Developmental transcriptomics of the brittle star Amphiura filiformis reveals gene regulatory network rewiring in echinoderm larval skeleton evolution

Genome Biology
David Viktor DylusPaola Oliveri

Abstract

Amongst the echinoderms the class Ophiuroidea is of particular interest for its phylogenetic position, ecological importance and developmental and regenerative biology. However, compared to other echinoderms, notably echinoids (sea urchins), relatively little is known about developmental changes in gene expression in ophiuroids. To address this issue, we have generated and assembled a large RNAseq data set of four key stages of development in the brittle star Amphiura filiformis and a de novo reference transcriptome of comparable quality to that of a model echinoderm-the sea urchin Strongylocentrotus purpuratus. Furthermore, we provide access to the new data via a web interface: http://www.echinonet.eu/shiny/Amphiura_filiformis/ . We have identified highly conserved genes associated with the development of a biomineralised skeleton. We also identify important class-specific characters, including the independent duplication of the msp130 class of genes in different echinoderm classes and the unique occurrence of spicule matrix (sm) genes in echinoids. Using a new quantification pipeline for our de novo transcriptome, validated with other methodologies, we find major differences between brittle stars and sea urchins in the tempor...Continue Reading

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Citations

Sep 29, 2018·Genesis : the Journal of Genetics and Development·Tanvi ShashikantCharles A Ettensohn
May 10, 2019·Communications Biology·Eric M Erkenbrack, Jeffrey R Thompson
May 1, 2020·Cell and Tissue Research·Cinzia FerrarioPaola Oliveri
Jun 20, 2018·Integrative and Comparative Biology·Selene L Fernandez-ValverdeRené Alexander Ramos-Díaz
Dec 18, 2020·Frontiers in Genetics·Jian Ming Khor, Charles A Ettensohn
Jan 12, 2020·Communications Biology·Eric M Erkenbrack, Jeffrey R Thompson

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Methods Mentioned

BETA
PCR
RNA-seq

Software Mentioned

InterProScan
WMISH
MODAL
RSEM
interpro
RefTr
scripts
shiny
R
Nanostring

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