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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.
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  • baseline
    • PRJNA605699:
          Individually indexed RNAseq data from liver, testis and ovary tissue of 4 different species (reptiles: Anolis carolinensis, Sceloporus undulatus; fish: Astyanax mexicanus and Clupea harengus).
      • key word
        • baseline;PRDM9;meiotic double strand breaks;phylogenetic;vertebrates;interdigitate across species;TEX15;ZCWPW1;ZCWPW2;double strand break repair
      • publication
        • Cavassim, Maria Izabel Alves , et al. "PRDM9 losses in vertebrates are coupled to the loss of at least three other meiotic genes." (2021).
      • abstract
        • In most mammals and likely throughout vertebrates, the gene PRDM9 specifies the locations of meiotic double strand breaks; in mice and humans at least, it also aids in their repair. For both roles, many of the molecular partners remain unknown. Here, we take a phylogenetic approach to identify genes that may be interacting with PRDM9, by leveraging the fact that PRDM9 arose before the origin of vertebrates, but was lost many times, either partially or entirely––and with it, its role in recombination. As a first step, we characterize PRDM9 domain composition across 379 vertebrate species, inferring at least eight independent losses. We then use the interdigitation of PRDM9 orthologs across vertebrates to test whether it co-evolved with any of 241 candidate genes co-expressed with PRDM9 in mice or associated with recombination phenotypes in mammals. Accounting for the phylogenetic relationship among species, we identify three genes whose presence and absence is unexpectedly coincident with that of PRDM9 : ZCWPW1 , which was recently shown to be recruited to sites of PRDM9 binding and to facilitate double strand break repair; TEX15 , which has also been suggested to play a role in repair; and ZCWPW2 , the paralog of ZCWPW1 . ZCWPW2 is expected to be recruited to sites of PRDM9 binding as well; its tight coevolution with PRDM9 across vertebrates suggests that it is a key interactor, with a role either in recruiting the recombination machinery or in double strand break repair. Author Summary Our understanding of meiotic recombination in mammals has seen great progress over the past 15 years, spurred in part by the convergence of lines of evidence from molecular biology, statistical genetics and evolutionary biology. We now know that in most mammals and likely in many vertebrates, the gene PRDM9 specifies the location of meiotic double strand breaks and that in mice and humans at least, it also aids in their repair. For both roles, however, many of the molecular partners remain unknown. To search for these, we take a phylogenetic approach, leveraging the fact that the complete PRDM9 has been lost at least eight times in vertebrates and thus that its presence is interdigitated across species. By this approach, we identify three genes whose presence or absence across vertebrates is significantly coupled to the presence or absence of PRDM9 : TEX15 , ZCWPW1 and the paralog of ZCWPW1 , ZCWPW2 . ZCWPW1 was recently shown to be recruited to sites of PRDM9 binding and to aid in the repair of double strand breaks. TEX15 has also been suggested to be involved in the repair process. ZCWPW2 is likely recruited to sites of PRDM9 binding; its tight coevolution with PRDM9 across vertebrates suggests that it plays an important role either in double strand break formation, potentially as the missing link that recruits the recombination machinery to sites of PRDM9 binding, or in double strand break repair.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR11050678 Sample_D01 male gonad surface nan untreatment RNA-seq of Astyanax mexicanus: male gonad surface
    • PRJEB15867:
          We found higher substitution rates in cavefish compared with surface fish, in accordance with a smaller cavefish population size which has allowed more rapid fixation of derived alleles present in the ancestral population. This result also implies that the Pachón cave population is much “younger” than previously estimated. The comparison of these data with simulations suggests that the Pachón cavefish population has probably been underground less than 30,000 years. This new time frame, together with other evidence, indicate that the evolution of cave phenotypes mainly involves the fixation of cryptic genetic variants present in surface fish populations within a short period of time.
      • key word
        • baseline;Cavefish;Adaptation;High-throughput sequencing;Microsatellites;SNPs;Molecular dating;EVOLUTIONARY GENETICS;BLIND CAVEFISH;CONVERGENT EVOLUTION;FASCIATUS CHARACIDAE;SURFACE-POPULATIONS;EYE LOSS;FISH;TELEOSTEI;DIVERGENCE;SIZES
      • publication
        • Fumey, J. , et al. "Evidence for late Pleistocene origin of Astyanax mexicanus cavefish." Bmc Evolutionary Biology 18.1(2018):43.
      • abstract
        • Background: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. Results: We reanalyzed the geographic distribution of mitochondria! and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachon cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years. Conclusions: Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.
      • sample list
        • sample id sample name tissue strain treatment description
          ERR1679845 E-MTAB-5142:ESF whole organism nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679848 E-MTAB-5142:Pa2_B brain nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679849 E-MTAB-5142:Pa2_OE olfactory epithelium nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679850 E-MTAB-5142:SF1_B brain nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679852 E-MTAB-5142:SF2_B brain nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679853 E-MTAB-5142:SF2_OE olfactory epithelium nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679846 E-MTAB-5142:Pa1_B brain nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679844 E-MTAB-5142:EPa whole organism nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679851 E-MTAB-5142:SF1_OE olfactory epithelium nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
          ERR1679847 E-MTAB-5142:Pa1_OE olfactory epithelium nan untreatment Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish
    • PRJNA285202:
          Transcriptome analysis of 11 tissues in Mexican tetra surface fish
      • key word
        • baseline;Gene duplication;Teleosts;Holostean;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 theimportance 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
          SRR2045426 S_Am_1 ovary surface fish untreatment Mexican tetra ovary
          SRR2045427 S_Am_2 brain surface fish untreatment Mexican tetra brain
          SRR2045428 S_Am_3 gills surface fish untreatment Mexican tetra gills
          SRR2045429 S_Am_4 heart surface fish untreatment Mexican tetra heart
          SRR2045430 S_Am_5 muscle surface fish untreatment Mexican tetra muscle
          SRR2045431 S_Am_6 liver surface fish untreatment Mexican tetra liver
          SRR2045432 S_Am_7 head kidney surface fish untreatment Mexican tetra kidney
          SRR2045433 S_Am_8 bones surface fish untreatment Mexican tetra bones
          SRR2045434 S_Am_9 intestine surface fish untreatment Mexican tetra intestine
          SRR2045435 S_Am_10 testis surface fish untreatment Mexican tetra testis
          SRR2045436 S_Am_11 embryos surface fish untreatment Mexican tetra embryo
    • PRJNA285201:
          Transcriptome analysis of 11 tissues in Mexican tetra Pachon cave fish
      • key word
        • baseline;Gene duplication;Teleosts;Holostean;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 theimportance 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
          SRR2045404 T_Am_12 ovary Pachon cave untreatment Mexican tetra ovary: Sample T_Am_12
          SRR2045405 T_Am_2 brain Pachon cave untreatment Mexican tetra brain: Sample T_Am_2
          SRR2045406 T_Am_3 gills Pachon cave untreatment Mexican tetra gills: Sample T_Am_3
          SRR2045407 T_Am_4 heart Pachon cave untreatment Mexican tetra heart: Sample T_Am_4
          SRR2045408 T_Am_5 muscle Pachon cave untreatment Mexican tetra muscle: Sample T_Am_5
          SRR2045409 T_Am_6 testis Pachon cave untreatment Mexican tetra testis: Sample T_Am_6
          SRR2045410 T_Am_7 head kidney Pachon cave untreatment Mexican tetra kidney: Sample T_Am_7
          SRR2045411 T_Am_8 bones Pachon cave untreatment Mexican tetra bones: Sample T_Am_8
          SRR2045412 T_Am_9 intestine Pachon cave untreatment Mexican tetra intestine: Sample T_Am_9
          SRR2045413 T_Am_13 testis Pachon cave untreatment Mexican tetra testis: Sample T_Am_13
          SRR2045414 T_Am_11 embryos Pachon cave untreatment Mexican tetra embryo: Sample T_Am_11
    • PRJNA545230:
          RNA sequencing of 2-cells eggs of Astyanax mexicanus (cavefish, surface fish and hybrids coming from reciprocal crosses) to compare maternally deposit RNAs and link them to the developmental variations observed between the two morphotypes.
      • key word
        • baseline;GERM-LAYER FORMATION;ONE-EYED-PINHEAD;BLIND CAVEFISH;PRECHORDAL PLATE;AXIAL MESENDODERM;AST
      • publication
        • Torres-Paz, J. , J. Leclercq , and S Rétaux. "Maternally-regulated gastrulation as a source of variation contributing to cavefish forebrain evolution." eLife Sciences 8(2019).
      • abstract
        • Sequential developmental events, starting from the moment of fertilization, are crucial for the acquisition of animal body plan. Subtle modifications in such early events are likely to have major impacts in later morphogenesis, bringing along morphological diversification. Here, comparing the blind cave and the surface morphotypes of Astyanax mexicanus fish, we found heterochronies during gastrulation that produce organizer and axial mesoderm tissues with different properties (including differences in the expression of dkk1b) that may have contributed to cavefish brain evolution. These variations observed during gastrulation depend fully on maternal factors. The developmental evolution of retinal morphogenesis and hypothalamic patterning are among those traits that retained significant maternal influence at larval stages. Transcriptomic analysis of fertilized eggs from both morphotypes and reciprocal F-1 hybrids showed a strong and specific maternal signature. Our work strongly suggests that maternal effect genes and developmental heterochronies that occur during gastrulation have impacted morphological brain change during cavefish evolution.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR9141190 Hybrid CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid cavefish: 2-cells stage Replicate 2
          SRR9141191 Hybrid CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid cavefish: 2-cells stage Replicate 3
          SRR9141192 SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus surface fish: 2-cells stage Replicate 3
          SRR9141193 CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus cavefish: 2-cells stage Replicate 1
          SRR9141194 SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus surface fish: 2-cells stage Replicate 1
          SRR9141195 SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus surface fish: 2-cells stage Replicate 2
          SRR9141196 Hybrid SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid surface fish: 2-cells stage Replicate 1
          SRR9141197 Hybrid SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid surface fish: 2-cells stage Replicate 2
          SRR9141198 CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus cavefish: 2-cells stage Replicate 2
          SRR9141199 CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus cavefish: 2-cells stage Replicate 3
          SRR9141200 Hybrid SF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid surface fish: 2-cells stage Replicate 3
          SRR9141201 Hybrid CF 2-cells egg nan untreatment RNA-Seq of Astyanax mexicanus hybrid cavefish: 2-cells stage Replicate 1
  • light
    • PRJNA557727:
          A widely accepted model for the evolution of cave animals posits cave colonization by surface dwelling ancestors followed by the acquisition of adaptive traits over many generations. However, the speed of cave adaptation in some species is difficult to reconcile with this conventional viewpoint, suggesting the importance of alternative mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with multiple populations of conspecific cave-dwelling morphs (cavefish, CF) and an ancestral-like surface dwelling morph (surface fish, SF) . We exposed SF to completely dark (D/D) conditions during early development and compared them to siblings placed on a standard photoperiod (L/D). Numerous altered traits were identified in D/D SF compared to L/D SF at both the gene expression and phenotypic levels, including changes related to endocrine signaling, circadian rhythms, metabolism (especially in lipids), eye anatomy, pigmentation, metabolic rates, starvation resistance, and neurotransmitter levels. Remarkably, most of these alterations mimicked CF phenotypes. Contrary to the widely accepted view that cave-related traits result from long-term genetic processes, our results indicate that many such traits can appear within a single generation by phenotypic plasticity. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of adaptive evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits, enabling a successful transition of A. mexicanus to dark cave habitats.
      • key word
        • light;GENE FLOW;POPULATION-STRUCTURE;SURFACE-POPULATIONS;EVOLUTION;CRUSTACEA;PATHWAY;LIGHT;DIFFERENTIATION;PHYLOGEOGRAPHY;DEGENERATION
      • publication
        • Bilandzija, H., et al. "Phenotypic plasticity as a mechanism of cave colonization and adaptation." eLife(2020).
      • abstract
        • A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that many cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR9878551 Light whole body without spleen and liver nan untreatment Control
          SRR9878552 Light whole body without spleen and liver nan untreatment Control
          SRR9878553 Light whole body without spleen and liver nan untreatment Control
          SRR9878554 Dark whole body without spleen and liver nan untreatment Dark Only
          SRR9878555 Dark whole body without spleen and liver nan untreatment Dark Only
          SRR9878556 Dark whole body without spleen and liver nan untreatment Dark Only
    • PRJNA605208:
          This study examines whole genome expression of surface and cave morphotypes of Astyanax mexicanus reared under different photic conditions. A subset of both cavefish and surface fish were reared under a 12 hour light dark cycle and separate subsets of both cavefish and surface fish were reared under 24 darkness - restoring the natural photic condition of the cave. RNA sequencing was performed after 5 years of rearing under either light:dark or dark:dark rearing.
      • key word
        • light;RNA-seq, Mexican tetra, troglomorphy, regressive evolution
      • publication
        • Sears, Connor R. , T. E. Boggs , and J. B. Gross . "Dark‐rearing uncovers novel gene expression patterns in an obligate caveヾwelling fish." Journal of Experimental Zoology Part B: Molecular and Developmental Evolution(2020).
      • abstract
        • Extreme environments often result in the evolution of dramatic adaptive features. The Mexican tetra, Astyanax mexicanus, includes 30 different populations of cave-dwelling forms that live in perpetual darkness. As a consequence, many populations have evolved eye loss, reduced pigmentation, and amplification of non-visual sensory systems. Closely-related surface-dwelling morphs demonstrate typical vision, pigmentation, and sensation. Transcriptomic assessments in this system have revealed important developmental changes associated with the cave morph, however they have not accounted for photic rearing conditions. Prior studies reared individuals under a 12:12 hr light/dark (LD) cycle. Here, we reared cavefish under constant darkness (DD) for 5+ years. From these experimental individuals, we performed mRNA sequencing and compared gene expression of surface fish reared under LD conditions to cavefish reared under DD conditions to identify photic-dependent gene expression differences. GO enrichment analyses revealed a number of previously underappreciated cave-associated changes impacting blood physiology and olfaction. We further evaluated the position of differentially expressed genes relative to QTL positions from prior studies, and found several candidate genes associated with these ecologically relevant lighting conditions. In sum, this work highlights photic condition as a key environmental factor impacting gene expression patterns in blind cave-dwelling fish.
      • sample list
        • sample id sample name tissue strain treatment description
          SRR11035213 Pachon-LD head nan 12 hour light cycle RNA-Seq of Astyanax mexicanus Pachon cavefish: head tissue: 12 hour light dark cycle
          SRR11035214 Surface-LD head nan 12 hour light cycle RNA-Seq of Astyanax mexicanus surface fish: head tissue: 12 hour light dark cycle
          SRR11035215 Surface-DD head nan 24 hour darkness RNA-Seq of Astyanax mexicanus surface fish: head tissue: 24 hour darkness
          SRR11035216 Pachon-DD head nan 24 hour darkness RNA-Seq of Astyanax mexicanus Pachon cavefish: head tissue: 24 hour darkness

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copyright 2021-present@Lab of Aquatic Bioinfomatics, Institute of Hydrobiology, Chinese Academy of Sciences