The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity
Abstract Background Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against in...
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| Format: | Article |
| Language: | English |
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BMC
2020-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-020-6488-1 |
| _version_ | 1818408590392688640 |
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| author | Yan Zhou Yuan Liang Qing Yan Liang Zhang Dianbao Chen Lingwei Ruan Yuan Kong Hong Shi Mingliang Chen Jianming Chen |
| author_facet | Yan Zhou Yuan Liang Qing Yan Liang Zhang Dianbao Chen Lingwei Ruan Yuan Kong Hong Shi Mingliang Chen Jianming Chen |
| author_sort | Yan Zhou |
| collection | DOAJ |
| description | Abstract Background Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear. Results Here, we describe the 2.06 Gbp genome assembly of Tachypleus tridentatus with 24,222 predicted protein-coding genes. Comparative genomics shows that T. tridentatus and the Atlantic horseshoe crab Limulus polyphemus have the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (including T. tridentatus and C. rotundicauda) and L. polyphemus appeared approximately 130 Mya (121–141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57–69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in the T. tridentatus genome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified in T. tridentatus with their potentially effective antimicrobial sites. Conclusions The draft genome of T. tridentatus would provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides in T. tridentatus constitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments. |
| first_indexed | 2024-12-14T09:46:09Z |
| format | Article |
| id | doaj.art-e2da106be326420882cf91380a388dc2 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-14T09:46:09Z |
| publishDate | 2020-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-e2da106be326420882cf91380a388dc22022-12-21T23:07:37ZengBMCBMC Genomics1471-21642020-02-0121111510.1186/s12864-020-6488-1The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunityYan Zhou0Yuan Liang1Qing Yan2Liang Zhang3Dianbao Chen4Lingwei Ruan5Yuan Kong6Hong Shi7Mingliang Chen8Jianming Chen9State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan UniversityState Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan UniversityShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at ShanghaiShanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at ShanghaiInstitute of Oceanography, Minjiang UniversityState Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural ResourcesInstitute of Oceanography, Minjiang UniversityState Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural ResourcesState Key Laboratory Breeding Base of Marine Genetic Resources, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural ResourcesInstitute of Oceanography, Minjiang UniversityAbstract Background Horseshoe crabs are ancient marine arthropods with a long evolutionary history extending back approximately 450 million years, which may benefit from their innate immune systems. However, the genetic mechanisms underlying their abilities of distinguishing and defending against invading microbes are still unclear. Results Here, we describe the 2.06 Gbp genome assembly of Tachypleus tridentatus with 24,222 predicted protein-coding genes. Comparative genomics shows that T. tridentatus and the Atlantic horseshoe crab Limulus polyphemus have the most orthologues shared among two species, including genes involved in the immune-related JAK-STAT signalling pathway. Divergence time dating results show that the last common ancestor of Asian horseshoe crabs (including T. tridentatus and C. rotundicauda) and L. polyphemus appeared approximately 130 Mya (121–141), and the split of the two Asian horseshoe crabs was dated to approximately 63 Mya (57–69). Hox gene analysis suggests two clusters in both horseshoe crab assemblies. Surprisingly, selective analysis of immune-related gene families revealed the high expansion of conserved pattern recognition receptors. Genes involved in the IMD and JAK-STAT signal transduction pathways also exhibited a certain degree of expansion in both genomes. Intact coagulation cascade-related genes were present in the T. tridentatus genome with a higher number of coagulation factor genes. Moreover, most reported antibacterial peptides have been identified in T. tridentatus with their potentially effective antimicrobial sites. Conclusions The draft genome of T. tridentatus would provide important evidence for further clarifying the taxonomy and evolutionary relationship of Chelicerata. The expansion of conserved immune signalling pathway genes, coagulation factors and intact antimicrobial peptides in T. tridentatus constitutes its robust and effective innate immunity for self-defence in marine environments with an enormous number of invading pathogens and may affect the quality of the adaptive properties with regard to complicated marine environments.https://doi.org/10.1186/s12864-020-6488-1Tachypleus tridentatusGenomeEvolutionInnate immunityCoagulation |
| spellingShingle | Yan Zhou Yuan Liang Qing Yan Liang Zhang Dianbao Chen Lingwei Ruan Yuan Kong Hong Shi Mingliang Chen Jianming Chen The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity BMC Genomics Tachypleus tridentatus Genome Evolution Innate immunity Coagulation |
| title | The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity |
| title_full | The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity |
| title_fullStr | The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity |
| title_full_unstemmed | The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity |
| title_short | The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity |
| title_sort | draft genome of horseshoe crab tachypleus tridentatus reveals its evolutionary scenario and well developed innate immunity |
| topic | Tachypleus tridentatus Genome Evolution Innate immunity Coagulation |
| url | https://doi.org/10.1186/s12864-020-6488-1 |
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