The impact of next-generation sequencing technology on genetics, Trends Genet, vol.24, pp.133-174, 2008. ,
Harnessing genomics for evolutionary insights, Trends Ecol. Evol. (Amst.), vol.24, pp.192-200, 2009. ,
Next-generation biology: sequencing and data analysis approaches for non-model organisms, Mar. Genomics, vol.30, pp.3-11, 2016. ,
RNA-seq: a method for comprehensive transcriptome analysis, Curr. Protoc. Mol. Biol, vol.4, pp.1-13, 2010. ,
A survey of best practices for RNA-seq data analysis, Genome Biol, vol.17, p.13, 2016. ,
RNA-seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet, vol.10, pp.57-63, 2009. ,
RNA sequencing: advances, challenges and opportunities, Nat. Rev. Genet, vol.12, pp.87-98, 2011. ,
Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics, Mol. Biol. Evol, vol.26, pp.2731-2775, 2009. ,
Applications of next generation sequencing in molecular ecology of non-model organisms, Heredity (Edinburgh), vol.107, pp.1-15, 2011. ,
Life-history evolution and mitogenomic phylogeny of caecilian amphibians, Mol. Phylogenet. Evol, vol.73, pp.177-89, 2014. ,
, Caecilians, Curr. Biol, vol.22, p.668, 2012.
A nine-family classification of caecilians (Amphibia: Gymnophiona), Evol. Biol, vol.41, pp.528-64, 2014. ,
Discovery of a new family of amphibians from northeast India with ancient links to Africa, Proc. Biol. Sci, vol.279, pp.2396-401, 2012. ,
Amphibian Species of the World: Version 6.0. AMNH, 2016. ,
Global patterns of diversification in the history of modern amphibians, Proc. Natl. Acad. Sci. USA, vol.104, pp.887-92, 2007. ,
Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes, Mol. Phylogenet. Evol, vol.53, pp.492-508, 2009. ,
A multilocus timescale for the origin of extant amphibians, Mol. Phylogenet. Evol, vol.56, pp.554-61, 2010. ,
Divergence time estimation using fossils as terminal taxa and the origins of lissamphibia, Syst. Biol, vol.60, pp.466-81, 2011. ,
An updated paleontological timetree of lissamphibians, with comments on the anatomy of Jurassic crown-group salamanders (Urodela), J. Hist. Biol, vol.26, pp.535-50, 2014. ,
RNA integrity number (RIN)-standardization of RNA quality control application, Agil. Appl. Note, pp.5989-1165, 2016. ,
Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-867, 2011. ,
FastQC: a quality control tool for high throughput sequence data, 2010. ,
Base-calling of automated sequencer traces using phred. I. Accuracy assessment, Genome Res, vol.8, pp.175-85, 1998. ,
TRUFA: a user-friendly web server for de novo RNA-seq analysis using cluster computing, Evol. Bioinform. Online, vol.11, pp.97-104, 2015. ,
Full-length transcriptome assembly from RNA-seq data without a reference genome, Nat. Biotechnol, vol.29, pp.644-52, 2011. ,
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis, Nat. Protoc, vol.8, pp.1494-512, 2013. ,
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, p.25, 2009. ,
The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2087, 2009. ,
HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-175, 2015. ,
Assessing de novo transcriptome assembly metrics for consistency and utility, BMC Genomics, vol.14, p.465, 2013. ,
Assembly, assessment, and availability of de novo generated eukaryotic transcriptomes, Front. Genet, vol.6, pp.1-9, 2016. ,
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes, Bioinformatics, vol.23, pp.1061-1068, 2007. ,
, Xenbase, the Xenopusmodel organism database; new virtualized system, data types and genomes, vol.43, pp.756-63, 2015.
Phylotranscriptomic consolidation of the jawed vertebrate timetree, Nat. Ecol. Evol, vol.1, pp.1370-1378, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01879160
Basic local alignment search tool, J. Mol. Biol, vol.215, pp.403-413, 1990. ,
EggNOG v4.0: nested orthology inference across 3686 organisms, Nucleic Acids Res, vol.42, pp.231-240, 2014. ,
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation, Bioinformatics, vol.23, pp.127-135, 2007. ,
CD-HIT: accelerated for clustering the next-generation sequencing data, Bioinformatics, vol.28, pp.3150-3152, 2012. ,
The axolotl genome and the evolution of key tissue formation regulators, Nature, vol.554, pp.50-55, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01874591
Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes, Proc. Natl. Acad. Sci. USA, vol.112, pp.1257-62, 2015. ,
The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA, Nat. Commun, vol.8, p.1433, 2017. ,
, R: A Language and Environment for Statistical Computing. R Found Stat Comput, 2016.
STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-52, 2015. ,
The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res, vol.44, pp.279-85, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01294685
HMMER: biosequence analysis using profile hidden Markov models, 2010. ,
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy, Genome Biol, vol.16, p.157, 2015. ,
MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol, vol.30, pp.772-80, 2013. ,
Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix, Mol. Biol. Evol, vol.26, pp.1641-50, 2009. ,
Phylogenetic mixture models for proteins, Philos. Trans. R Soc. Lond. B Biol. Sci, vol.363, pp.3965-76, 2008. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00365645
ASTRAL: genome-scale coalescent-based species tree estimation, Bioinformatics, vol.30, pp.541-549, 2014. ,
Fast coalescent-based computation of local branch support from quartet frequencies, Mol. Biol. Evol, vol.33, pp.1654-68, 2016. ,
Long non-coding RNAs: insights into functions, Nat. Rev. Genet, vol.10, pp.155-164, 2009. ,
Gene number expansion and contraction in vertebrate genomes with respect to invertebrate genomes, Genome Res, vol.18, pp.221-253, 2008. ,
Evolution by gene loss, Nat. Rev. Genet, vol.17, pp.379-91, 2016. ,
, Therapy of Skin Diseases: A Worldwide Perspective on Therapeutic Approaches and Their Molecular Basis, pp.3-14, 2010.
, Biology of Amphibians, 1994.
The natural history of amphibian skin secretions, their normal functioning and potential medical applications, Biol. Rev. Camb. Philos. Soc, vol.72, pp.365-79, 1997. ,
Cutaneous granular glands and amphibian venoms, Comp. Biochem. Physiol. A: Physiol, vol.111, pp.1-29, 1995. ,
Granular gland transcriptomes in stimulated amphibian skin secretions, Biochem. J, vol.371, pp.125-155, 2003. ,
The toad, ugly and venomous, wears yet a precious jewel in his skin, Prog. Neurobiol, vol.41, pp.473-507, 1993. ,
Identical skin toxins by convergent molecular adaptation in frogs, Curr. Biol, vol.20, pp.125-155, 2010. ,
Comparative transcriptome analyses of seven anurans reveal functions and adaptations of amphibian skin, Sci. Rep, vol.6, p.24069, 2016. ,
The first salamander defensin antimicrobial peptide, PLoS One, vol.8, p.83044, 2013. ,
Parental investment by skin feeding in a caecilian amphibian, Nature, vol.440, pp.926-935, 2006. ,
One hundred million years of skin feeding? Extended parental care in a Neotropical caecilian (Amphibia: Gymnophiona), Biol. Lett, vol.4, pp.358-61, 2008. ,
, Squamation in caecilians, with an atlas of scales, vol.49, pp.989-164, 1972.
Phallus morphology in caecilians (Amphibia, Gymnophiona) and its systematic utility, Bull. Nat. Hist. Museum Zool. Ser, vol.68, pp.143-54, 2002. ,
, Review of the reproductive biology of caecilians (Amphibia, Gymnophiona), vol.7, pp.191-202, 2012.
Functional and evolutionary implications of gene orthology, Nat. Rev. Genet, vol.14, pp.360-366, 2013. ,
Conservation biology of caecilian amphibians, Conserv. Biol, vol.19, pp.45-55, 2005. ,
, Genome 10K: a proposal to obtain whole-genome sequence for 10000 vertebrate species, Genome 10K Community of Scientists, vol.100, pp.659-74, 2009.
The Genome 10K Project: a way forward, Annu. Rev. Anim. Biosci, vol.3, pp.57-111, 2015. ,
, Sal-Site: integrating new and existing ambystomatid salamander research and informational resources, vol.6, p.181, 2005.
, Conservation genetics and genomics of amphibians and reptiles, vol.3, pp.113-151, 2015.