Diversity and Evolution of Clostridium beijerinckii and
Complete Genome of the Type Strain DSM 791(T)

J 2021

Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T)

SEDLAR, Karel, Marketa NYKRYNOVA, Matěj BEZDÍČEK, Barbora BRANSKA, Martina LENGEROVÁ et. al.

Basic information

Original name

Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T)

Authors

SEDLAR, Karel (203 Czech Republic, guarantor), Marketa NYKRYNOVA (203 Czech Republic), Matěj BEZDÍČEK (203 Czech Republic, belonging to the institution), Barbora BRANSKA (203 Czech Republic), Martina LENGEROVÁ (203 Czech Republic), Petra PATAKOVA (203 Czech Republic) and Helena SKUTKOVA (203 Czech Republic)

Edition

PROCESSES, Vilnius, MDPI, 2021, 2227-9717

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

30204 Oncology

Country of publisher

Switzerland

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.352

RIV identification code

RIV/00216224:14110/21:00124062

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.3390/pr9071196

UT WoS

000676954500001

Keywords in English

butanol; ABE; IBE; core genome; accessory genome; pan genome

Abstract

V originále

Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791(T), composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.

Citovat

SEDLAR, Karel, Marketa NYKRYNOVA, Matěj BEZDÍČEK, Barbora BRANSKA, Martina LENGEROVÁ, Petra PATAKOVA and Helena SKUTKOVA. Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T). PROCESSES. Vilnius: MDPI, 2021, vol. 9, No 7, p. 1-16. ISSN 2227-9717. Available from: https://dx.doi.org/10.3390/pr9071196.

@article{1831973,
   author = {Sedlar, Karel and Nykrynova, Marketa and Bezdíček, Matěj and Branska, Barbora and Lengerová, Martina and Patakova, Petra and Skutkova, Helena},
   article_location = {Vilnius},
   article_number = {7},
   doi = {http://dx.doi.org/10.3390/pr9071196},
   keywords = {butanol; ABE; IBE; core genome; accessory genome; pan genome},
   language = {eng},
   issn = {2227-9717},
   journal = {PROCESSES},
   title = {Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T)},
   url = {https://www.mdpi.com/2227-9717/9/7/1196/htm},
   volume = {9},
   year = {2021}
}

TY  - JOUR
ID  - 1831973
AU  - Sedlar, Karel - Nykrynova, Marketa - Bezdíček, Matěj - Branska, Barbora - Lengerová, Martina - Patakova, Petra - Skutkova, Helena
PY  - 2021
TI  - Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T)
JF  - PROCESSES
VL  - 9
IS  - 7
SP  - 1-16
EP  - 1-16
PB  - MDPI
SN  - 22279717
KW  - butanol
KW  - ABE
KW  - IBE
KW  - core genome
KW  - accessory genome
KW  - pan genome
UR  - https://www.mdpi.com/2227-9717/9/7/1196/htm
N2  - Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791(T), composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology.
ER  -

SEDLAR, Karel, Marketa NYKRYNOVA, Matěj BEZDÍČEK, Barbora BRANSKA, Martina LENGEROVÁ, Petra PATAKOVA and Helena SKUTKOVA. Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791(T). \textit{PROCESSES}. Vilnius: MDPI, 2021, vol.~9, No~7, p.~1-16. ISSN~2227-9717. Available from: https://dx.doi.org/10.3390/pr9071196.

Detailed Information on Publication Record