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Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

Wygoda JA, Yang Y, Byrne M, Wray GA - Genome Biol Evol (2014)

Bottom Line: With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians.Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University.

ABSTRACT
With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians. Although early development has been intensively studied, the molecular mechanisms underlying development of the adult echinoderm and its unusual radial body plan are largely unknown. To investigate the evolution of developmental changes in gene expression underlying radial body plan development and metamorphosis, we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across larval, metamorphic, and postmetamorphic life cycle phases in the sea urchin Heliocidaris erythrogramma. Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases. These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.

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Fuzzy c-means clustering identifies general patterns of gene expression across development. To illustrate major patterns of gene expression, five clusters detected by fuzzy c-means clustering of the average expression value of 4,421 genes (log2FC ≥ 2, FDR ≤ 0.001) are shown (see supplementary fig. S1, Supplementary Material online, for additional clusters). The ms of a given gene within a cluster is represented by color, with red (ms = 1) indicating high association. For each cluster, significantly enriched PANTHER biological process categories identified by a Wilcoxon signed rank test are shown. For clarity, only the top ten categories are displayed (see supplementary table S5, Supplementary Material online, for additional categories).
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evu070-F4: Fuzzy c-means clustering identifies general patterns of gene expression across development. To illustrate major patterns of gene expression, five clusters detected by fuzzy c-means clustering of the average expression value of 4,421 genes (log2FC ≥ 2, FDR ≤ 0.001) are shown (see supplementary fig. S1, Supplementary Material online, for additional clusters). The ms of a given gene within a cluster is represented by color, with red (ms = 1) indicating high association. For each cluster, significantly enriched PANTHER biological process categories identified by a Wilcoxon signed rank test are shown. For clarity, only the top ten categories are displayed (see supplementary table S5, Supplementary Material online, for additional categories).

Mentions: Although our comparisons of advanced rudiment, early juvenile, and late juvenile stages provide important insights into the differences in pre- and postmetamorphic development, they do not take the full time-course into account. To further investigate the large-scale patterns of gene expression across juvenile body plan development and metamorphosis, we used fuzzy c-means clustering to group differentially expressed genes (log fold-change ≥ 2, FDR ≤ 0.001) into 16 distinct clusters (see Materials and Methods). We kept 3,316 clustered genes for further analysis based on their membership score (ms) within a cluster (ms ≥ 0.5). The majority of clusters exhibited both stage-specific expression profiles (supplementary fig. S1, Supplementary Material online) and significant enrichment of PANTHER biological process categories (Wilcoxon rank test; supplementary table S5, Supplementary Material online). Generally, the patterns that we observed could be summarized by Clusters 2, 5, 6, 13, and 16 (fig. 4).Fig. 4.—


Transcriptomic analysis of the highly derived radial body plan of a sea urchin.

Wygoda JA, Yang Y, Byrne M, Wray GA - Genome Biol Evol (2014)

Fuzzy c-means clustering identifies general patterns of gene expression across development. To illustrate major patterns of gene expression, five clusters detected by fuzzy c-means clustering of the average expression value of 4,421 genes (log2FC ≥ 2, FDR ≤ 0.001) are shown (see supplementary fig. S1, Supplementary Material online, for additional clusters). The ms of a given gene within a cluster is represented by color, with red (ms = 1) indicating high association. For each cluster, significantly enriched PANTHER biological process categories identified by a Wilcoxon signed rank test are shown. For clarity, only the top ten categories are displayed (see supplementary table S5, Supplementary Material online, for additional categories).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4007537&req=5

evu070-F4: Fuzzy c-means clustering identifies general patterns of gene expression across development. To illustrate major patterns of gene expression, five clusters detected by fuzzy c-means clustering of the average expression value of 4,421 genes (log2FC ≥ 2, FDR ≤ 0.001) are shown (see supplementary fig. S1, Supplementary Material online, for additional clusters). The ms of a given gene within a cluster is represented by color, with red (ms = 1) indicating high association. For each cluster, significantly enriched PANTHER biological process categories identified by a Wilcoxon signed rank test are shown. For clarity, only the top ten categories are displayed (see supplementary table S5, Supplementary Material online, for additional categories).
Mentions: Although our comparisons of advanced rudiment, early juvenile, and late juvenile stages provide important insights into the differences in pre- and postmetamorphic development, they do not take the full time-course into account. To further investigate the large-scale patterns of gene expression across juvenile body plan development and metamorphosis, we used fuzzy c-means clustering to group differentially expressed genes (log fold-change ≥ 2, FDR ≤ 0.001) into 16 distinct clusters (see Materials and Methods). We kept 3,316 clustered genes for further analysis based on their membership score (ms) within a cluster (ms ≥ 0.5). The majority of clusters exhibited both stage-specific expression profiles (supplementary fig. S1, Supplementary Material online) and significant enrichment of PANTHER biological process categories (Wilcoxon rank test; supplementary table S5, Supplementary Material online). Generally, the patterns that we observed could be summarized by Clusters 2, 5, 6, 13, and 16 (fig. 4).Fig. 4.—

Bottom Line: With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians.Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases.These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Duke University.

ABSTRACT
With their complex life cycle and highly derived body plan, echinoderms are unique among bilaterians. Although early development has been intensively studied, the molecular mechanisms underlying development of the adult echinoderm and its unusual radial body plan are largely unknown. To investigate the evolution of developmental changes in gene expression underlying radial body plan development and metamorphosis, we assembled a reference transcriptome de novo and used RNA-seq to measure gene expression profiles across larval, metamorphic, and postmetamorphic life cycle phases in the sea urchin Heliocidaris erythrogramma. Our results present a high-resolution view of gene expression dynamics during the complex transition from pre- to postmetamorphic development and suggest that distinct sets of regulatory and effector proteins are used during different life history phases. These analyses provide an important foundation for more detailed analyses of the evolution of the radial adult body of echinoderms.

Show MeSH