood, Mol. Biol. Evol, vol.4, pp.1586-1591, 2007. ,
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis, Nucleic Acids Res, vol.38, pp.196-203, 2010. ,
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol, vol.16, p.157, 2015. ,
MCScanX: a toolkit for detection and evolutionary analysis of gene Version postprint Comment citer ce document ,
Pseudo-chromosome-length genome assembly of a double haploid "Bartlett" pear (Pyrus synteny and collinearity, Nucleic Acids Res, vol.40, pp.49-49, 2012. ,
D-GENIES: dot plot large genomes in an interactive, efficient and simple way, PeerJ, vol.6, p.4958, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-02625819
, Comment citer ce document
Pseudo-chromosome-length genome assembly of a double haploid, Troggio, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02563877
Pseudo-chromosome-length genome assembly of a double haploid, Troggio, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02563877
Pseudo-chromosome-length genome assembly of a double haploid, Troggio, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02563877
Pseudo-chromosome-length genome assembly of a double haploid, Troggio, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02563877
, , 2019.