Work

Draft genome sequence data of Serratia nematodiphila AMFE 036/1 from Nham (Thai fermented beef sausage) revealing serralysin-family metalloproteases and secondary metabolite biosynthetic gene clusters

Year: 2026

Type: data-paper

Abstract: The draft genome sequence dataset of Serratia nematodiphila strain AMFE 036/1 was generated from an isolate obtained from Nham, a traditional Thai fermented beef sausage in Amnatcharoen province, Thailand. Whole-genome sequencing was performed using the DNBSEQ platform. Following quality filtering and preprocessing, 4,975,255 high-quality paired-end reads were retained, corresponding to an average sequencing depth of approximately 44×. A 5.4-Mbp draft genome comprising 53 contigs was generated by de novo assembly, with an N50 value of 245,680 bp and a GC content of 59.5%. Genome quality assessment using CheckM2 indicated a completeness of 100.00% and contamination of 0.07%, while BUSCO analysis yielded a completeness of 96.4% (pseudomonadota_odb12.2); both estimates indicate a near-complete genome. Genome annotation using the NCBI Prokaryotic Genome Annotation Pipeline identified 5,196 predicted genes, including 5,111 coding DNA sequences and 85 RNA genes. Functional annotation identified genes associated with hydrolytic enzyme activities, including five putative extracellular serralysin-family metalloprotease genes (EC 3.4.24.40), three of which were co-localised with cognate Inh-type metalloprotease inhibitor genes. Secondary metabolite biosynthetic gene cluster (BGC) prediction using antiSMASH identified ten BGC regions across the genome, of which two exhibited 100% similarity to known clusters in the MIBiG database, corresponding to prodigiosin and yersinopine biosynthetic pathways. Genome-based taxonomic analyses confirmed the closest relationship with S. nematodiphila DSM 21420 T (dDDH, 95.30%; ANIb, 99.17%; ANIm, 99.39%). The dataset can be used for comparative genomics, phylogenomics, genome mining, and functional annotation studies involving food-associated Serratia species.

Source: Data in Brief

DOI: 10.1016/j.dib.2026.113353