Philippe Rigault

Philippe Rigault
Gydle Inc. · Department of Bioinformatics

Ingénieur de l'École Centrale de Paris (M.Sc.Eng.)

About

130
Publications
20,937
Reads
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6,379
Citations
Additional affiliations
May 2008 - present
Gydle Inc.
Position
  • Founder and CEO
July 2004 - December 2008
Centre de Recherche du CHUL/CHUQ, Université Laval, Québec, CANADA
Position
  • Researcher, Professeur Associé, Director of bioinformatics platform
January 2001 - June 2004
Illumina
Position
  • Director of Bioinformatics
Education
September 1988 - July 1991
CentraleSupélec
Field of study
  • Engineering & Bioengineering

Publications

Publications (130)
Article
A continuous array of overlapping clones covering the entire human chromosome 21q was constructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of...
Article
Full-text available
Excerpt The genetic factors underlying common disease arelargely unknown. Discovery of disease-causing genes willtransform our knowledge of the genetic contribution tohuman disease, lead to new genetic screens, and underpinresearch into new cures and improved lifestyles. The sequencing of the human genome has catalyzed efforts tosearch for disease...
Article
Full-text available
Several angiosperm plant genomes, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), and grapevine (Vitis vinifera), have been sequenced, but the lack of reference genomes in gymnosperm phyla reduces our understanding of plant evolution and restricts the potential impacts of genomics research. A gene ca...
Article
Full-text available
Eucalypts are the world’s most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest p...
Article
A yeast artificial chromosome library containing 33,000 clones with an average insert size of one megabase of human genomic DNA was extensively analysed by several different procedures for detecting overlaps and positional information. We developed an analysis strategy that resulted, after confirmatory tests, in a YAC contig map reliably covering a...
Article
Full-text available
The evolutionary trajectory of a population both influences and is influenced by characteristics of its genome. A disjunct population, for example is likely to exhibit genomic features distinct from those of continuous populations, reflecting its specific evolutionary history and influencing future recombination outcomes. We examined genetic divers...
Article
Full-text available
Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has...
Article
Full-text available
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myriad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of poole...
Preprint
Full-text available
Cannabis sativa L. is an important yet controversial plant with a long history of recreational, medicinal, industrial, and agricultural use, and together with its sister genus Humulus, it represents a group of plants with a myr-iad of academic, agricultural, pharmaceutical, industrial, and social interests. We have performed a meta-analysis of pool...
Article
Full-text available
The NLRs or NBS-LRRs (nucleotide-binding, leucine-rich-repeat) form the largest resistance gene family in plants, with lineage-specific contingents of TNL, CNL and RNL subfamilies and a central role in resilience to stress. The origin, evolution and distribution of NLR sequences has been unclear owing in part to the variable size and diversity of t...
Article
Full-text available
Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combi...
Article
Full-text available
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly e...
Preprint
Full-text available
Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results Using chromosome 7A of wheat as a model, sequence-finished megabase scale sections of this chromosome were established by combining...
Article
Full-text available
Background At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. Yet the status of these regions as refuge areas with naturally existing populations has be...
Article
Full-text available
GK-G, PR, JT contributed equally to experimental design, data analysis andinterpretation/writing of manuscript;, RP, MH, KF, RA genome analyses andinterpretation; ZF, AK data analysis and physical map construction; EH, CC, JTMAGIC map construction; MA rice-wheat phylogenomic; AS, DK, mate-pairlibraries; PS. BD, FC, PL, Chinese Spring x Renan molecu...
Article
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly e...
Article
Temperatures are expected to increase over the next century in all terrestrial biomes and particularly in boreal forests, where drought-induced mortality has been predicted to rise. Genomics research is helping to develop hypotheses regarding the molecular basis of drought tolerance and recent work proposed that the osmo-protecting dehydrin protein...
Article
Full-text available
Background Climatic and edaphic conditions over geological timescales have generated enormous diversity of adaptive traits and high speciation within the genus Eucalyptus (L. Hér.). Eucalypt species occur from high rainfall to semi-arid zones and from the tropics to latitudes as high as 43°S. Despite several morphological and metabolomic characteri...
Poster
Full-text available
Background: RuBisCo, the key enzyme in fixation of carbon dioxide in photosynthetic organisms, is particularly interesting from an evolutionary point of view as both nuclear and organellar genomes co-operate to encode the holoenzyme. Because of its crucial role in Calvin Cycle of photosynthesis, the protein has been hypothesized to undergo fine-tun...
Article
Full-text available
Next-generation sequencing technologies provide new opportunities to identify the genetic components responsible for trait variation. However, in species with large polyploid genomes, such as bread wheat, the ability to rapidly identify genes underlying quantitative trait loci (QTL) remains non-trivial. To overcome this, we introduce a novel pipeli...
Article
Full-text available
A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be desc...
Article
We present a phylogenetic analysis and comparison of structural features of chloroplast genomes for 39 species of the eucalypt group (genera Eucalyptus, Corymbia, Angophora, and outgroups Allosyncarpia and Stockwellia). We use 41 complete chloroplast genome sequences, adding 39 finished-quality chloroplast genomes to two previously published genome...
Article
High-density SNP genotyping arrays can be designed for any species given sufficient sequence information of high quality. Two high-density SNP arrays relying on the Infinium iSelect technology (Illumina) were designed for use in the conifer white spruce (Picea glauca). One array contained 7338 segregating SNPs representative of 2814 genes of variou...
Conference Paper
The Eucalyptus grandis (Brasuz1) genome sequence was a milestone in the acceleration of eucalyptus genomics. Here we report novel methods and tools for the analysis of highly diverse genomes, together with their applications across eucalypts. We present Gydle software that enables the direct assembly of Illumina reads into finished-quality complet...
Article
Full-text available
Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the s...
Data
Parameters of the composite genus-level spruce gene linkage map.
Data
Full-text available
Gene ontology distribution. Gene ontology terms assigned to the 1,801 mapped spruce genes at the level 3 of the (A) molecular functions and (B) biological processes. Only categories including five genes or more are represented.
Data
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Conservation between the chromosomes from Picea and Pinus taeda or Pinus pinaster.
Data
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Coordinates and annotation of the conserved genes found on homoeologous Picea and Pinus chromosomes.
Data
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Unrooted majority-rule bootstrap trees obtained with the neighbour-joining (NJ) and the maximum parsimony (MP) methods for 157 gene families of seed plants.
Data
Full-text available
Parameters of expanded main gene linkage map for white spruce.
Data
Gene families and number of genes mapped on the spruce genome for each family.
Data
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Over-representation of gene ontology classes in the gene arrays based on Fisher exact tests.
Data
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Composite spruce gene linkage map. This composite linkage map consisted of 1,801 genes, including 1,743 genes from white spruce and 58 genes from black spruce, positioned onto the 12 linkage groups corresponding to the 12 spruce chromosomes. Genes highlighted in grey were positioned on both spruce genomes and genes written in red were positioned on...
Data
Gene position along the spruce chromosomes, accessions, sequence and annotation.
Data
Full-text available
Over-representation of gene ontology classes in the gene-rich regions based on Fisher exact tests.
Data
Full-text available
Cluster of co-localizing genes: annotation and expression. We collected expression data from a transcriptomic database covering eight tissues and including mature xylem, juvenile xylem, phelloderm (including phloem), young needles, vegetative buds, megagametophytes, adventitious roots and embryogenic cells [30]. A level of expression was assigned t...
Data