2026-10-13T02:24:39Z https://www.scidb.cn/oai

10.57760/sciencedb.v.00026 2026-05-28T15:23:34Z

2026-05-28 Molluscan Transcriptome RNA Virus Dataset doi:10.57760/sciencedb.v.00026 en This dataset comprises the complete collection of RNA viral sequences, phylogenetic reconstructions, and host prediction results generated from a large-scale metatranscriptomic survey of molluscan RNA viromes. The data were produced by mining 223 publicly available, de novo assembled metatranscriptomes deposited in MolluscDB (Liu et al., 2025), spanning eight molluscan classes (Bivalvia, Solenogastres, Gastropoda, Polyplacophora, Cephalopoda, Caudofoveata, Scaphopoda, and Monoplacophora) collected from diverse geographic locations globally. RNA virus identification was performed using a custom multi-stage RdRP (RNA-dependent RNA polymerase) discovery pipeline combining six-frame end-to-end translation, profile-based homology search (HMMER v3.4, PSI-BLAST v2.16.0+, DIAMOND v2.1.10, MMseqs2 v16.747c6), and phylogenetic validation (Palmscan v2.0, CD-HIT v4.8.1). High-stringency criteria (profile coverage ≥50%, E-value ≤1e−10, score ≥70) were applied, and candidate hits were validated for conserved polymerase motifs A–C–D. Complete RdRP open reading frames were reconstructed, and non-redundant sets were generated at 90% amino acid identity with ≥75% coverage. Taxonomic annotation employed three complementary approaches: VITAP v1.7, geNomad v1.9, and BLASTp against NCBI's non-redundant protein database (NR; accessed March 15, 2025). Phylogenetic reconstruction was conducted using IQ-TREE v3.0.1 with ModelFinder Plus (1,000 ultrafast bootstrap replicates), following MUSCLE5 alignment, trimAl trimming (≤20% gaps), and Markov clustering (MCL v.22.282, inflation value 3). Three-dimensional RdRP structures were modeled using ESMFold v1.0 and compared via FoldSeek v10.941cd33 (e-value ≤1e−5). Host predictions were generated through CRISPR spacer matching, taxonomic inference from known virus–host pairs (ICTV records), and machine-learning classification using RNAVirHost v1.0.5. Relative viral abundance was estimated by mapping quality-trimmed reads (BBDuk v37.62) to RdRP-bearing contigs using Bowtie2 v2.5.4, followed by TPM calculation with CoverM v0.7.0.The dataset includes 203 high-confidence RNA viral genomes assigned to five viral phyla (Pisuviricota, Kitrinoviricota, Lenarviricota, Negarnaviricota, and Duplornaviricota), spanning 15 established orders and 3 candidate order-level lineages.  Mollusca; RNA viruses; Metatranscriptomics; Virus diversity jiaxiang Li chenkewei chenxin zhengkaiyang sunshujuan yuhao dongyue wangziyue xuyixuan andrew.mcminn yeongyiksung wenjyemok lilianwang liangyantao wangmin PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset http://www.doi.org/10.1016/j.virs.2026.05.009 Science Data Bank