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PhyloFish specifications

Information


Unique identifier OMICS_32580
Name PhyloFish
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Julien Bobe

Publication for PhyloFish

PhyloFish citations

 (7)
library_books

De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species

2018
BMC Genomics
PMCID: 5759245
PMID: 29310597
DOI: 10.1186/s12864-017-4379-x

[…] ge and high quality of the assembly of the protein-coding transcriptomes for these species. We found that BUSCO recovery in the current assemblies was three times greater than that identified for the PhyloFish assembly of the corresponding species. For both the brown trout and European whitefish assemblies presented here, we recovered 78 and 76% of the BUSCOs completely, whereas only 26% of BUSCOs […]

library_books

De novo assembly and characterization of the Hucho taimen transcriptome

2017
Ecol Evol
PMCID: 5773338
PMID: 29375797
DOI: 10.1002/ece3.3735

[…] , ), zebrafish (Danio rerio) (Howe et al., ), and medaka (Oryzias latipes) (Kasahara et al., ). The transcript and protein sequences of brown trout, brook trout, and grayling were downloaded from the PhyloFish database (Pasquier et al., ). The eggNOG database (Huerta‐Cepas et al., ) was used to define the gene family, and eggNOG‐mapper was used to search the fiNOG dataset for orthologous groups (H […]

call_split

Evolutionary history of glucose 6 phosphatase encoding genes in vertebrate lineages: towards a better understanding of the functions of multiple duplicates

2017
BMC Genomics
PMCID: 5414149
PMID: 28464795
DOI: 10.1186/s12864-017-3727-1
call_split See protocol

[…] f rainbow trout g6pc genes and the genomic sequence of zebrafish g6pc (data not shown).Finally, tissue expression profiles of g6pc genes (Fig.  and Additional file : Figure S3) were identified in the PhyloFish database using the Blast tool []. In the case of ohnologs which possess highly similar sequences (such as g6pcb1a and g6pcb1b in trout; []), we considered fragments that included SNPs specif […]

call_split

Support for Lungfish as the Closest Relative of Tetrapods by Using Slowly Evolving Ray Finned Fish as the Outgroup

2017
Genome Biol Evol
PMCID: 5381532
PMID: 28082606
DOI: 10.1093/gbe/evw288
call_split See protocol

[…] ity or gaps were excluded. Genes of short length (<100 amino acids) were discarded.Next bowfin (Amia calva) data was added to data set I. The transcriptome data of the bowfin () was obtained from the PhyloFish database (http://phylofish.sigenae.org/). A Nucleotide BLAST search (r = 2, G = 2, E = 2, e-value cutoff of 1 × 10− 10) was performed with the bowfin contigs as the queries against the human […]

library_books

Sexually dimorphic gene expressions in eels: useful markers for early sex assessment in a conservation context

2016
Sci Rep
PMCID: 5034313
PMID: 27658729
DOI: 10.1038/srep34041

[…] Seven genes were selected based on a multi-tissue RNA-seq analysis originating from the PhyloFish project (http://phylofish.sigenae.org/index.html) that aimed at characterizing the transcriptome of 11 different tissues/organs in a wide variety of teleostean and holostean species, includi […]

library_books

Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database

2016
BMC Genomics
PMCID: 4870732
PMID: 27189481
DOI: 10.1186/s12864-016-2709-z

[…] n levels along the contigs in the different libraries. Expression data in the various libraries can be exported to generate expression profiles for the different tissues/organs. To our knowledge, the PhyloFish database is the only database that allows (i) the identification of contigs in such a large diversity of fish species, including many species with no or limited transcriptomic resources, and […]

Citations

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PhyloFish institution(s)
INRA, Laboratoire de Physiologie et Génomique des poissons, Campus de Beaulieu, Rennes, France; INRA, SIGENAE, GenPhySE, Castanet-Tolosan, France; INRA, SIGENAE, UR 875, MIAT INRA, Toulouse, France; CNRS, MGX-Montpellier GenomiX, Montpellier, France. 5 Aix-Marseille Université, CNRS, Centrale Marseille, I2M, UMR7373, Eccorev, équipe EBM, Marseille, France; Institute of Neuroscience, University of Oregon, Eugene, OR, USA; Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
PhyloFish funding source(s)
Supported by the French national research Agency (ANR-10-GENM-017–PhyloFish, ANR-13-BSV7-0015-Maternal Legacy, and ANR-13-ISV7-0005–PhyloSex) and by the National Institutes of Health (R01 OD011116 and R24 OD011199).

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