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Ecol Evol
2017 Mar 14;78:2798-2811. doi: 10.1002/ece3.2850.
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Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus.
Gaitán-Espitia JD
,
Hofmann GE
.
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In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins. From these transcripts, ~80% were functionally annotated allowing the identification of ~2,600 functional, structural, and regulatory genes involved in developmental process. Analysis of expression profiles between gastrula and pluteus stages of M. franciscanus revealed 791 differentially expressed genes with 251 GO overrepresented terms. For gastrula, up-regulated GO terms were mainly linked to cell differentiation and signal transduction involved in cell cycle checkpoints. In the pluteus stage, major GO terms were associated with phosphoprotein phosphatase activity, muscle contraction, and olfactory behavior, among others. Our evolutionary comparative analysis revealed that several of these genes and functional pathways are highly conserved among echinoids, holothuroids, and ophiuroids.
Figure 1. Gene Ontology categories for biological processes in the gastrula and pluteus transcriptomes of Mesocentrotus franciscanus. Categories are shown on the xâ€axis; while the right yâ€axis indicates the number of genes per category, the left yâ€axis indicates the percentage of genes in the main category
Figure 2. Protein clusters among early developmental transcriptomes of echinoderms. (a) Comparison between gastrula and pluteus stages of Mesocentrotus franciscanus. Analysis of orthologous clusters among gastrulas (b) and pluteus (c) stages of the sea urchins M. franciscanus, Strongylocentrotus purpuratus and Lytechinus variegatus, the sea cucumber Parastichopus parvimensis (gastrula), and the brittle star Amphiura filiformis (pluteus)
Figure 3. Unigenes homology to KEGG genes obtained from the KAAS server. (a) Number of sequences assigned to each subcategory of the reference hierarchy KOs. (b) Percentage distribution of the five top KEGG orthology categories in the reference, gastrula, and pluteus transcriptomes of Mesocentrotus franciscanus
Figure 4. Gene expression profiles during early development of Mesocentrotus franciscanus. (a) Heat map generated from differentially expressed genes between gastrula and pluteus stages. The bar color reflects the gene expression levels. (b) Volcano plot displaying the log2 fold change and the −log10 of the pâ€values from Kal's statistical test for the gastrula and pluteus stages. (c) Overview of log2 expression ratios of all transcripts differentially expressed between gastrula and pluteus stages
Figure 5. Gene Ontology treemaps for annotated differentially expressed genes. (a) Upâ€regulated GO terms in (a) gastrula and (b) pluteus stages of M. franciscanus. When GO terms are upâ€regulated in gastrula, they are downâ€regulated accordingly in the pluteus
Adams,
Rapid adaptation to food availability by a dopamine-mediated morphogenetic response.
2011, Pubmed,
Echinobase
Adams,
Rapid adaptation to food availability by a dopamine-mediated morphogenetic response.
2011,
Pubmed
,
Echinobase
Angerer,
Animal-vegetal axis patterning mechanisms in the early sea urchin embryo.
2000,
Pubmed
,
Echinobase
Arenas-Mena,
Histone H2A.Z expression in two indirectly developing marine invertebrates correlates with undifferentiated and multipotent cells.
2007,
Pubmed
,
Echinobase
Ashburner,
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
2000,
Pubmed
Bilic,
Wnt induces LRP6 signalosomes and promotes dishevelled-dependent LRP6 phosphorylation.
2007,
Pubmed
Brawand,
The evolution of gene expression levels in mammalian organs.
2011,
Pubmed
Byrne,
The stunting effect of a high CO2 ocean on calcification and development in sea urchin larvae, a synthesis from the tropics to the poles.
2013,
Pubmed
,
Echinobase
Cameron,
SpBase: the sea urchin genome database and web site.
2009,
Pubmed
,
Echinobase
Carrier,
Gene Expression Changes Associated With the Developmental Plasticity of Sea Urchin Larvae in Response to Food Availability.
2015,
Pubmed
,
Echinobase
Chomczynski,
Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction.
1987,
Pubmed
Conesa,
Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.
2005,
Pubmed
Cross,
Growth factors in development, transformation, and tumorigenesis.
1991,
Pubmed
Delroisse,
De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae.
2015,
Pubmed
,
Echinobase
Dilly,
Characterization of the Antarctic sea urchin (Sterechinus neumayeri) transcriptome and mitogenome: a molecular resource for phylogenetics, ecophysiology and global change biology.
2015,
Pubmed
,
Echinobase
Dylus,
Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.
2016,
Pubmed
,
Echinobase
Evans,
Glycosyltrasferase activity in developing sea-urchin embryos.
1977,
Pubmed
,
Echinobase
Filteau,
Gene coexpression networks reveal key drivers of phenotypic divergence in lake whitefish.
2013,
Pubmed
Gaitán-Espitia,
Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus.
2016,
Pubmed
,
Echinobase
Gaitán-Espitia,
Gene expression profiling during the embryo-to-larva transition in the giant red sea urchin Mesocentrotus franciscanus.
2021,
Pubmed
,
Echinobase
Gao,
Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution.
2008,
Pubmed
,
Echinobase
Garfield,
The impact of gene expression variation on the robustness and evolvability of a developmental gene regulatory network.
2013,
Pubmed
,
Echinobase
Gildor,
Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.
2016,
Pubmed
,
Echinobase
Gillard,
The transcriptome of the NZ endemic sea urchin Kina (Evechinus chloroticus).
2014,
Pubmed
,
Echinobase
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Hammond,
Early developmental gene regulation in Strongylocentrotus purpuratus embryos in response to elevated CO₂ seawater conditions.
2012,
Pubmed
,
Echinobase
Hinman,
Expression of AmKrox, a starfish ortholog of a sea urchin transcription factor essential for endomesodermal specification.
2003,
Pubmed
,
Echinobase
Hinman,
Expression of a gene encoding a Gata transcription factor during embryogenesis of the starfish Asterina miniata.
2003,
Pubmed
,
Echinobase
Hinman,
Expression and function of a starfish Otx ortholog, AmOtx: a conserved role for Otx proteins in endoderm development that predates divergence of the eleutherozoa.
2003,
Pubmed
,
Echinobase
Hinman,
Developmental gene regulatory network architecture across 500 million years of echinoderm evolution.
2003,
Pubmed
,
Echinobase
Hinman,
Evolutionary plasticity of developmental gene regulatory network architecture.
2007,
Pubmed
,
Echinobase
Israel,
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris.
2016,
Pubmed
,
Echinobase
Jackson,
The importance of evo-devo to an integrated understanding of molluscan biomineralisation.
2016,
Pubmed
Jaffe,
Ca2+ signalling during fertilization of echinoderm eggs.
2001,
Pubmed
,
Echinobase
Jones,
InterProScan 5: genome-scale protein function classification.
2014,
Pubmed
Kari,
Analysis of changes in a yolk glycoprotein complex in the developing sea urchin embryo.
1985,
Pubmed
,
Echinobase
Layden,
The rise of the starlet sea anemone Nematostella vectensis as a model system to investigate development and regeneration.
2016,
Pubmed
Lee,
Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida.
2003,
Pubmed
,
Echinobase
McAlister,
Evolutionary responses to environmental heterogeneity in central american echinoid larvae: plastic versus constant phenotypes.
2008,
Pubmed
,
Echinobase
McCauley,
Development of an embryonic skeletogenic mesenchyme lineage in a sea cucumber reveals the trajectory of change for the evolution of novel structures in echinoderms.
2012,
Pubmed
,
Echinobase
McCauley,
A conserved gene regulatory network subcircuit drives different developmental fates in the vegetal pole of highly divergent echinoderm embryos.
2010,
Pubmed
,
Echinobase
McIntyre,
Branching out: origins of the sea urchin larval skeleton in development and evolution.
2014,
Pubmed
,
Echinobase
Moriya,
KAAS: an automatic genome annotation and pathway reconstruction server.
2007,
Pubmed
Nakata,
Expression patterns of wnt8 orthologs in two sand dollar species with different developmental modes.
2009,
Pubmed
,
Echinobase
Ozaki,
L-malate dehydrogenase in the development of the sea urchin Strongylocentrotus purpuratus.
1970,
Pubmed
,
Echinobase
Padilla-Gamiño,
Temperature and CO(2) additively regulate physiology, morphology and genomic responses of larval sea urchins, Strongylocentrotus purpuratus.
2013,
Pubmed
,
Echinobase
Pérez-Portela,
Characterization of the transcriptome and gene expression of four different tissues in the ecologically relevant sea urchin Arbacia lixula using RNA-seq.
2016,
Pubmed
,
Echinobase
Peter,
The endoderm gene regulatory network in sea urchin embryos up to mid-blastula stage.
2010,
Pubmed
,
Echinobase
Raff,
Modularity and dissociation in the evolution of gene expression territories in development.
2000,
Pubmed
,
Echinobase
Rafiq,
Genome-wide analysis of the skeletogenic gene regulatory network of sea urchins.
2014,
Pubmed
,
Echinobase
Rafiq,
The genomic regulatory control of skeletal morphogenesis in the sea urchin.
2012,
Pubmed
,
Echinobase
Runcie,
Genetics of gene expression responses to temperature stress in a sea urchin gene network.
2012,
Pubmed
,
Echinobase
Stewart,
De novo assembly of the transcriptome of Acanthaster planci testes.
2015,
Pubmed
,
Echinobase
Sultan,
Development in context: the timely emergence of eco-devo.
2007,
Pubmed
Supek,
REVIGO summarizes and visualizes long lists of gene ontology terms.
2011,
Pubmed
Swezey,
Enzyme stimulation upon fertilization is revealed in electrically permeabilized sea urchin eggs.
1988,
Pubmed
,
Echinobase
Tu,
Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus.
2014,
Pubmed
,
Echinobase
Tu,
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
2012,
Pubmed
,
Echinobase
Tulin,
A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.
2013,
Pubmed
Ueno,
PTEN is required for the normal progression of gastrulation by repressing cell proliferation after MBT in Xenopus embryos.
2006,
Pubmed
Vaughn,
Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii.
2012,
Pubmed
,
Echinobase
Wang,
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species.
2015,
Pubmed
Wei,
A database of mRNA expression patterns for the sea urchin embryo.
2006,
Pubmed
,
Echinobase
Ye,
WEGO: a web tool for plotting GO annotations.
2006,
Pubmed
Yokota,
Degradation of yolk proteins in sea urchin eggs and embryos.
1988,
Pubmed
,
Echinobase
Yu,
Growth attenuation with developmental schedule progression in embryos and early larvae of Sterechinus neumayeri raised under elevated CO2.
2013,
Pubmed
,
Echinobase
Zhou,
Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers.
2014,
Pubmed
,
Echinobase
