A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights
Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-le...
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| Published in | Journal of bacteriology Vol. 196; no. 12; pp. 2210 - 2215 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
American Society for Microbiology
01.06.2014
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. |
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| AbstractList | Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. |
| Author | Chen, Xiu-Lan Zhou, Jizhong Zhang, Yu-Zhong Zhou, Bai-Cheng Xie, Bin-Bin Zhang, Xi-Ying Qin, Qi-Long Oren, Aharon |
| Author_xml | – sequence: 1 givenname: Qi-Long surname: Qin fullname: Qin, Qi-Long organization: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China, Marine Biotechnology Research Center, Shandong University, Jinan, China, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China – sequence: 2 givenname: Bin-Bin surname: Xie fullname: Xie, Bin-Bin organization: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China, Marine Biotechnology Research Center, Shandong University, Jinan, China, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China – sequence: 3 givenname: Xi-Ying surname: Zhang fullname: Zhang, Xi-Ying organization: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China, Marine Biotechnology Research Center, Shandong University, Jinan, China, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China – sequence: 4 givenname: Xiu-Lan surname: Chen fullname: Chen, Xiu-Lan organization: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China, Marine Biotechnology Research Center, Shandong University, Jinan, China, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China – sequence: 5 givenname: Bai-Cheng surname: Zhou fullname: Zhou, Bai-Cheng organization: Marine Biotechnology Research Center, Shandong University, Jinan, China – sequence: 6 givenname: Jizhong surname: Zhou fullname: Zhou, Jizhong organization: Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, USA – sequence: 7 givenname: Aharon surname: Oren fullname: Oren, Aharon organization: Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel – sequence: 8 givenname: Yu-Zhong surname: Zhang fullname: Zhang, Yu-Zhong organization: State Key Laboratory of Microbial Technology, Shandong University, Jinan, China, Marine Biotechnology Research Center, Shandong University, Jinan, China, Collaborative Innovation Center of Deep Sea Biology, Shandong University, Jinan, China |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24706738$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Archaea - classification Archaea - genetics Bacteria - classification Bacteria - genetics Bacteriology Biochemistry Evolution Genetic Variation Genomics Genomics - methods Genotype & phenotype Phylogeny Prokaryotes Proteins Taxonomy |
| Title | A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights |
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