Abstract
BackgroundThe marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. Its phylogenetic position within the spiralian/ lophotrochozoan clade, the comparatively high conservation of ancestral features in the Platynereis genome, and experimental access to any stage within its life cycle, make Platynereis an important model for elucidating the complex regulatory and functional molecular mechanisms governing early development, later organogenesis, and various features of its larval and adult life. High resolution RNA-seq gene expression data obtained from specific developmental stages can be used to dissect early developmental mechanisms. However, the potential for discovery of these mechanisms relies on tools to search, retrieve, and compare genome-wide information within Platynereis, and across other metazoan taxa.ResultsTo facilitate exploration and discovery by the broader scientific community, we have developed a web-based, searchable online research tool, PdumBase, featuring the first comprehensive transcriptome database for Platynereis dumerilii during early stages of development (2 h ~ 14 h). Our database also includes additional stages over the P. dumerilii life cycle and provides access to the expression data of 17,213 genes (31,806 transcripts) along with annotation information sourced from Swiss-Prot, Gene Ontology, KEGG pathways, Pfam domains, TmHMM, SingleP, and EggNOG orthology. Expression data for each gene includes the stage, the normalized FPKM, the raw read counts, and information that can be leveraged for statistical analyses of differential gene expression and the construction of genome-wide co-expression networks. In addition, PdumBase offers early stage transcriptome expression data from five further species as a valuable resource for investigators interested in comparing early development in different organisms. To understand conservation of Platynereis gene models and to validate gene annotation, most Platynereis gene models include a comprehensive phylogenetic analysis across 18 species representing diverse metazoan taxa.ConclusionsPdumBase represents the first online resource for the early developmental transcriptome of Platynereis dumerilii. It serves as a research platform for discovery and exploration of gene expression during early stages, throughout the Platynereis life cycle, and enables comparison to other model organisms. PdumBase is freely available at http://pdumbase.gdcb.iastate.edu.
Highlights
The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans
Over the last decade, Platynereis has emerged as a powerful spiralian model for comparative genomic analyses, evolutionary developmental biology studies, stem cells, regeneration, marine ecology, chronobiology and neurobiology [23,24,25,26,27]
More detailed annotation can be obtained from the interface with links to the gene ontology, Pfam, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, EggNOG, SignalP and tmHMM information of the corresponding genes
Summary
The marine polychaete annelid Platynereis dumerilii has recently emerged as a prominent organism for the study of development, evolution, stem cells, regeneration, marine ecology, chronobiology and neurobiology within metazoans. The morphological and genomic attributes exhibited by Platynereis have been useful for inferring ancestral gene structures and ancient cell types representative of ancestral bilaterian species [17, 18] These inferences are based on the findings that Platynereis shares many common features with vertebrates, including similar gene expression profiles during the development of the brain, the central nervous system, the eye, appendages, and muscles. These features have been instrumental in developing and testing hypotheses about the urbilaterian body plan and the origin of complex organ systems during animal evolution [3, 4, 19,20,21,22] For these reasons, over the last decade, Platynereis has emerged as a powerful spiralian model for comparative genomic analyses, evolutionary developmental biology (evo-devo) studies, stem cells, regeneration, marine ecology, chronobiology and neurobiology [23,24,25,26,27]. Platynereis as a laboratory organism boasts an ever-increasing experimental toolkit, expanding the usefulness of this species in identifying and dissecting gene function: during early and late development; during organogenesis; in various cell types; and in neuronal circuits that dictate the circadian and lunar rhythm-controlled swimming behaviors [27,28,29,30,31,32,33,34,35]
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