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EXAMPLES:

gene XLOC_000007
f7
RNA TCONS_00000019
bioproject PRJEB12982


  •   bowfin
    (Amia calva)
  •   eurasian perch
    (Perca fluviatilis)
  •   grass carp
    (Ctenopharyngodon idella)
  •   mexican tetra
    (Astyanax mexicanus)
  •   rainbow trout
    (Oncorhynchus mykiss)
  •   striped catfish
    (Pangasianodon hypophthalmus)
  •   tiger barb
    (Puntius tetrazona)
  •   zebrafish
    (Danio rerio)
  • simplified version

  •   bowfin
    (Amia calva)
  •   eurasian perch
    (Perca fluviatilis)
  •   grass carp
    (Ctenopharyngodon idella)
  •   mexican tetra
    (Astyanax mexicanus)
  •   rainbow trout
    (Oncorhynchus mykiss)
  •   striped catfish
    (Pangasianodon hypophthalmus)
  •   tiger barb
    (Puntius tetrazona)
  •   zebrafish
    (Danio rerio)
  • simplified version

Bioproject

  • Please select the sample of bioproject for visualization of expression.
  • Click on the node of the fold tree to expand the information about the bioproject and sample.
  • Check the sample checkbox for sample selection.
  • baseline
    • PRJNA659268:
          Amia calva developmental genomics
      • key word
        • baseline;APICAL ECTODERMAL RIDGE;TOLL-LIKE RECEPTORS;SPOTTED GAR;TRANSCRIPTION FACTORS;READ ALIGNMENT;SCPP GENES;VERTEBRATE;TRANSITION;EXPRESSION;CHROMATIN
      • publication
        • Thompson, A. , et al. "The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes." Nature Genetics.
      • abstract
        • Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR12613066 Amia_stage_26_fin_bud_mRNA_Pool_1 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1986).)
          SRR12613069 Amia_stage_25_fin_bud_mRNA_Pool_1 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1987).)
          SRR12613070 Amia_stage_24_fin_bud_mRNA_Pool_3 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1988).)
          SRR12613073 Amia_stage_23_fin_bud_mRNA_Pool_3 fin bud nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1989).)
          SRR12613082 Amia_stage_30-31_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1990).)
          SRR12613083 Amia_stage_28-29_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1991).)
          SRR12613084 Amia_stage_26-27_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1992).)
          SRR12613085 Amia_stage_24-25_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1993).)
          SRR12613088 Amia_stage_23-24_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1994).)
          SRR12613089 Amia_stage_22-23_embryo_mRNA whole embryo nan untreatment Morphological classification reference Ballard's research.(Ballard, W. W. Stages and rates of normal development in the holostean fish, Amia calva. J. Exp. Zool. 238, 337–354 (1986).)
    • PRJNA612482:
          In an effort to an accurate immune-transcriptome, RNA from spleen, gill, liver and gut were individually isolated and then pooled together in equal amounts prior to next-gen sequencing.
      • key word
        • baseline;APICAL ECTODERMAL RIDGE;TOLL-LIKE RECEPTORS;SPOTTED GAR;TRANSCRIPTION FACTORS;READ ALIGNMENT;SCPP GENES;VERTEBRATE;TRANSITION;EXPRESSION;CHROMATIN
      • publication
        • Thompson, A. , et al. "The genome of the bowfin (Amia calva) illuminates the developmental evolution of ray-finned fishes." Nature Genetics.
      • abstract
        • Analysis of a chromosome-level bowfin genome assembly sheds light into neopterygian fish evolution. Chromatin accessibility and gene expression profiling provides insight into bowfin embryonic development.The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR11303972 Bowfin-0039 spleen,liver,gill,gut wild type untreatment In an effort to an accurate immune-transcriptome, RNA from spleen, gill, liver and gut were individually isolated and then pooled together in equal amounts prior to next-gen sequencing.
    • PRJNA599026:
          The project is to study the oldest fish lineages in the ray-finned fishes. Although they belong to fish, their body structure and behavior remain highly similar to that of the tetrapods. Through comparative genome analysis with living vertebrates, we provides insights into the molecular basis of terrestrial adaptation of basal ray-finned fishes.
      • key word
        • baseline;[1]COMPARATIVE GENOME ANALYSIS;ACIPENSER-NACCARII HEART;CONUS ARTERIOSUS;PHYLOGENETIC ANALYSIS;LIMB TRANSITION;PECTORAL FIN;EVOLUTION;ORIGIN;LUNG;SEQUENCE;[2]mitogenome;actinopterygii;ancient fish;teleostei;taxonomic sampling;higher-level relationships;MITOCHONDRIAL-DNA SEQUENCE;COMPLETE NUCLEOTIDE-SEQUENCE;DEEP-SEA FISH;SPLICEOSOMAL INTRONS;VERTEBRATE EVOLUTION;MOLECULAR PHYLOGENY;GENE ORDER;GENOME;TELEOSTEI;INFERENCE
      • publication
        • [1]Bi X et al., "Tracing the genetic footprints of vertebrate landing in non-teleost ray-finned fishes.", Cell, 2021 Mar 4;184(5):1377-1391.e14;[2]Inoue JG et al., "Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish".", Mol Phylogenet Evol, 2003 Jan;26(1):110-20
      • abstract
        • [1]Rich fossil evidence suggests that many traits and functions related to terrestrial evolution were present long before the ancestor of lobe- and ray-finned fishes. Here, we present genome sequences of the bichir, paddlefish, bowfin, and alligator gar, covering all major early divergent lineages of ray-finned fishes. Our analyses show that these species exhibit many mosaic genomic features of lobe- and ray-finned fishes. In particular, many regulatory elements for limb development are present in these fishes, supporting the hypothesis that the relevant ancestral regulation networks emerged before the origin of tetrapods. Transcriptome analyses confirm the homology between the lung and swim bladder and reveal the presence of functional lung-related genes in early ray-finned fishes. Furthermore, we functionally validate the essential role of a jawed vertebrate highly conserved element for cardiovascular development. Our results imply the ancestors of jawed vertebrates already had the potential gene networks for cardio-respiratory systems supporting air breathing.[2]The basal actinopterygians comprise four major lineages (polypteriforms, acipenseriforms, lepisosteids, and Amia) and have been collectively called "ancient fish." We investigated the phylogeny of this group of fishes in relation to teleosts using mitochondrial genomic (mitogenomic) data, and compared this to the various alternative phylogenetic hypotheses that have been proposed previously. In addition to the previously determined complete mitochondrial DNA (mtDNA) sequences from 14 teleosts and two outgroups, we used newly determined mitogenomic sequences of 12 purposefully chosen species representing all the ancient fish lineages plus related teleosts. This data set comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding the ND6 gene and third codon positions) and 22 transfer RNA (tRNA) genes (stem regions only) and these data were subjected to maximum parsimony, maximum likelihood, and Bayesian analyses. The resultant trees from the three methods were well resolved and largely congruent, with most internal branches being supported by high statistical values. Mitogenomic data strongly supported not only the monophyly of the teleosts (osteoglossomorphs and above), but also a sister-group relationship between the teleosts and a clade comprising the acipenseriforms, lepisosteids, and Amia, with the polypteriforms occupying the most basal position in the actinopterygian phylogeny. Although the tree topology differed from any of the previously proposed hypotheses based on morphology, it exhibited congruence with a recently proposed novel hypothesis based on nuclear markers. (C) 2002 Elsevier Science (USA). All rights reserved.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR11149343 Bowfin_002 liver nan untreatment RNA-Seq of Amia calva : adult
    • PRJNA398732:
          Fish-T1K_Phylogeny Project
      • key word
        • baseline;Fish-T1K;Fish;Transcriptome;RNA;Database;Biodiversity
      • publication
        • Ying, S. , et al. "Fish-T1K (Transcriptomes of 1,000 Fishes) Project: Large-scale transcriptome data for fish evolution studies." Gigascience 5.1(2016).
      • abstract
        • Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in 'omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the "Transcriptomes of 1,000 Fishes" (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5997676 Amia calva gill nan untreatment Fish-T1K (Transcriptomes of 1000 fishes)_Phylogeny Project Raw sequence reads
    • PRJNA357627:
          Transcriptomes of developing jaws of vertebrates, sequenced for develelopmental study and phylotranscriptomic assessment of the vertebrate tree of life
      • key word
        • baseline;PLACENTAL MAMMAL PHYLOGENY;MOLECULAR CLOCK;MITOCHONDRIAL GENOMES;SQUAMATE TREE;DIVERSIFICATION;ORIGIN;ROOT;TURTLES;DIVERSITY;EVOLUTION
      • publication
        • Irisarri, I. , et al. "Phylotranscriptomic consolidation of the jawed vertebrate timetree." Nature Ecology & Evolution (2017).
      • abstract
        • Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on 'standards' for data selection, curation and tree inference. We use jawedvertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accurate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance oflarge, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR5114777 ROSC3 developing tissue from jaw/mandible nan untreatment Transcriptomes of developing jaws of vertebrates, sequenced for develelopmental study and phylotranscriptomic assessment of the vertebrate tree of life
    • PRJNA292033:
          Vertebrate phototransduction represents the best understood example of response activation in a G protein cascade. Not only have the protein components been characterised comprehensively, but in addition the molecular mechanisms that mediate high amplification and rapid response kinetics are understood in sufficient detail to predict the onset phase of the response to light absorption. Although the phylogeny of the phototransduction proteins has been studied extensively in jawed vertebrates (gnathostomes), there is a paucity of information about the corresponding proteins in the jawless branch of vertebrates (agnathans), from which gnathostomes diverged around 500 million years ago. The only surviving jawless vertebrates are lampreys (around 40 species) and hagfish (around 80 species). We have applied high-throughput sequencing to eye tissue from one species of hagfish, two species of lamprey and five species of gnathostome fish, to obtain mRNA sequences for the components of the phototransduction cascade
      • key word
        • baseline;phototransduction;rhodopsin;transducin;phosphodiesterase;cyclic nucleotide-gated channel;VISUAL PIGMENTS;GAF DOMAINS;ROD;PHOTORECEPTORS;SENSITIVITY;VISION;OPSINS;GENES;DUPLICATION;DETERMINANT
      • publication
        • Lamb, T. D. , and D. M. Hunt . "Evolution of the vertebrate phototransduction cascade activation steps." Developmental Biology (2017):S0012160616308326.
      • abstract
        • We applied high-throughput sequencing to eye tissue from several species of basal vertebrates (a hagfish, two species of lamprey, and five species of gnathostome fish), and we analyzed the mRNA sequences for the proteins underlying activation of the phototransduction cascade. The molecular phylogenies that we constructed from these sequences are consistent with the 2R WGDmodel of two rounds of whole genome duplication. Our analysis suggests that agnathans retain an additional representative (that has been lost in gnathostomes) in each of the gene families we studied; the evidence is strong for the G-protein a subunit (GNAT) and the cGMP phosphodiesterase (PDE6), and indicative for the cyclic nucleotide-gated channels (CNGA and CNGB). Two of the species (the hagfish Eptatretus cirrhatus and the lamprey Mordacia mordax) possess only a single class of photoreceptor, simplifying deductions about the composition of cascade protein isoforms utilized in their photoreceptors. For the other lamprey, Geotria australis, analysis of the ratios of transcript levels in downstream and upstream migrant animals permits tentative conclusions to be drawn about the isoforms used in four ofthe five spectral classes of photoreceptor. Overall, our results suggest that agnathan rod-like photoreceptors utilize the same GNAT1 as gnathostomes, together with a homodimeric PDE6 that may be agnathanspecific, whereas agnathan cone-like photoreceptors utilize a GNAT that may be agnathan-specific, together with the same PDE6C as gnathostomes. These findings help elucidate the evolution of the vertebrate phototransduction cascade from an ancestral chordate phototransduction cascade that existed prior to the vertebrate radiation.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR2146931 AMICA1 retina nan untreatment Evolution of the activation steps in the vertebrate phototransduction cascade analysed using agnathan eye transcriptomes
    • PRJNA255850:
          Transcriptome analysis of 10 bowfin tissues
      • key word
        • baseline;Gene duplication;TeleostsHolostean;Gene expression;Gar;Salmonids;Assembly;Stra8;Mcam;SPOTTED GAR;DIVERSIFICATION;RESOLUTION;PHYLOGENY;STRA8;CD146;TIME
      • publication
        • Pasquier, J. , et al. "Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. " Bmc Genomics 17.1(2016):368.
      • abstract
        • 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 salmonids, carps, suckers and others. In plants and animals, WGD events are associated with adaptive radiations and evolutionary innovations. WGD-spurred innovation may be especially relevant in the case of teleost fish, which colonized a wide diversity of habitats on earth, including many extreme environments. Fish biodiversity, the use of fish models for human medicine and ecological studies, and the importance of fish in human nutrition, fuel an important need for the characterization of gene expression repertoires and corresponding evolutionary histories of ray-finned fish genes. To this aim, we performed transcriptome analyses and developed the PhyloFish database to provide (i) de novo assembled gene repertoires in 23 different ray-finned fish species including two holosteans (i.e. a group that diverged from teleosts before TGD) and 21 teleosts (including six salmonids), and (ii) gene expression levels in ten different tissues and organs (and embryos for many) in the same species. This resource was generated using a common deep RNA sequencing protocol to obtain the most exhaustive gene repertoire possible in each species that allows between-species comparisons to study the evolution of gene expression in different lineages. The PhyloFish database described here can be accessed and searched using RNAbrowse, a simple and efficient solution to give access to RNA-seq de novo assembled transcripts.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR1524261 A_Ac_2 brain nan untreatment Bowfin brain
          SRR1524262 A_Ac_3 gill nan untreatment Bowfin gills
          SRR1524263 A_Ac_4 heart nan untreatment Bowfin heart
          SRR1524264 A_Ac_5 muscle nan untreatment Bowfin muscle
          SRR1524265 A_Ac_6 liver nan untreatment Bowfin liver
          SRR1524266 A_Ac_7 kidney nan untreatment Bowfin kidney
          SRR1524267 A_Ac_8 bones nan untreatment Bowfin bones
          SRR1524268 A_Ac_9 intestine nan untreatment Bowfin intestine
          SRR1524269 A_Ac_12 ovary nan untreatment Bowfin ovary
          SRR1524270 A_Ac_13 testis nan untreatment Bowfin testis

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Gene / RNA

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