The lab released the most comprehensive functional and evolutionary genomics database for molluscs

     On November 12, 2024, our research group launched MolluscDB 2.0, the most comprehensive functional and evolutionary genomics database for molluscs to date. The research was published in Nucleic Acids Research under the title "MolluscDB 2.0: A Comprehensive Functional and Evolutionary Genomics Database for Over 1,400 Molluscan Species".

    Mollusca, the second-largest phylum in the animal kingdom and the largest marine animal group, originated approximately 540 million years ago. With over 100,000 extant species, molluscs represent one of the most evolutionarily successful invertebrate groups. Furthermore, many molluscs are economically important in fisheries and aquaculture, comprising ∼27% of global aquaculture production. With the rapid development of molluscan genomics, significant scientific discoveries have been made continuously, greatly enhancing the depth of understanding of animal origins and adaptive evolution. In collaboration with leading global institutions, our research team initiated the Mollusca 10,000 Genomes Project (M10K+ project) and constructed the first comprehensive genomic database for Mollusca in 2021, named MolluscDB (http://mgbase.qnlm.ac). This database integrated 1,000 genomic and transcriptomic datasets and provided tools for comparative genomic analyses. Since its release, MolluscDB has attracted nearly 15,000 accesses from over 70 countries, becoming the largest molluscan genomic resources center in the world.

Fig. 1 The impact of MolluscDB. (a The global visits of MolluscDB; b The citation of MolluscDB from diverse research areas; c The rank of MolluscDB; d The initiation ceremony of M10K project.)

    In recent years, the booming of high-quality genomes and diverse functional genomic data has propelled molluscan research into the era of systems biology, unlocking new opportunities for scientific exploration. However, integrating multi-omics resources characterized by "complexity, high dimensionality, and huge amount" to build customized analytical platforms tailored to molluscan biological characteristics remains a critical challenge in the field. To address these challenges, we have substantially upgraded MolluscDB 1.0 to MolluscDB 2.0 (http://mgbase.qnlm.ac), integrating a vast array of functional genomic resources and providing tools for multilevel integrative and comparative analyses.

    MolluscDB 2.0 integrates nearly 4,200 multi-omics datasets comprised of almost all public molluscan datasets, achieving the coverage of six multi-omics layers, including high-quality genomes, bulk transcriptomes, single-cell transcriptomes, proteomes, epigenomes, and metagenomes. These multi-omics resources span 1,450 molluscan species, covering all 8 classes and 92% of the 76 orders, with geographic distributions ranging from terrestrial, freshwaterr, offshore and deep-sea ecosystems. MolluscDB 2.0 significantly improves 14 original modules including genome assembly, genome annotation, gene family clustering, transcription factor, transposable element, gene expression profiles, and gene co-expression networks of various developmental stages and adult tissues/ organs, and develops more than 20 special customized modules including pan-evolutionary modules (utilizing the PanSyn toolkit developed by our group; Nature Protocols 2024), evo-devo modules, and functional genomics modules related to single-cell transcriptome, proteome, epigenome, and metagenome datasets. The complex information is also integrated into a customized genome browser, enabling multi-dimensional visualization of genetic information.  

    MolluscDB 2.0 serves as an open-access database platform for molluscan research, with the most representative taxonomic coverage, the most abundant multi-omics datasets and the most comprehensive analytical functions. It enables systematic integration and in-depth analysis of ever-growing related resources, facilitating a more comprehensive understanding of the biological mysteries and evolutionary history of molluscs. The platform will also promote the understanding of the evolution of the unique life processes of marine organisms, and provide strong support for the genetic breeding of molluscs.

Fig. 2 Overview of taxonomy coverage in MolluscDB 2.0

Fig. 3. Overview of MolluscDB 2.0 database architecture and function.

    Professors Yuli Li, Shi Wang and Lingling Zhang of the Key Laboratory of Marine Genetics and Breeding (Ministry of Education), and the Center for Marine Biology Evolution and Development led by Fang Zongxi, serve as co-corresponding authors of the paper, with Dr. Fuyun Liu, Master's candidate Bingcheng Cai and Associate Professor Shanshan Lian as co-first authors. This research was supported by National Key R&D Program of China, National Natural Science Foundation of China, Fundamental Research Funds for the Central Universities, Science & Technology Innovation Project of Laoshan Laboratory, Key Research and Development Program of Shandong Province, Taishan Scholar Project of Shandong Province. This work was also supported by the High-Performance Computing and System Simulation Center of the Laoshan National Laboratory and the High-Performance Biological Supercomputing Center of the Ocean University of China.

Paper links:：https://doi.org/10.1093/nar/gkae1026