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The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity
Jianming Chen
Corresponding Author
ORCiD: https://orcid.org/0000-0003-0400-3092
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
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 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.
Keywords
Tachypleus tridentatus, Genome, Evolution, Innate immunity, Coagulation
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CURRENT STATUS: Published
Version 6
Posted 14 Jan, 2020
Published
On 10 Feb, 2020
No community comments so far
Editor assigned
On 13 Jan, 2020
Editorial decision: Accept
On 13 Jan, 2020
Submission checks complete
On 12 Jan, 2020
Editor invited
On 12 Jan, 2020
No comments provided
Submission checks complete
On 08 Jan, 2020
Editorial decision: Minor revision
On 08 Jan, 2020
No comments provided
Editorial decision: Minor revision
On 03 Jan, 2020
Editor assigned
On 27 Dec, 2019
Submission checks complete
On 26 Dec, 2019
Editor invited
On 26 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 17 Dec, 2019
Review #2 received
Received 05 Dec, 2019
Review #1 received
Received 05 Dec, 2019
Reviewers invited
Invitations sent on 20 Nov, 2019
Reviewer #1 agreed
On 20 Nov, 2019
Reviewer #2 agreed
On 20 Nov, 2019
Editor assigned
On 12 Nov, 2019
Submission checks complete
On 11 Nov, 2019
Editor invited
On 11 Nov, 2019
No comments provided
Editorial decision: Major revision
On 20 Oct, 2019
Review #2 received
Received 17 Oct, 2019
Review #1 received
Received 11 Sep, 2019
Reviewer #2 agreed
On 25 Aug, 2019
Reviewers invited
Invitations sent on 25 Aug, 2019
Reviewer #1 agreed
On 25 Aug, 2019
Editor assigned
On 12 Aug, 2019
Submission checks complete
On 11 Aug, 2019
Editor invited
On 11 Aug, 2019
No comments provided
Editorial decision: Major revision
On 22 Jun, 2019
Review #2 received
Received 16 Jun, 2019
Review #1 received
Received 14 Jun, 2019
Reviewer #2 agreed
On 27 May, 2019
Reviewer #1 agreed
On 25 May, 2019
Reviewers invited
Invitations sent on 07 May, 2019
Submission checks complete
On 30 Apr, 2019
Editor invited
On 30 Apr, 2019
Editor assigned
On 30 Apr, 2019
First submitted
On 21 Apr, 2019
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Subject Areas
Molecular Biology & Genetics
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
The draft genome of horseshoe crab Tachypleus tridentatus reveals its evolutionary scenario and well-developed innate immunity
Jianming Chen
Corresponding Author
ORCiD: https://orcid.org/0000-0003-0400-3092
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 6
Posted 14 Jan, 2020
Published
On 10 Feb, 2020
No community comments so far
Editor assigned
On 13 Jan, 2020
Editorial decision: Accept
On 13 Jan, 2020
Submission checks complete
On 12 Jan, 2020
Editor invited
On 12 Jan, 2020
No comments provided
Submission checks complete
On 08 Jan, 2020
Editorial decision: Minor revision
On 08 Jan, 2020
No comments provided
Editorial decision: Minor revision
On 03 Jan, 2020
Editor assigned
On 27 Dec, 2019
Submission checks complete
On 26 Dec, 2019
Editor invited
On 26 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 17 Dec, 2019
Review #2 received
Received 05 Dec, 2019
Review #1 received
Received 05 Dec, 2019
Reviewers invited
Invitations sent on 20 Nov, 2019
Reviewer #1 agreed
On 20 Nov, 2019
Reviewer #2 agreed
On 20 Nov, 2019
Editor assigned
On 12 Nov, 2019
Submission checks complete
On 11 Nov, 2019
Editor invited
On 11 Nov, 2019
No comments provided
Editorial decision: Major revision
On 20 Oct, 2019
Review #2 received
Received 17 Oct, 2019
Review #1 received
Received 11 Sep, 2019
Reviewer #2 agreed
On 25 Aug, 2019
Reviewers invited
Invitations sent on 25 Aug, 2019
Reviewer #1 agreed
On 25 Aug, 2019
Editor assigned
On 12 Aug, 2019
Submission checks complete
On 11 Aug, 2019
Editor invited
On 11 Aug, 2019
No comments provided
Editorial decision: Major revision
On 22 Jun, 2019
Review #2 received
Received 16 Jun, 2019
Review #1 received
Received 14 Jun, 2019
Reviewer #2 agreed
On 27 May, 2019
Reviewer #1 agreed
On 25 May, 2019
Reviewers invited
Invitations sent on 07 May, 2019
Submission checks complete
On 30 Apr, 2019
Editor invited
On 30 Apr, 2019
Editor assigned
On 30 Apr, 2019
First submitted
On 21 Apr, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Molecular Biology & Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Genomics.
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 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.
Figure 1
Figure 2
Figure 3
Figure 4