2026-10-14T22:38:03Z https://www.scidb.cn/oai

10.57760/sciencedb.39389 2026-06-11T15:15:23Z

2026-06-11 Genome assembly accession numbers of strains used for multilocus phylogenetic analysis doi:10.57760/sciencedb.39389 en This dataset includes two supplementary tables that provide information on the strains and sequence data used in multilocus phylogenetic analysis. Supplementary Table 1, “Genome assembly accession numbers of strains,” lists the GenBank/RefSeq accession numbers of the whole-genome assemblies of Enterobacter strains and closely related taxa used for phylogenetic analysis. Supplementary Table 2, “16S rRNA and housekeeping gene accession numbers of strains,” lists the accession numbers or location identifiers for the 16S rRNA gene and four housekeeping genes (rpoB, atpD, gyrB, and infB) used for DNA-based phylogenetic analysis. Together, these two tables provide a reference for the source of sequences used in the multilocus phylogenetic analysis, allowing traceability of each strain’s genome and target gene sequences.The strains included in the dataset are primarily from the genus Enterobacter, with additional related taxa including Leclercia adecarboxylata, Leclercia pneumoniae, and Escherichia coli K-12 GM4792 serving as comparative or outgroup material. Genome assembly accessions, 16S rRNA sequences, and housekeeping gene sequences were retrieved from NCBI GenBank/RefSeq databases or associated publicly available genome datasets. The dataset was generated by selecting representative and type strains for the study, retrieving their publicly available genome assemblies, and then extracting the 16S rRNA, rpoB, atpD, gyrB, and infB sequences from the corresponding genome assembly files, gene records, protein IDs, or old locus tags. Extracted sequences were curated and formatted consistently for multilocus sequence alignment and phylogenetic tree construction. Sequence retrieval, annotation checks, and alignments can be performed using standard bioinformatics tools, such as NCBI BLAST, NCBI Genome/GenBank, MEGA, DNAMAN, or Geneious.Supplementary Table 1 contains 26 strain records, with columns including Strain, Species, and Genome assembly. Here, “Strain” denotes the strain name or identifier, “Species” denotes the taxonomic species name, and “Genome assembly” denotes the corresponding whole-genome assembly accession number in NCBI (e.g., starting with GCA_ or GCF_). No measurement units are applicable, as these are identifiers for locating and downloading genome sequences. Supplementary Table 2 contains 27 strain records, with columns including Strains, Species, 16S, rpoB, atpD, gyrB, and infB. “Strains” denotes the strain name or identifier, “Species” the taxonomic species name, and the subsequent columns list accession numbers, protein IDs, or old locus tags for the corresponding genes. All accession numbers, protein IDs, and locus tags are database identifiers without measurement units.This dataset represents genome and gene sequence source information only; it does not include field sampling, and therefore does not contain specific temporal or spatial data or resolution. For strains where an individual housekeeping gene does not have a nucleotide accession number, the corresponding protein ID, old locus tag, or whole-genome assembly number is used, as noted in the table footnotes. Some entries may vary due to database updates, genome re-annotations, or accession version changes; users should refer to the latest NCBI records. The data do not involve experimental measurements with units and do not have measurement error, although minor discrepancies may arise due to differences in sequencing platforms, assembly quality, annotation strategies, and database version updates. To minimize the impact of these variations on phylogenetic analysis, sequences should be checked for length, orientation, homology, and alignment quality prior to tree construction.The dataset is provided in standard spreadsheet formats (Excel, CSV, or Word tables). Supplementary Table 1 provides the genome assembly accession numbers for each strain, while Supplementary Table 2 provides 16S rRNA and housekeeping gene accession numbers or location information used for multilocus phylogenetic analysis. These files can be opened and edited using Microsoft Excel, WPS Office, R, Python (pandas), or similar software. Sequence retrieval, alignment, and phylogenetic analysis can be performed using NCBI, MEGA, MAFFT, MUSCLE, IQ-TREE, PhyML, Geneious, or similar tools. genome assembly; phylogenetic analysis; Enterobacter chen hao jian Chen Qichun Xiao Yong Peng Zhengke Hu Qiongbo Yin Fei PUBLIC https://creativecommons.org/licenses/by/4.0/ dataset Science Data Bank