Cédric Cabau

Cédric Cabau
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Department of Animal Physiology and Livestock Systems

About

108
Publications
21,900
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,033
Citations
Introduction

Publications

Publications (108)
Article
Full-text available
Objective Causal mutations for major genes that underlie a broad range of morphological traits are often located within exons of genes that then affect protein functions. Non-model organism genetic studies are not easy to perform due to the lack of genome-wide molecular tools such as SNP genotyping array. Genotyping-By-Sequencing (GBS) methods offe...
Article
Full-text available
The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and pre...
Preprint
Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the to...
Article
Evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex‐determining genes identified. Pangasiids are economically important catfishes in South‐Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized th...
Preprint
Full-text available
The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex deter...
Article
Full-text available
Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chrom...
Article
Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.¹,² B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species³,⁴ that have often been considered as selfish genetic element...
Article
Full-text available
The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Cras- sostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were d...
Article
Full-text available
Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality tran...
Article
Full-text available
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the deca...
Article
Full-text available
Background: Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures b...
Article
Full-text available
Whole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to re...
Article
Full-text available
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chr...
Article
Full-text available
Siberian sturgeon, Acipenser baerii, is a commercially valuable fish for flesh and caviar production and a threatened species. We produced transcriptomic data for ten tissues with relevance to puberty, reproduction, early development, growth and food intake. The data includes RNA-Seq read sets of brain, pituitary, anterior-kidney, kidney, stomach,...
Preprint
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during v...
Preprint
Full-text available
Whole genome duplications (WGD) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to re...
Article
Full-text available
The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approa...
Article
Full-text available
Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture manage...
Article
Full-text available
Background: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-Ag...
Preprint
Full-text available
Background: Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures be...
Presentation
Characterization of neuroendocrine signalling systems during gametogenesis in the Pacific oyster, Crassostrea gigas Emilie Realis-Doyelle1, Julie Schwartz1, Cedric Cabau2, Christophe Klopp2, Marie-Pierre Dubos1, Guillaume Rivière1, Pascal Favrel1. 1 UMR BOREA, Normandie Université, UNICAEN, MNHN, CNRS-7208, IRD-207, Sorbonne Universités, Esplanade...
Preprint
Full-text available
Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquacu...
Presentation
Title of the communication: Characterization of neuroendocrine signalling systems during gametogenesis in the Pacific oyster, Crassostrea gigas Emilie Realis-Doyelle1, Julie Schwartz1, Cedric Cabau2, Christophe Klopp2, Marie-Pierre Dubos1, Guillaume Rivière1, Pascal Favrel1. 1 UMR BOREA, Normandie Université, UNICAEN, MNHN, CNRS-7208, IRD-207, Sorb...
Preprint
Full-text available
Background The genus Oryzias is constituted of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparati...
Article
Full-text available
Background The sustainability of poultry farming relies on the development of more efficient and autonomous production systems in terms of feed supply. This implies a better integration of adaptive traits in breeding programs, including digestive efficiency, in order to favor the use of a wider variety of feedstuffs. The aim of the project was to i...
Preprint
Full-text available
Background Functional annotation of livestock genomes is a critical step to decipher the genotype-to-phenotype relationship underlying complex traits. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project ( http://www.fragencode.org ) aimed to profile the landscape of transcription (RNA-seq), chromatin acces...
Article
Whole-genome duplications (WGDs) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however, remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of...
Preprint
Full-text available
Whole genome duplications (WGD) are important evolutionary events. Our understanding of underlying mechanisms, including the evolution of duplicated genes after WGD, however remains incomplete. Teleost fish experienced a common WGD (teleost-specific genome duplication, or TGD) followed by a dramatic adaptive radiation leading to more than half of a...
Article
Full-text available
Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error co...
Data
Details about consensus error rates
Data
Additional descriptions and validations
Data
Default command lines of DRAP third party tools
Article
Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error co...
Article
Full-text available
Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error co...
Article
Full-text available
With more than 30,000 species, ray-finned fish represent approximately half of vertebrates. The evolution of ray-finned fish was impacted by several whole genome duplication (WGD) events including a teleost-specific WGD event (TGD) that occurred at the root of the teleost lineage about 350 million years ago (Mya) and more recent WGD events in salmo...
Article
Full-text available
[This corrects the article DOI: 10.1371/journal.pone.0086227.].
Article
Full-text available
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model...
Article
FOXL2 loss-of-function in goats leads to the early trans-differentiation of ovaries into testes, then to the full sex-reversal of XX homozygous mutants. By contrast, Foxl2 loss of function in mice induces an arrest of follicle formation after birth, followed by complete female sterility. In order to understand the molecular role of FOXL2 during ova...
Article
Full-text available
Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and...
Article
Full-text available
Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due to an additional round of WGD, the rainbow trout genome offers a unique opportunity to investigate the early evolutionary fate of a duplicated vertebrate geno...
Article
Full-text available
The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate...
Article
Full-text available
Successful early folliculogenesis is crucial for female reproductive function. It requires appropriate gene specific expression of the different types of ovarian cells at different developmental stages. To date, most gene expression studies on the ovary were conducted in rodents and did not distinguish the type of cell. In mono-ovulating species, f...
Article
Full-text available
Not much is known about the molecular and functional features of pluripotent stem cells (PSCs) in rabbits. To address this, we derived and characterized 2 types of rabbit PSCs from the same breed of New Zealand White rabbits: 4 lines of embryonic stem cells (rbESCs), and 3 lines of induced PSCs (rbiPSCs) that were obtained by reprogramming adult sk...
Article
Pluripotent stem cells (PSCs) can exist in at least two morphologically, molecularly and functionally distinct pluripotent states, designated as the naïve and primed states; PSC exist in both states in rodents, whereas only the primed stated has been described in primates so far. Not much is known about the pluripotent state of PSCs in rabbits. To...
Article
Full-text available
Background As for other non-model species, genetic analyses in quail will benefit greatly from a higher marker density, now attainable thanks to the evolution of sequencing and genotyping technologies. Our objective was to obtain the first genome wide panel of Japanese quail SNP (Single Nucleotide Polymorphism) and to use it for the fine mapping of...
Data
Figure S2. Distribution of the trait in both AIL populations. TI : Tonic Immobility.
Data
Table S2. List of the genes localized in the candidate interval. Source : Biomart, Ensembl Genes 61 (Sanger UK), Gallus Gallus Genes (WASHUCS52).
Data
Figure S3. Quail in a tonic immobility state. Immobilization is induced by keeping the animal on its back in a U-shaped cradle for 10 seconds.
Data
Figure S1. Distribution of the functional annotation of the detected SNP (log scale). Annotations are from the Ensembl APIs (Application Programme Interface): the functional consequence of each SNP in each transcript has been predicted using the Variant Effect Predictor (VEP). All the non intergenic consequences are represented.
Data
Table S1. List of the 384 SNP used in this study.
Article
Full-text available
Background Most egg yolk precursors are synthesized by the liver, secreted into the blood and transferred into oocytes, to provide nutrients and bioactive molecules for the avian embryo. Three hundred and sixteen distinct proteins have been identified in egg yolk. These include 37 proteases and antiproteases, which are likely to play a role in the...
Article
Since the discovery of Sry in mammals [1, 2], few other master sex-determining genes have been identified in vertebrates [3-7]. To date, all of these genes have been characterized as well-known factors in the sex differentiation pathway, suggesting that the same subset of genes have been repeatedly and independently selected throughout evolution as...
Article
Full-text available
Background There is considerable interest in developing high-throughput genotyping with single nucleotide polymorphisms (SNPs) for the identification of genes affecting important ecological or economical traits. SNPs are evenly distributed throughout the genome and are likely to be functionally relevant. In rainbow trout, in silico screening of EST...
Data
Minor sequence frequencies, heterozygosity and PIC values were indicated for all SNPs in the INRA Sigenae database (worksheet 1) and for the validation panel (worksheet 2). Allele frequencies were calculated by direct count of sequence depth for each allele, expected heterozygosities per locus (He) were estimated by He = 2pq and PIC values were est...
Data
Illumina quality design scores for the validation panel.
Data
INRA rainbow trout linkage maps. Newly integrated SNPs were highlighted in red.