PdumBase: a transcriptome database and research tool for Platynereis dumerilii and early development of other metazoans

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4987-0) contains supplementary material, which is available to authorized users.

FoxA expression pattern in two polychaete species, Alitta virens and Platynereis dumerilii: Examination of the conserved key regulator of the gut development from cleavage through larval life, postlarval growth, and regeneration

“…foxA expression in P. dumerilii is first detected during cleavage, just before the start of gastrulation movements. This is consistent with mRNA-seq data (http:// pdumbase.gdcb.iastate.edu, Chou et al, 2018) that show a reliable foxA transcription as early as 6 hpf with a maximum at 8 hpf. Zygotic expression encompasses the ventral and the lateral lips of the blastopore and, for a short time, also the 4dderived endomesodermal material in the dorsal lip ( Fig.…”

DNA methylation during development and regeneration of the annelidPlatynereis dumerilii

“…We next aimed to characterize expression of DNA methylation and NuRD genes in P. dumerilii . We first took advantage of two previously published transcriptomic datasets corresponding to various developmental stages and adult condition of P. dumerilii [45,54], available in a public database (Pdumbase) [55]. The first dataset corresponds to embryonic developmental stages, ranging from 2 to 14hhpf, with a time point every two hours [45].…”

The development of early pioneer neurons in the annelid Malacoceros fuliginosus

“…The evolution of this group is in lophotrochozoans seemingly more complex than hitherto anticipated, since many species have several gene copies, many of which are poorly studied. Mfu-ASCa1 and Mfu-ASCa2 are closely related to P. dumerilli Achaete-scute 1 and to C. teleta Achaete scute 2 (Additional file 21), but also to two more transcripts from P. dumerilii, which we received from the Genbank TSA database, for which no cellular expression data exist, but according to PdumBase [37] are highly expressed in larvae from early on. To give a final answer on clear orthology relationships amongst these 6 genes is not possible based on our tree.…”