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Research article
Aide Macias Munoz
University of California Irvine
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8755-123X
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions.
Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades.
Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.
Keywords
Cnidaria, opsin, gene expression, open chromatin, phylogenetics
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CURRENT STATUS: Published
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 28 Nov, 2019
Editor assigned
On 25 Nov, 2019
Submission checks complete
On 24 Nov, 2019
Editor invited
On 24 Nov, 2019
Version 2
Posted 11 Nov, 2019
No comments provided
Editorial decision: Minor revision
On 14 Nov, 2019
Review #2 received
Received 12 Nov, 2019
Review #3 received
Received 12 Nov, 2019
Review #1 received
Received 08 Nov, 2019
Reviewer #3 agreed
On 07 Nov, 2019
Reviewers invited
Invitations sent on 06 Nov, 2019
Reviewer #1 agreed
On 06 Nov, 2019
Reviewer #2 agreed
On 06 Nov, 2019
Editor assigned
On 05 Nov, 2019
Submission checks complete
On 04 Nov, 2019
Editor invited
On 04 Nov, 2019
No comments provided
Editorial decision: Major revision
On 03 Oct, 2019
Review #7 received
Received 02 Oct, 2019
Review #4 received
Received 02 Oct, 2019
Review #1 received
Received 27 Sep, 2019
Review #2 received
Received 27 Sep, 2019
Review #6 received
Received 20 Sep, 2019
Review #3 received
Received 20 Sep, 2019
Reviewer #7 agreed
On 17 Sep, 2019
Reviewer #6 agreed
On 16 Sep, 2019
Reviewers invited
Invitations sent on 12 Sep, 2019
Reviewer #1 agreed
On 12 Sep, 2019
Reviewer #2 agreed
On 12 Sep, 2019
Reviewer #3 agreed
On 12 Sep, 2019
Reviewer #4 agreed
On 12 Sep, 2019
Reviewer #5 agreed
On 12 Sep, 2019
Submission checks complete
On 06 Sep, 2019
Editor invited
On 06 Sep, 2019
Editor assigned
On 27 Aug, 2019
First submitted
On 22 Aug, 2019
Metrics
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PDF Downloads: ...
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Subject Areas
Epigenetics & Genomics
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A new preprint design is coming!
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See the published version of this preprint at BMC Genomics.
This is a preprint, 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
Aide Macias Munoz
University of California Irvine
Corresponding Author
ORCiD: https://orcid.org/0000-0002-8755-123X
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
View the published article at BMC Genomics.
No community comments so far
Editorial decision: Accept
On 28 Nov, 2019
Editor assigned
On 25 Nov, 2019
Submission checks complete
On 24 Nov, 2019
Editor invited
On 24 Nov, 2019
Version 2
Posted 11 Nov, 2019
No comments provided
Editorial decision: Minor revision
On 14 Nov, 2019
Review #2 received
Received 12 Nov, 2019
Review #3 received
Received 12 Nov, 2019
Review #1 received
Received 08 Nov, 2019
Reviewer #3 agreed
On 07 Nov, 2019
Reviewers invited
Invitations sent on 06 Nov, 2019
Reviewer #1 agreed
On 06 Nov, 2019
Reviewer #2 agreed
On 06 Nov, 2019
Editor assigned
On 05 Nov, 2019
Submission checks complete
On 04 Nov, 2019
Editor invited
On 04 Nov, 2019
No comments provided
Editorial decision: Major revision
On 03 Oct, 2019
Review #7 received
Received 02 Oct, 2019
Review #4 received
Received 02 Oct, 2019
Review #1 received
Received 27 Sep, 2019
Review #2 received
Received 27 Sep, 2019
Review #6 received
Received 20 Sep, 2019
Review #3 received
Received 20 Sep, 2019
Reviewer #7 agreed
On 17 Sep, 2019
Reviewer #6 agreed
On 16 Sep, 2019
Reviewers invited
Invitations sent on 12 Sep, 2019
Reviewer #1 agreed
On 12 Sep, 2019
Reviewer #2 agreed
On 12 Sep, 2019
Reviewer #3 agreed
On 12 Sep, 2019
Reviewer #4 agreed
On 12 Sep, 2019
Reviewer #5 agreed
On 12 Sep, 2019
Submission checks complete
On 06 Sep, 2019
Editor invited
On 06 Sep, 2019
Editor assigned
On 27 Aug, 2019
First submitted
On 22 Aug, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: The evolution of opsin genes is of great interest because it can provide insight into the evolution of light detection and vision. An interesting group in which to study opsins is Cnidaria because it is a basal phylum sister to Bilateria with much visual diversity within the phylum. Hydra vulgaris (H. vulgaris) is a cnidarian with a plethora of genomic resources to characterize the opsin gene family. This eyeless cnidarian has a behavioral reaction to light, but it remains unknown which of its many opsins functions in light detection. Here, we used phylogenetics and RNA-seq to investigate the molecular evolution of opsin genes and their expression in H. vulgaris. We explored where opsin genes are located relative to each other in an improved genome assembly and where they belong in a cnidarian opsin phylogenetic tree. In addition, we used RNA-seq data from different tissues of the H. vulgaris adult body and different time points during regeneration and budding stages to gain insight into their potential functions.
Results: We identified 45 opsin genes in H. vulgaris, many of which were located near each other suggesting evolution by tandem duplications. Our phylogenetic tree of cnidarian opsin genes supported previous claims that they are evolving by lineage-specific duplications. We identified two H. vulgaris genes (HvOpA1 and HvOpB1) that fall outside of the two commonly determined Hydra groups; these genes possibly have a function in nematocytes and mucous gland cells respectively. We also found opsin genes that have similar expression patterns to phototransduction genes in H. vulgaris. We propose a H. vulgaris phototransduction cascade that has components of both ciliary and rhabdomeric cascades.
Conclusions: This extensive study provides an in-depth look at the molecular evolution and expression of H. vulgarisopsin genes. The expression data that we have quantified can be used as a springboard for additional studies looking into the specific function of opsin genes in this species. Our phylogeny and expression data are valuable to investigations of opsin gene evolution and cnidarian biology.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
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