Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA.
Wake Forest Institute for Regenerative Medicine, 91 Technology Way NE, Winston-Salem, NC, 27101, USA.
BMC Genom Data. 2022 Oct 23;23(1):75. doi: 10.1186/s12863-022-01090-6.
Here we release a new version of EchinoDB, EchinoDB v2.0 ( https://echinodb.uncc.edu ). EchinoDB is a database of genomic and transcriptomic data on echinoderms. The initial database consisted of groups of 749,397 orthologous and paralogous transcripts arranged in orthoclusters by sequence similarity.
The updated version of EchinoDB includes two new major datasets: the RNA-Seq data of the brittle star Ophioderma brevispinum and the high-quality genomic assembly data of the green sea urchin Lytechinus variegatus. In addition, we enabled keyword searches for annotated data and installed an updated version of Sequenceserver to allow Basic Local Alignment Search Tool (BLAST) searches. The data are downloadable in FASTA format. The first version of EchinoDB appeared in 2016 and was implemented in GO on a local server. The new version has been updated using R Shiny to include new features and improvements in the application. Furthermore, EchinoDB now runs entirely in the cloud for increased reliability and scaling.
EchinoDB serves a user base drawn from the fields of phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration. As use cases, we illustrate the function of EchinoDB in retrieving components of signaling pathways involved in the tissue regeneration process of different echinoderms, including the emerging model species Ophioderma brevispinum. Moreover, we use EchinoDB to shed light on the conservation of the molecular components involved in two echinoderm-specific phenomena: spicule matrix proteins involved in the formation of stereom endoskeleton and the tensilin protein that contributes to the capacity of the connective tissues to quickly change its mechanical properties. The genes involved in the former had been previously studied in echinoids, while gene sequences involved in the latter had been previously described in holothuroids. Specifically, we ask (a) if the biomineralization-related proteins previously reported only in sea urchins are also present in other, non-echinoid, echinoderms and (b) if tensilin, the protein responsible for the control of stiffness of the mutable collagenous tissue, previously described in sea cucumbers, is conserved across the phylum.
我们发布了 EchinoDB 的新版本，EchinoDB v2.0（https://echinodb.uncc.edu）。EchinoDB 是一个棘皮动物基因组和转录组数据的数据库。最初的数据库由 749397 个直系同源和旁系同源转录本组成，这些转录本通过序列相似性被排列在直系同源簇中。
EchinoDB 的更新版本包括两个新的主要数据集：短腕海星 Ophioderma brevispinum 的 RNA-Seq 数据和绿海胆 Lytechinus variegatus 的高质量基因组组装数据。此外，我们启用了对注释数据的关键字搜索，并安装了更新版本的 Sequenceserver 以允许进行基本局部比对搜索工具（BLAST）搜索。这些数据以 FASTA 格式下载。EchinoDB 的第一个版本于 2016 年出现，在本地服务器上使用 GO 实现。新版本使用 R Shiny 进行了更新，以包含应用程序中的新功能和改进。此外，EchinoDB 现在完全在云中运行，以提高可靠性和可扩展性。
EchinoDB 的用户群体来自系统发生学、发育生物学、基因组学、生理学、神经生物学和再生等领域。作为用例，我们说明了 EchinoDB 在检索不同棘皮动物组织再生过程中涉及信号通路的组件的功能，包括新兴的模式物种短腕海星 Ophioderma brevispinum。此外，我们使用 EchinoDB 阐明了参与两种棘皮动物特有现象的分子成分的保守性：参与 Stereom 内骨骼形成的骨针基质蛋白和有助于结缔组织快速改变其机械性能的 tensilin 蛋白。前者涉及的基因以前在海胆中进行过研究，而后者涉及的基因序列以前在海参中进行过描述。具体来说，我们提出了以下问题：（a）以前仅在海胆中报道的与生物矿化相关的蛋白是否也存在于其他非棘皮动物棘皮动物中；（b）负责控制可变形胶原组织硬度的蛋白 tensilin 是否在整个门中保守。
