CrusTF: a comprehensive resource of transcriptomes for evolutionary and functional studies of crustacean transcription factors

Abstract

BackgroundCrustacea, the second largest subphylum of Arthropoda, includes species of major ecological and economic importance, such as crabs, lobsters, crayfishes, shrimps, and barnacles. With the rapid development of crustacean aquaculture and biodiversity loss, understanding the gene regulatory mechanisms of growth, reproduction, and development of crustaceans is crucial to both aquaculture development and biodiversity conservation of this group of organisms. In these biological processes, transcription factors (TFs) play a vital role in regulating gene expression. However, crustacean transcription factors are still largely unknown, because the lack of complete genome sequences of most crustacean species hampers the studies on their transcriptional regulation on a system-wide scale. Thus, the current TF databases derived from genome sequences contain TF information for only a few crustacean species and are insufficient to elucidate the transcriptional diversity of such a large animal group.ResultsOur database CrusTF (http://qinlab.sls.cuhk.edu.hk/CrusTF) provides comprehensive information for evolutionary and functional studies on the crustacean transcriptional regulatory system. CrusTF fills the knowledge gap of transcriptional regulation in crustaceans by exploring publicly available and newly sequenced transcriptomes of 170 crustacean species and identifying 131,941 TFs within 63 TF families. CrusTF features three categories of information: sequence, function, and evolution of crustacean TFs. The database enables searching, browsing and downloading of crustacean TF sequences. CrusTF infers DNA binding motifs of crustacean TFs, thus facilitating the users to predict potential downstream TF targets. The database also presents evolutionary analyses of crustacean TFs, which improve our understanding of the evolution of transcriptional regulatory systems in crustaceans.ConclusionsGiven the importance of TF information in evolutionary and functional studies on transcriptional regulatory systems of crustaceans, this database will constitute a key resource for the research community of crustacean biology and evolutionary biology. Moreover, CrusTF serves as a model for the construction of TF database derived from transcriptome data. A similar approach could be applied to other groups of organisms, for which transcriptomes are more readily available than genomes.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4305-2) contains supplementary material, which is available to authorized users.

CrusTome: A transcriptome database resource for large-scale analyses across Crustacea

“…The underrepresentation of non-hexapod pancrustaceans in publicly available databases could be attributed to challenges of a technical nature rather than to a lack of effort or adoption of genomic methodologies by researchers. This disparity is exemplified by the rapid increase of raw sequencing reads in the NCBI’s Sequence Read Archive (SRA) (Havird and Santos 2016; Qin et al . 2017; Hyde et al .…”

“…Several approaches have been previously taken to address this knowledge gap representing crustaceans and other non-traditional model organisms (Qin et al . 2017; Nong et al .…”

“…2020). For example, CrusTF is a web-based database resource containing sequence data, with an emphasis on transcription factors, mined from multiple transcriptomic sources (Qin et al . 2017).…”

“…The underrepresentation of non-hexapod pancrustaceans in publicly available databases could be attributed to challenges of a technical nature rather than to a lack of effort or adoption of genomic methodologies by researchers. This disparity is exemplified by the rapid increase of raw sequencing reads in the NCBI's Sequence Read Archive (SRA) (Havird and Santos 2016;Qin et al 2017;Hyde et al 2020), in contrast to the Transcriptome Shotgun Assembly (TSA) database. Since the SRA database is comprised of raw sequencing reads, accessing information stored therein requires a specific expertise and set of skills, oftentimes with steep learningcurves.…”

Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

“…Transcription is the first step in gene expression, while transcription factors control whether genes are transcribed and the rate of transcription [36]. Those transcription factors that had a higher expression level in the cement glands might play transcriptional regulatory roles during the initial expression of cement proteins and other related proteins in the cement glands [37].…”