Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential
The genus <i>Geobacillus</i> is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that <i>Geobacillus</i> evolved from <i>Bacillus</i>, relatively little knowledg...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/9/3393 |
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| author | Mengmeng Wang Han Zhu Zhijian Kong Tuo Li Lei Ma Dongyang Liu Qirong Shen |
| author_facet | Mengmeng Wang Han Zhu Zhijian Kong Tuo Li Lei Ma Dongyang Liu Qirong Shen |
| author_sort | Mengmeng Wang |
| collection | DOAJ |
| description | The genus <i>Geobacillus</i> is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that <i>Geobacillus</i> evolved from <i>Bacillus</i>, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two <i>Geobacillus</i> genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of <i>Geobacillus</i> strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the <i>Geobacillus</i> strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of <i>Geobacillus</i> seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different <i>Geobacillus</i> species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and <i>Geobacillus</i>’ evolution was directed by the environment and HGT events. |
| first_indexed | 2024-03-10T19:54:38Z |
| format | Article |
| id | doaj.art-905cb00ac72e438a90289599f94e4b26 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T19:54:38Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-905cb00ac72e438a90289599f94e4b262023-11-20T00:04:48ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-05-01219339310.3390/ijms21093393Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting PotentialMengmeng Wang0Han Zhu1Zhijian Kong2Tuo Li3Lei Ma4Dongyang Liu5Qirong Shen6Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaJiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University, Nanjing 210095, ChinaThe genus <i>Geobacillus</i> is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that <i>Geobacillus</i> evolved from <i>Bacillus</i>, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two <i>Geobacillus</i> genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of <i>Geobacillus</i> strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the <i>Geobacillus</i> strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of <i>Geobacillus</i> seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different <i>Geobacillus</i> species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and <i>Geobacillus</i>’ evolution was directed by the environment and HGT events.https://www.mdpi.com/1422-0067/21/9/3393<i>Geobacillus</i>comparative genomicspan-genomecore genomegenomic featuresevolutionary events |
| spellingShingle | Mengmeng Wang Han Zhu Zhijian Kong Tuo Li Lei Ma Dongyang Liu Qirong Shen Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential International Journal of Molecular Sciences <i>Geobacillus</i> comparative genomics pan-genome core genome genomic features evolutionary events |
| title | Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential |
| title_full | Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential |
| title_fullStr | Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential |
| title_full_unstemmed | Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential |
| title_short | Pan-Genome Analyses of <i>Geobacillus</i> spp. Reveal Genetic Characteristics and Composting Potential |
| title_sort | pan genome analyses of i geobacillus i spp reveal genetic characteristics and composting potential |
| topic | <i>Geobacillus</i> comparative genomics pan-genome core genome genomic features evolutionary events |
| url | https://www.mdpi.com/1422-0067/21/9/3393 |
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