AnnelidaDB: a comprehensive platform of taxonomic and multi-omic resources across annelids
8 affiliations
- 1Department of Biology, Hong Kong Baptist University , Hong Kong SAR ,
- 2Data Darkness Lab, School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China , Suzhou, Jiangsu 215000 ,
- 3Laboratory of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences , Qingdao 266071 ,
- 4School of Biological and Behavioural Sciences, Queen Mary University of London , London E1 4NS ,
- 5Scripps Institution of Oceanography, University of California , San Diego 92093-0202 ,
- 6Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) , Guangzhou, Guangdong 511458 ,
- 7Department of Ocean Science, The Hong Kong University of Science and Technology , Hong Kong SAR ,
- 8Department of Computer Science, Hong Kong Baptist University , Hong Kong SAR ,
Abstract
Annelids inhabit marine, freshwater, and terrestrial ecosystems and are important models for studying animal evolution, regeneration, and host–microbe interactions, yet their rapidly growing omics resources remain dispersed across repositories and publications. We developed AnnelidaDB (www.annelidadb.com), a species-centred database built on an updated phylogenetic framework that integrates genomes, mitochondrial genomes, transcriptomes, proteomes, epigenomes, single-cell datasets, host-associated symbiont genomes, and comparative synteny for Annelida. The current release covers 1121 species, including 152 species with nuclear genomes, 177 with mitochondrial genomes, 591 with transcriptome data, 5 with single-cell datasets comprising 209 802 cells, and 30 bacterial symbiont genomes. AnnelidaDB organizes these resources through 10 navigation directories and connects species, genome, gene, functional annotation, and gene-family records. Users can browse genomic assemblies, explore interactive single-cell atlases and 12 200 precomputed Oxford plots, run BLAST queries and search genes against the annelid-specific database, and submit chromosome-level data for syntenic analysis against 20 Annelida linkage groups. Sequences, annotations, and private results are available for download. As a comprehensive multi-omics resource dedicated to annelids, AnnelidaDB provides an accessible platform for comparative investigations of annelid genome evolution, adaptation, regeneration, and symbiosis.
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BibTeX
@article{li2026annelidadb,
title = {{AnnelidaDB: a comprehensive platform of taxonomic and multi-omic resources across annelids}},
author = {Yunlong Li and Haokun Liu and Maeva Perez and Yi-Xuan Li and Fan Hui and Zihui Shen and Yanan Sun and José M Martín-Durán and Greg W Rouse and Pei-Yuan Qian and Jianliang Xu and Xike Xie and Jian-Wen Qiu},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1087},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1087/9005756},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - AnnelidaDB: a comprehensive platform of taxonomic and multi-omic resources across annelids
AU - Yunlong Li
AU - Haokun Liu
AU - Maeva Perez
AU - Yi-Xuan Li
AU - Fan Hui
AU - Zihui Shen
AU - Yanan Sun
AU - José M Martín-Durán
AU - Greg W Rouse
AU - Pei-Yuan Qian
AU - Jianliang Xu
AU - Xike Xie
AU - Jian-Wen Qiu
PY - 2026
DA - 2026/10/31
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1087
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1087/9005756
AB - Annelids inhabit marine, freshwater, and terrestrial ecosystems and are important models for studying animal evolution, regeneration, and host–microbe interactions, yet their rapidly growing omics resources remain dispersed across repositories and publications. We developed AnnelidaDB (www.annelidadb.com), a species-centred database built on an updated phylogenetic framework that integrates genomes, mitochondrial genomes, transcriptomes, proteomes, epigenomes, single-cell datasets, host-associated symbiont genomes, and comparative synteny for Annelida. The current release covers 1121 species, including 152 species with nuclear genomes, 177 with mitochondrial genomes, 591 with transcriptome data, 5 with single-cell datasets comprising 209 802 cells, and 30 bacterial symbiont genomes. AnnelidaDB organizes these resources through 10 navigation directories and connects species, genome, gene, functional annotation, and gene-family records. Users can browse genomic assemblies, explore interactive single-cell atlases and 12 200 precomputed Oxford plots, run BLAST queries and search genes against the annelid-specific database, and submit chromosome-level data for syntenic analysis against 20 Annelida linkage groups. Sequences, annotations, and private results are available for download. As a comprehensive multi-omics resource dedicated to annelids, AnnelidaDB provides an accessible platform for comparative investigations of annelid genome evolution, adaptation, regeneration, and symbiosis.
SN - 0305-1048
SN - 1362-4962
ER -