CrustyBase: an interactive online database for crustacean transcriptomes

Abstract

Transcriptome sequencing has opened the field of genomics to a wide variety of researchers, owing to its efficiency, applicability across species and ability to quantify gene expression. The resulting datasets are a rich source of information that can be mined for many years into the future, with each dataset providing a unique angle on a specific context in biology. Maintaining accessibility to this accumulation of data presents quite a challenge for researchers. The primary focus of conventional genomics databases is the storage, navigation and interpretation of sequence data, which is typically classified down to the level of a species or individual. The addition of expression data adds a new dimension to this paradigm – the sampling context. Does gene expression describe different tissues, a temporal distribution or an experimental treatment? These data not only describe an individual, but the biological context surrounding that individual. The structure and utility of a transcriptome database must therefore reflect these attributes. We present an online database which has been designed to maximise the accessibility of crustacean transcriptome data by providing intuitive navigation within and between datasets and instant visualization of gene expression and protein structure. The site is accessible at https://crustybase.org and currently holds 10 datasets from a range of crustacean species. It also allows for upload of novel transcriptome datasets through a simple web interface, allowing the research community to contribute their own data to a pool of shared knowledge.

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

“…However, despite the taxonomic breadth covered across Crustacea, ease of access, and web-based tools and operability, its present scope is limited, as it pertains exclusively to transcription factors. CrustyBase, a recently published interactive database of crustacean transcriptomes, also employs a web-based approach with a Graphical User Interface (GUI) that excels in terms of accessibility, navigation, and operability (Hyde et al, 2020). It also leverages the advantages of being able to process gene expression data that can be linked directly to each submitted transcriptome, an integrated BLAST interface, and intuitive visualization features.…”

“…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.…”

“…2022). Nevertheless, similar to other non-model invertebrates, they are severely underrepresented in publicly accessible (and readily available) databases such as those maintained by the National Center for Biotechnology Information (NCBI) (GIGA Community of Scientists 2014; Havird and Santos 2016; Hyde et al . 2020).…”

The Crustacean Antennule: A Complex Organ Adapted for Lifelong Function in Diverse Environments and Lifestyles

“…Comparative biologists, especially those using modern methods, have an open slate to explore the diversity of antennules in this fascinating group of animals. The availability of more crustacean species with sequenced genomes and a greater arsenal of molecular techniques to identify specifically expressed RNA or protein in individual cells, or to up-or downregulate RNA or protein expression (Sagi et al, 2013;Martin et al, 2016;Burnett et al, 2020;Hyde et al, 2020;Kozma et al, 2020a), now allows researchers to study antennular systems in greater depth at the molecular level. Such studies, combined with the ability to monitor the physicochemical environment around the animal, and even to record antennular function in live animals in real time, will allow a much deeper understanding of these intriguing and complex organs.…”

A Tale of Two Lobsters—Transcriptomic Analysis Reveals a Potential Gap in the RNA Interference Pathway in the Tropical Rock Lobster Panulirus ornatus

“…RNAi gene orthologues were submitted to a tBLASTN search on CrustyBase ( , accessed on 4 July 2022) utilising both the metamorphic stages and adult tissues databases for P. ornatus and the multiple sub-adult tissues database for T. australiensis [ 68 , 69 , 83 ]. The most complete sequences with e-values of <1.0 × 10 −30 and >50% query coverage, were selected for further analysis.…”