Genome Analysis of a Newly Sequenced B. subtilis SRCM117797 and Multiple Public B. subtilis Genomes Unveils Insights into Strain Diversification and Biased Core Gene Distribution.

Haftom Baraki Abraha, Rathnayaka Mudiyanselage Ramesha, Mokhammad Khoiron Ferdiansyah, Hyeonro Son, Gayeong Kim, Beomseok Park, Do-Youn Jeong, Kwang-Pyo Kim

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Article in Current microbiology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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8 authors.

Haftom Baraki AbrahaDepartment of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Rathnayaka Mudiyanselage RameshaDepartment of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Mokhammad Khoiron FerdiansyahDepartment of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Hyeonro SonDepartment of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Gayeong KimDepartment of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Beomseok ParkDepartment of Agricultural Convergence Technology, Jeonbuk National University, Jeonju, 54896, South Korea.

Do-Youn JeongMicrobial Institute for Fermentation Industry, Sunchang, 56048, South Korea.

Kwang-Pyo KimDepartment of Food Science and Technology, Jeonbuk National University, Jeonju, 54896, South Korea. kpkim@jbnu.ac.kr.ORCID http://orcid.org/0000-0002-3724-4151

Funding

National Research Foundation of Korea 2021R1A2C2008022

6 · The paper itself

Abstract

The bacterium Bacillus subtilis is a widely used study model and industrial workhorse organism that belongs to the group of gram-positive bacteria. In this study, we report the analysis of a newly sequenced complete genome of B. subtilis strain SRCM117797 along with a comparative genomics of a large collection of B. subtilis strain genomes. B. subtilis strain SRCM117797 has 4,255,638 bp long chromosome with 43.4% GC content and high coding sequence association with macromolecules, metabolism, and phage genes. Genomic diversity analysis of 232 B. subtilis strains resulted in the identification of eight clusters and three singletons. Of 147 B. subtilis strains included, 89.12% had strain-specific genes, of which 6.75% encoded strain-specific insertion sequence family transposases. Our analysis showed a potential role of strain-specific insertion sequence family transposases in intra-cellular accumulation of strain-specific genes. Furthermore, the chromosomal layout of the core genes was biased: overrepresented on the upper half (closer to the origin of replication) of the chromosome, which may explain the fast-growing characteristics of B. subtilis. Overall, the study provides a complete genome sequence of B. subtilis strain SRCM117797, show an extensive genomic diversity of B. subtilis strains and insights into strain diversification mechanism and non-random chromosomal layout of core genes.

Indexed as

Bacillus subtilisGenome, BacterialBase CompositionChromosomes, BacterialGenetic VariationGenomicsPhylogenySequence Analysis, DNA

Identifiers

PMID39133322

DOI10.1007/s00284-024-03819-1

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.