SAGER: a database of Symbiodiniaceae and Algal Genomic Resource.

Ling Li,Hongfei Li,Liying Yu,Chichi Liu,Tangcheng Li,Senjie Lin,Chentao Guo,Xin Lin

doi:10.1093/database/baaa051

Abstract

Symbiodiniaceae dinoflagellates are essential endosymbionts of reef building corals and some other invertebrates. Information of their genome structure and function is critical for understanding coral symbiosis and bleaching. With the rapid development of sequencing technology, genome draft assemblies of several Symbiodiniaceae species and diverse marine algal genomes have become publicly available but spread in multiple separate locations. Here, we present a Symbiodiniaceae and Algal Genomic Resource Database (SAGER), a user-friendly online repository for integrating existing genomic data of Symbiodiniaceae species and diverse marine algal gene sets from MMETSP and PhyloDB databases. Relevant algal data are included to facilitate comparative analyses. The database is freely accessible at http://sampgr.org.cn. It provides comprehensive tools for studying gene function, expression and comparative genomics, including search tools to identify gene information from Symbiodiniaceae species, and BLAST tool to find orthologs from marine algae and protists. Moreover, SAGER integrates transcriptome datasets derived from diverse culture conditions of corresponding Symbiodiniaceae species. SAGER was developed with the capacity to incorporate future Symbiodiniaceae and algal genome and transcriptome data, and will serve as an open-access and sustained platform providing genomic and molecular tools that can be conveniently used to study Symbiodiniaceae and other marine algae.Database URL: http://sampgr.org.cn

Highlights

Symbiodiniaceae, symbiotic dinoflagellates, are well known as essential endosymbionts of reef building corals and some other invertebrates [1]
In face of stress resulting from climate change and anthropogenic disturbance, there has been increasingly widespread and severe coral degradation in recent decades, largely due to the disruption of the coral-dinoflagellate symbiosis [7, 8]
To understand molecular mechanisms underpinning symbiosis and its disruption and develop strategies to conserve coral reefs, there have been dedicated efforts employing the high-throughput “omics” technologies to identify genomic and genetic elements associated with these processes [9,10,11,12,13]

Summary

Introduction

Symbiodiniaceae, symbiotic dinoflagellates, are well known as essential endosymbionts of reef building corals and some other invertebrates [1]. Tools such as keyword search, BLAST [20, 21], JBrowse [22] and download will allow Symbiodiniaceae and marine alga researchers to perform various tasks including manual check of gene model annotation and obtaining updates of marine algal genomic resources. This includes assembled genomes, CDS and amino acid sequences, re-annotated gene annotation and gene expression from different culture conditions of six Symbiodiaceae species

Results

Conclusion