The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters
Abstract Background We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet includes carrion, and a complex milieu of bacteria, including potential...
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| Format: | Article |
| Language: | English |
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BMC
2019-08-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-019-6029-y |
| _version_ | 1818452113336827904 |
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| author | Monique L. van Hoek M. Dennis Prickett Robert E. Settlage Lin Kang Pawel Michalak Kent A. Vliet Barney M. Bishop |
| author_facet | Monique L. van Hoek M. Dennis Prickett Robert E. Settlage Lin Kang Pawel Michalak Kent A. Vliet Barney M. Bishop |
| author_sort | Monique L. van Hoek |
| collection | DOAJ |
| description | Abstract Background We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet includes carrion, and a complex milieu of bacteria, including potentially pathogenic strains, has been detected in the saliva of wild dragons. They appear to be unaffected, suggesting that dragons have robust defenses against infection. While little information is available regarding the molecular biology of reptile immunity, it is believed that innate immunity, which employs antimicrobial host-defense peptides including defensins and cathelicidins, plays a more prominent role in reptile immunity than it does in mammals. . Results High molecular weight genomic DNA was extracted from Komodo dragon blood cells. Subsequent sequencing and assembly of the genome from the collected DNA yielded a genome size of 1.6 Gb with 45x coverage, and the identification of 17,213 predicted genes. Through further analyses of the genome, we identified genes and gene-clusters corresponding to antimicrobial host-defense peptide genes. Multiple β-defensin-related gene clusters were identified, as well as a cluster of potential Komodo dragon ovodefensin genes located in close proximity to a cluster of Komodo dragon β-defensin genes. In addition to these defensins, multiple cathelicidin-like genes were also identified in the genome. Overall, 66 β-defensin genes, six ovodefensin genes and three cathelicidin genes were identified in the Komodo dragon genome. Conclusions Genes with important roles in host-defense and innate immunity were identified in this newly sequenced Komodo dragon genome, suggesting that these organisms have a robust innate immune system. Specifically, multiple Komodo antimicrobial peptide genes were identified. Importantly, many of the antimicrobial peptide genes were found in gene clusters. We found that these innate immunity genes are conserved among reptiles, and the organization is similar to that seen in other avian and reptilian species. Having the genome of this important squamate will allow researchers to learn more about reptilian gene families and will be a valuable resource for researchers studying the evolution and biology of the endangered Komodo dragon. |
| first_indexed | 2024-12-14T21:17:56Z |
| format | Article |
| id | doaj.art-187d18fdb1d7470480631d3cf45a54f9 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T21:17:56Z |
| publishDate | 2019-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-187d18fdb1d7470480631d3cf45a54f92022-12-21T22:47:01ZengBMCBMC Genomics1471-21642019-08-0120111810.1186/s12864-019-6029-yThe Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clustersMonique L. van Hoek0M. Dennis Prickett1Robert E. Settlage2Lin Kang3Pawel Michalak4Kent A. Vliet5Barney M. Bishop6School of Systems Biology, George Mason UniversityDipartimento di Scienze della Vita-Edif. C11, Università di TriesteAdvanced Research Computing, Virginia Polytechnic Institute and State UniversityEdward Via College of Osteopathic MedicineEdward Via College of Osteopathic MedicineDepartment of Biology, University of FloridaDepartment of Chemistry, George Mason UniversityAbstract Background We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet includes carrion, and a complex milieu of bacteria, including potentially pathogenic strains, has been detected in the saliva of wild dragons. They appear to be unaffected, suggesting that dragons have robust defenses against infection. While little information is available regarding the molecular biology of reptile immunity, it is believed that innate immunity, which employs antimicrobial host-defense peptides including defensins and cathelicidins, plays a more prominent role in reptile immunity than it does in mammals. . Results High molecular weight genomic DNA was extracted from Komodo dragon blood cells. Subsequent sequencing and assembly of the genome from the collected DNA yielded a genome size of 1.6 Gb with 45x coverage, and the identification of 17,213 predicted genes. Through further analyses of the genome, we identified genes and gene-clusters corresponding to antimicrobial host-defense peptide genes. Multiple β-defensin-related gene clusters were identified, as well as a cluster of potential Komodo dragon ovodefensin genes located in close proximity to a cluster of Komodo dragon β-defensin genes. In addition to these defensins, multiple cathelicidin-like genes were also identified in the genome. Overall, 66 β-defensin genes, six ovodefensin genes and three cathelicidin genes were identified in the Komodo dragon genome. Conclusions Genes with important roles in host-defense and innate immunity were identified in this newly sequenced Komodo dragon genome, suggesting that these organisms have a robust innate immune system. Specifically, multiple Komodo antimicrobial peptide genes were identified. Importantly, many of the antimicrobial peptide genes were found in gene clusters. We found that these innate immunity genes are conserved among reptiles, and the organization is similar to that seen in other avian and reptilian species. Having the genome of this important squamate will allow researchers to learn more about reptilian gene families and will be a valuable resource for researchers studying the evolution and biology of the endangered Komodo dragon.http://link.springer.com/article/10.1186/s12864-019-6029-yKomodo dragonVaranus komodoensisMonitor lizardInnate immunityAntimicrobial peptideDefensin |
| spellingShingle | Monique L. van Hoek M. Dennis Prickett Robert E. Settlage Lin Kang Pawel Michalak Kent A. Vliet Barney M. Bishop The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters BMC Genomics Komodo dragon Varanus komodoensis Monitor lizard Innate immunity Antimicrobial peptide Defensin |
| title | The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters |
| title_full | The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters |
| title_fullStr | The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters |
| title_full_unstemmed | The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters |
| title_short | The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters |
| title_sort | komodo dragon varanus komodoensis genome and identification of innate immunity genes and clusters |
| topic | Komodo dragon Varanus komodoensis Monitor lizard Innate immunity Antimicrobial peptide Defensin |
| url | http://link.springer.com/article/10.1186/s12864-019-6029-y |
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