Armstrong AF and Grosberg RK (2018), The developmental transcriptomes of two sea bis...

ECB-ART-46343

BMC Genomics 2018 May 18;191:368. doi: 10.1186/s12864-018-4768-9.

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The developmental transcriptomes of two sea biscuit species with differing larval types.

Armstrong AF , Grosberg RK .

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BACKGROUND: Larval developmental patterns are extremely varied both between and within phyla, however the genetic mechanisms leading to this diversification are poorly understood. We assembled and compared the developmental transcriptomes for two sea biscuit species (Echinodermata: Echinoidea) with differing patterns of larval development, to provide a resource for investigating the evolution of alternate life cycles. One species (Clypeaster subdepressus) develops via an obligately feeding larva which metamorphoses 3-4 weeks after fertilization; the other (Clypeaster rosaceus) develops via a rare, intermediate larval type-facultative feeding- and can develop through metamorphosis entirely based on egg provisioning in under one week. RESULTS: Overall, the two transcriptomes are highly similar, containing largely orthologous contigs with similar functional annotation. However, we found distinct differences in gene expression patterns between the two species. Larvae from C. rosaceus, the facultative planktotroph, turned genes on at earlier stages and had less differentiation in gene expression between larval stages, whereas, C. subdepressus showed a higher degree of stage-specific gene expression. CONCLUSION: This study is the first genetic analysis of a species with facultatively feeding larvae. Our results are consistent with known developmental differences between the larval types and raise the question of whether earlier onset of developmental genes is a key step in the evolution of a reduced larval period. By publishing a transcriptome for this rare, intermediate, larval type, this study adds developmental breadth to the current genetic resources, which will provide a valuable tool for future research on echinoderm development as well as studies on the evolution of development in general.

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Genes referenced: LOC100887844

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	Fig. 1. Summary of orthogroups between Clypeaster rosaceus (red), C. subdepressus (yellow), and Strongylocentrotus purpuratus (purple). Orthogroups with all three species present are shown overlapping in the middle (10,779). Orthogroups shared exclusively by the Clypeaster species are shown in orange (2625)
	Fig. 2. Distribution of biological process gene ontology terms in each transcriptome. The category and percent of GO terms belonging to that category are labeled for both Clypeaster rosaceus (a) and C. subdepressus (b)
	Fig. 3. Heatmaps of the Euclidean distance between samples for each Clypeaster rosaceus (a), and C. subdepressus (b). Dark purple colors represent highly similar samples, while lighter, yellow colors reflect more distant samples. The order of samples is denoted below each column with the sample names indicating first the developmental stage, followed by experiment (1â€“3), and replicate within experiment (a or b). The branching pattern at the top of each plot represents relative distances between samples
	Fig. 4. Scatterplots of stage specific gene expression. a-c Clypeaster rosaceus, (d-f) C. subdepressus. Expression levels are displayed in counts per million contrasted pairwise between developmental stages as labeled on the x- and y-axes. Red points represent genes identified as significantly differentially expressed, using a false discovery rate of 0.05, between stages while black dots are not significantly different. The number (and percent) of differentially expressed genes is indicated in each plot

References [+] :

Allen, Intermediate modes of larval development: bridging the gap between planktotrophy and lecithotrophy. 2007, Pubmed