The Marine Fish Database (MFDB) is developed, the first integrative genomics platform specifically designed for marine teleosts, and establishes a scalable framework to accelerate hypothesis-driven discoveries in marine fish biology, evolutionary adaptation, and ecological resilience research.
Abstract
Marine fishes are important contributors to biodiversity conservation and socioeconomic sustainability. While genomic and multi-omics datasets for marine fish species have expanded exponentially in recent years, their systematic integration remains underexplored, hindering comprehensive investigations into gene regulation and biological systems. To bridge this gap, we developed the Marine Fish Database (MFDB; http://marinefishdb.cn), the first integrative genomics platform specifically designed for marine teleosts. MFDB compiles fragmented multi-omics resources across 89 species, encompassing genome assemblies, phylogenomic reconstructions, collinearity maps, pan gene sets, gene architectures, functional annotations, expression profiles, and evolutionary gene family analyses. MFDB further delivers specialized analytical modules, including tissue-specific gene co-expression networks, lineage-defining core gene repertoires, and macrosynteny-driven chromosomal evolution models. The platform features an intuitive and programmable interface, enabling multiscale queries, cross-omics data mining, and dynamic visualization of multidimensional biological interactions. These functionalities collectively empower users to decipher how genomic elements orchestrate phenotypic outcomes through multi-layered regulatory cascades. By integrating rapidly expanding omics datasets with robust analytical pipelines, MFDB establishes a scalable framework to accelerate hypothesis-driven discoveries in marine fish biology, evolutionary adaptation, and ecological resilience research, and further provides an easy-to-operate information platform for the molecular breeding of marine fish species.
This work provides a critical evaluation of the functional gaps between genomic potential and in situ microbial activity and offers a novel synthesis of how multiomics integration and predictive modeling can move beyond species cataloging toward a more robust, evidence‐based framework for environmental sustainability.
The SAR11 Genome Atlas is presented, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information.
To improve cross‐species comparability, standardized annotations for 27 high‐quality genomes are generated with a unified pipeline, thereby minimizing annotation biases that often hinder comparative analyses across data sets produced by different studies.
Zhen‐Zhen Liu, Qing Xu, Yu Han et al.· Journal of Systematics and E...· 0 citations
ABSTRACT Earth's biodiversity is central to ecosystem health and resilience, providing essential functions and services. The Red Sea is a recognised marine biodiversity hotspot with high endemism and unique environmental conditions that support extensive but poorly resolved biodiversity. Here, we applied metagenomic analyses to sediment samples collected from coastal to deep‐sea environments during the Red Sea Decade Expedition 2022 to characterise biodiversity across the web of life. From a single shotgun assay per sample, this approach simultaneously characterised the sediment microbiome, which amplicon‐based surveys recover only through parallel, targeted assays, and extended detection to higher eukaryotes. Using high‐throughput sequencing, we generated 12.8 billion sequences, revealing taxa covering all domains of life. Although eukaryotic sequences represented only 0.7% of the taxonomically annotated dataset, we managed to identify 679 eukaryotic families. Prokaryotic diversity was high, as expected in a basin‐scale sampling coupled with high sequencing depth, with groups covering a wide functional array. Community structure analyses revealed depth‐driven stratification of open‐ocean benthic microbial communities and latitudinal structuring of coastal benthic eukaryotes. Overall, this dataset provides an empirical reliability–coverage trade‐off with direct consequences for the design of eDNA monitoring programmes targeting conservation‐priority taxa, and clear priorities for taxa specific reference‐database expansion.
Elisa Laiolo, Christopher A. Hempel, Balegh A. Abukabbos et al.· Environmental Microbiology· 0 citations
Penaeid shrimp are among the most commercially important aquaculture species globally, yet no dedicated integrated functional annotation and enrichment analysis platform currently for penaeid shrimp. Researchers working with shrimp transcriptomic data currently rely on generic enrichment tools built around model organisms that provide limited or no coverage for most penaeid species. In this context, current study aims to develop annotation and enrichment analysis platform for commercially important shrimp species.
ShEnrich was developed using a multi-tiered annotation pipeline combining BLASTP searches against the NCBI non-redundant database, InterProScan domain prediction, and eggNOG-mapper orthology assignments. Cross-species ortholog clustering was performed using OrthoMCL across five commercially farmed penaeid species. GMT libraries for each species were constructed for KEGG and GO enrichment analysis, implemented using the clusterProfiler R package. The platform was built on a MySQL 8.0 relational database with a PHP 8.1 backend and an integrated JBrowse2 genome browser.
The database integrates 61,287 annotated proteins representing 34,169 genes, with 178,595 gene-pathway associations across 442 KEGG pathways and 138,077 proteins mapped to 12,897 GO terms across five species:
Penaeus vannamei
,
Penaeus monodon
,
Penaeus indicus
,
Penaeus chinensis
, and
Penaeus japonicus
. Cross-species comparative genomics is supported through 18,031 ortholog groups identified using OrthoMCL. The web platform provides KEGG and GO enrichment analysis, protein annotation search, ortholog browsing, and genome visualization. ShEnrich is freely available at
https://bioinfo.ciba.res.in/shenrich/
.
ShEnrich provides the first dedicated functional annotation and enrichment analysis resource for penaeid shrimp, filling a gap that has limited biological interpretation of transcriptomic data in this economically important group. The platform supports functional analysis of gene expression studies across disease, stress, and environmental conditions in commercially farmed shrimp species.
Harikrishnan Udayakumar Geetha, Ashok Kumar Jangam, V. K. Katneni et al.· BMC Bioinformatics· 0 citations
The GenomeCompendium is released, a public database and interactive analysis tool for complete prokaryotic genomes and it is shown that complex, repeat-rich genomes are more common than previously estimated.
Tiberiu Totu, Garance Jaques, B. Heiniger et al.· bioRxiv· 0 citations
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