title: Genomic Analysis of a Marine Bacterium: Bioinformatics for Comparison, Evaluation, and Interpretation of DNA Sequences.
abstract: A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709-AM260713). Genome-to-Genome Distance (GGDC) showed high similarity toPseudoalteromonas haloplanktis(X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR) indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains. Maximum GC content for the marine bacterium strains ranged 53-54%. The use of QR codes, CGR, FCGR, and GC dataset helped in identifying and interpreting short genome sequences from specific isolates. A phylogenetic tree was constructed with the bootstrap test (1000 replicates) using MEGA6 software. Principal Component Analysis (PCA) was carried out using EMBL-EBI MUSCLE program. Thus, generated genomic data are of great assistance for hierarchical classification in Bacterial Systematics which combined with phenotypic features represents a basic procedure for a polyphasic approach on unambiguous bacterial isolate taxonomic classification.
authors.affiliation: School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, India.
authors.forename: Bhagwan N
authors.identifier: 0000-0002-0954-0180
authors.initials: BN
authors.lastname: Rekadwad
authors.affiliation: Institute of Natural Resources and Agrobiology, Spanish National Research Council, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain.
authors.forename: Juan M
authors.identifier: 0000-0003-4746-6775
authors.initials: JM
authors.lastname: Gonzalez
authors.affiliation: School of Life Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, India.
authors.forename: Chandrahasya N
authors.initials: CN
authors.lastname: Khobragade
mesh_terms: D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D025341:Principal Component Analysis; D031161:Pseudoalteromonas / Q000235:genetics*; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*
chemical_list: D012336:RNA, Ribosomal, 16S