SKLB CoralBioinfo Database

Although reef-building corals play an important role in the global marine ecosystem, there emerges a huge lack of bioinformatics data as well as databases from these species, exerting negative effects on exploring their biology. Here we introduce the construction of SKLB CoralBioinfo database series. Developed under the Docker-based LEMP tech-stack, these databases integrate our own data from full-length transcriptome sequencing and small RNA sequencing of several main reef-building coral species with other existing coral bio-data. It is expected for this work to fulfill the “data gap” and boost the virtuous 3A (Acquisition-Analysis-Application) cycle in coral multi-omics research.

1. DATABASE CONTENT

CoralBioinfo, which stores basic bioinformatics data such as ▼sequence and ▼gene information, is first developed to lay the foundation for down-stream database construction.

1.1. Sequence

All raw sequences are available on NCBI:

Species	Full-length transcript	Small RNA	Illumina RNA-seq^*
Acropora muricata	SRR9613488	SRR13442147 SRR13442146 SRR13442145	SRR12904786 SRR12904785 SRR12904784
Montipora foliosa	SRR9129316	SRR13442144 SRR13442143 SRR13442142	SRR12904783 SRR12904782 SRR12904781
Montipora capricornis	SRR9129315	SRR13442141 SRR13442150 SRR13442149	SRR12904780 SRR12904792 SRR12904791
Pocillopora verrucosa	SRR9129314	SRR13442152 SRR13442151 SRR13442148	SRR12904794 SRR12904793 SRR12904787
Pocillopora damicornis	SRR9613489	NULL	SRR12904790 SRR12904789 SRR12904788

^*Illumina RNA-seqs are not stored in CoralBioinfo. However, URLs of their mirrors on public database must be listed according to 4.2.

These raw data are processed through mature bioinformatics pipelines to get Unigene and miRNA sequences, which have been transformed into ncbi-blast databases for alignment tasks.

1.2. Gene

Gene information mined from Unigene is consisted of transcript structure and annotations from seven databases: GO, KEGG, KOG, Nr, Nt, Pfam and Swiss-Prot.

Every gene page demonstrates sequence, annotation and structure information of the transcript. There will be 7 buttons labelled "GO", "KEGG", "KOG", "Nr", "Nt", "Pfam" and "SwissProt" for users to get annotation details. If there are no annotation results for the transcript in one database, corresponding button will be unclickable.

1.2.1. Structure

CDS

Name	Description	Sample
gene	gene/transcript name	...SH_FW_transcript13494/f2p0/1891
type	<tag>-<completeness> \| 3UTR \| 5UTR <tag> = confident \| likely \| suspicious \| dumb <completeness> = compl \| 5/3partial \| internal \| NA	confident-compl
seq	CDS/UTR sequence	ATGCCGTCGAT...
start	start site	255
end	end site	782
species	-	Montipora capricornis

SSR

Name	Description	Sample
gene	gene/transcript name	...SH_WP_transcript13616/f12p0/2318
type	c (complex repeat) pn (n nt repeat)	p3
SSR	SSR sequence	(ATT)14
start	start site	1808
end	end site	1849
species	-	Montipora foliosa

1.2.2. Annotation

GO

Name	Description	Sample
gene	gene/transcript name	...HQ_SH_981_transcript2380/f3p0/3329
term	GO term	GO:0007049
type	ontology type	biological_process
description	-	cell cycle
species	coral species	Pocillopora verrucosa

KEGG

Name	Description	Sample
gene	gene/transcript name	...HQ_Formosa_2_transcript11807/f44p0/2477
subject	target label	nve:NEMVE_v1g190252
ko_id	KO ID	K03083
ko_name	KO name	GSK3B
definition	KO description	glycogen synthase kinase 3 beta
ec	-	2.7.11.26
pathway	KO pathway	ko04012; Environmental Information Process...
species	coral species	Acropora muricata

KOG

Name	Description	Sample
gene	gene/transcript name	...HQ_SH_981_transcript6218/f4p0/2707
identity	-	83.7
E_value	-	4.40E-160
kog_gene	KOG gene ID	Hs19924133
kog_id	KOG number	KOG1433
function	function description	DNA repair protein RAD51/RHP55
class	KOG classification	L
description	KOG class description	Replication, recombination and repair
species	coral species	Pocillopora verrucosa

Nr

Name	Description	Sample
gene	gene/transcript name	...HQ_Formosa_2_transcript13610/f3p0/2327
identity	-	87.5
E_value	-	7.20E-168
subject	target label	XP_001627328.1
description	-	predicted protein [Nematostella vectensis]
species	coral species	Acropora muricata

Nt

Name	Description	Sample
gene	gene/transcript name	...HQ_SH_FW_transcript9634/f2p0/2180
identity	-	78.743
E_value	-	2.52E-93
subject	target label	XM_008286923.1
description	-	Stegastes partitus rho-related GTP-bind...
species	coral species	Montipora capricornis

Pfam

Name	Description	Sample
gene	gene/transcript name	...HQ_SH_WP_transcript19522/f3p0/1726
id	PFAM ID	PF06293
description	PFAM description	Lipopolysaccharide kinase (Kdo/WaaP) family
species	coral species	Montipora foliosa

SwissProt

Name	Description	Sample
gene	gene/transcript name	...HQ_SH_WP_transcript22309/f13p0/1307
identity	-	88.5
E_value	-	1.50E-196
subject	target label	sp\|P62335\|PRS10_ICTTR
description	-	26S protease regulatory subunit...
species	coral species	Montipora foliosa

1.3. Other data

2. WEB SERVICE

Tool module development is carried out simultaneously with data curation.

CoralSeqServer
Optimized from Sequenceserver, it provides a more user-friendly BLAST interface. Click the "Format" button in the upper right corner to display data lists ordered by type, where sub-titles offer links to BLAST service for specific data.
Tips: Genomes have not been uploaded yet.
SKLB Genome Browser
It is customized by GIVE to help gaining deeper insights into multi-omics data.
CoralAPI
It offers users capability of acquiring data in-batch through URLs.

3. SUB-DATABASE

Two miRNA-centered sub-databases are built based on sequences and annotations from ▲CoralBioinfo.

CoralmiR
It turns out to be the first database demonstrating reef-building coral miRNAs and their 3'UTR targeting sites.
CoralSym
It publishes a novel C1-clade Symbiodiniaceae miRNA set identified in four coral species.

4. INCLUSION CRITERIA

Contribution requests are always welcome, while they are ought to meet the basic requirement that all raw data must have mirrors on main public bioinformatics database such as NCBI. Please contact 📧Dr. Yunchi Zhu to offer your data after reading the following rules.

4.1. Genome

CoralBioinfo accepts reef-building coral genomes assembled to the chromosome level. The following data are required to be provided:

Raw genome URLs on public database
Assembled sequence (.fasta)
Annotation (.gpd/.gff/.gtf)

CoralSym accepts C-clade Symbiodiniaceae genomes. The following data are required to be provided:

Raw data URLs on public database
Assembled sequence (.fasta/.fastq)
Annotation (.gpd/.gff/.gtf)

Other genome-related data, which can be embedded into GIVE-customized genome browsers, are welcome as well.

4.2. Transcript

CoralBioinfo accepts reef-building coral full-length transcripts. Each full-length sample must be coupled with at least 3 NGS samples for correction and down-stream analysis such as DEG. The following data are required to be provided:

Raw data URLs on public database (1 full-length sample against 3 NGS samples)
Unigene sequence (.fasta)
▲Formatted annotation from at least 5 databases

4.3. Small RNA

CoralmiR accepts reef-building coral miRNAs. Submitted data format should be strictly in line with table structure of coralmir.info and coralmir.pair. In addition, the following data are required to be provided:

Raw data URLs on public database
miRNA-precursor structure (.ps/.pdf)

CoralSym accepts C-clade Symbiodiniaceae miRNAs. Before contribution, corresponding genomes need to be uploaded according to 4.1. Data format should be strictly in line with table structure of coralsym.info and coralsym.pair. In addition, the following data are required to be provided:

Raw data URLs on public database
miRNA-precursor structure (.ps/.pdf)