Ocean Genomics: Banking & Sequencing Survey

1.

The purpose of this survey is:

1. To identify marine species that should be top priorities for sequencing and/or biobanking due to their conservation value.

2. To identify critical sequencing or biobanking resource gaps that may be limiting the conservation benefits of genetic rescue techniques in marine conservation.

3. To target funding recommendations to address critical resource gaps.

The survey needs to be completed for a specific species or taxon. If you work on multiple species, it would be ideal if you would complete a survey for each species. You may take the survey as many times as you want. The more data we get the better.

The survey is 18 questions and should take you less than 10 minutes.

Many thanks!

Section 1: Overview

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* 1. What marine organism or system do you study?

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* 2. Rank the significance (a combination of severity and scope) of the following threats to the species/system that you work on:

	Highest Priority	High Priority	Medium Concern	Low Priority	Lowest Priority	Not Applicable
Disease	Disease Highest Priority	Disease High Priority	Disease Medium Concern	Disease Low Priority	Disease Lowest Priority	Disease Not Applicable
Pollution	Pollution Highest Priority	Pollution High Priority	Pollution Medium Concern	Pollution Low Priority	Pollution Lowest Priority	Pollution Not Applicable
Habitat Loss / Alteration	Habitat Loss / Alteration Highest Priority	Habitat Loss / Alteration High Priority	Habitat Loss / Alteration Medium Concern	Habitat Loss / Alteration Low Priority	Habitat Loss / Alteration Lowest Priority	Habitat Loss / Alteration Not Applicable
Climate Change	Climate Change Highest Priority	Climate Change High Priority	Climate Change Medium Concern	Climate Change Low Priority	Climate Change Lowest Priority	Climate Change Not Applicable
Invasive Species	Invasive Species Highest Priority	Invasive Species High Priority	Invasive Species Medium Concern	Invasive Species Low Priority	Invasive Species Lowest Priority	Invasive Species Not Applicable
Over-Exploitation	Over-Exploitation Highest Priority	Over-Exploitation High Priority	Over-Exploitation Medium Concern	Over-Exploitation Low Priority	Over-Exploitation Lowest Priority	Over-Exploitation Not Applicable

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* 3. Which of the following sequencing resources do you use in your research?

	Never	Rarely	Often	Planning On It
Barcoding	Barcoding Never	Barcoding Rarely	Barcoding Often	Barcoding Planning On It
Specific Gene Markers	Specific Gene Markers Never	Specific Gene Markers Rarely	Specific Gene Markers Often	Specific Gene Markers Planning On It
Microsatellite Markers	Microsatellite Markers Never	Microsatellite Markers Rarely	Microsatellite Markers Often	Microsatellite Markers Planning On It
RADseq	RADseq Never	RADseq Rarely	RADseq Often	RADseq Planning On It
SNP Array / SNP Chips	SNP Array / SNP Chips Never	SNP Array / SNP Chips Rarely	SNP Array / SNP Chips Often	SNP Array / SNP Chips Planning On It
Whole Genomes (Low or High Coverage)	Whole Genomes (Low or High Coverage) Never	Whole Genomes (Low or High Coverage) Rarely	Whole Genomes (Low or High Coverage) Often	Whole Genomes (Low or High Coverage) Planning On It
Gene Expression / RNAseq	Gene Expression / RNAseq Never	Gene Expression / RNAseq Rarely	Gene Expression / RNAseq Often	Gene Expression / RNAseq Planning On It

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* 4. Indicate which (if any) of the following are limiting your use of genomics for guiding conservation efforts?

Expense

My lab lacks technical expertise to process samples for sequencing.

My lab lacks technical expertise to process bioinformatic data.

I am unaware of how these techniques can improve / benefit my work.

I do not believe genomics will improve / benefit my work.

Not applicable.

Other (please specify)

Section 2: Sequencing Data
Please select a single priority species for which to answer the following questions.

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* 5. Identify the species:

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* 6. Has the genome sequence of this species been published?

Yes

Unsure

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* 7. If yes, where are the sequence data available?

Not Applicable

GenBank

And / or another shared repository (please specify):

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* 8. If the genome sequence is complete but unpublished, which of the following reasons why it is not publicly available is most applicable?

The sequence will be published as part of a specific research inquiry.

There is uncertainty on the quality of the data.

The team is still annotating the genome.

The status of the project is unknown.

Not Applicable

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* 9. To what level of assembly is the current state of your species' genome or the best reference genome?

Contigs Only

Contigs and Scaffolds

Linkage Groups, Scaffolds, and Contigs

Complete Chromosomal Assembly

Unknown

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* 10. What is the quality of the annotation for your reference genome?

Not Annotated

Partially Annotated

Well Annotated

Not Applicable

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* 11. From where are annotations derived?

Mostly from predictive algorithms and gene models.

RNA-seq, transcriptome mapping, and gene prediction.

Annotated but uncertain of technique used.

Not Applicable

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* 12. Identify how you use (or would use) genomic information in your research and prioritize its importance:

	Critical	Very Important	Somewhat Important	Potentially Important	Not Important
Biodiversity assessments.	Biodiversity assessments. Critical	Biodiversity assessments. Very Important	Biodiversity assessments. Somewhat Important	Biodiversity assessments. Potentially Important	Biodiversity assessments. Not Important
Identifying adaptive variation across geographic and environmental gradient.	Identifying adaptive variation across geographic and environmental gradient. Critical	Identifying adaptive variation across geographic and environmental gradient. Very Important	Identifying adaptive variation across geographic and environmental gradient. Somewhat Important	Identifying adaptive variation across geographic and environmental gradient. Potentially Important	Identifying adaptive variation across geographic and environmental gradient. Not Important
Identifying mechanisms underlying resilience / tolerance / resistance to disease.	Identifying mechanisms underlying resilience / tolerance / resistance to disease. Critical	Identifying mechanisms underlying resilience / tolerance / resistance to disease. Very Important	Identifying mechanisms underlying resilience / tolerance / resistance to disease. Somewhat Important	Identifying mechanisms underlying resilience / tolerance / resistance to disease. Potentially Important	Identifying mechanisms underlying resilience / tolerance / resistance to disease. Not Important
Marine Spacial Planning (MPAs).	Marine Spacial Planning (MPAs). Critical	Marine Spacial Planning (MPAs). Very Important	Marine Spacial Planning (MPAs). Somewhat Important	Marine Spacial Planning (MPAs). Potentially Important	Marine Spacial Planning (MPAs). Not Important
Improving fisheries management.	Improving fisheries management. Critical	Improving fisheries management. Very Important	Improving fisheries management. Somewhat Important	Improving fisheries management. Potentially Important	Improving fisheries management. Not Important
Disease surveillance and reporting.	Disease surveillance and reporting. Critical	Disease surveillance and reporting. Very Important	Disease surveillance and reporting. Somewhat Important	Disease surveillance and reporting. Potentially Important	Disease surveillance and reporting. Not Important
Identifying critical genetic elements (promoters, CDS, terminators, etc).	Identifying critical genetic elements (promoters, CDS, terminators, etc). Critical	Identifying critical genetic elements (promoters, CDS, terminators, etc). Very Important	Identifying critical genetic elements (promoters, CDS, terminators, etc). Somewhat Important	Identifying critical genetic elements (promoters, CDS, terminators, etc). Potentially Important	Identifying critical genetic elements (promoters, CDS, terminators, etc). Not Important
Identifying mechanisms underlying resilience / tolerance / resistance to climate change.	Identifying mechanisms underlying resilience / tolerance / resistance to climate change. Critical	Identifying mechanisms underlying resilience / tolerance / resistance to climate change. Very Important	Identifying mechanisms underlying resilience / tolerance / resistance to climate change. Somewhat Important	Identifying mechanisms underlying resilience / tolerance / resistance to climate change. Potentially Important	Identifying mechanisms underlying resilience / tolerance / resistance to climate change. Not Important
Monitoring or Managing invasive species.	Monitoring or Managing invasive species. Critical	Monitoring or Managing invasive species. Very Important	Monitoring or Managing invasive species. Somewhat Important	Monitoring or Managing invasive species. Potentially Important	Monitoring or Managing invasive species. Not Important
Gene editing or genetic engineering.	Gene editing or genetic engineering. Critical	Gene editing or genetic engineering. Very Important	Gene editing or genetic engineering. Somewhat Important	Gene editing or genetic engineering. Potentially Important	Gene editing or genetic engineering. Not Important

Section 3: Cryopreservation, Cell Culturing, Etc.

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* 13. Identify the availability of the following technologies in your research area:

	Not Available or Not Applicable	Partially Available	Widely Available	Generally Available
Established Immortalized Cell Lines	Established Immortalized Cell Lines Not Available or Not Applicable	Established Immortalized Cell Lines Partially Available	Established Immortalized Cell Lines Widely Available	Established Immortalized Cell Lines Generally Available
Primary Cell Sorting Capabilities	Primary Cell Sorting Capabilities Not Available or Not Applicable	Primary Cell Sorting Capabilities Partially Available	Primary Cell Sorting Capabilities Widely Available	Primary Cell Sorting Capabilities Generally Available
Functional Primary Cell Culture Protocols	Functional Primary Cell Culture Protocols Not Available or Not Applicable	Functional Primary Cell Culture Protocols Partially Available	Functional Primary Cell Culture Protocols Widely Available	Functional Primary Cell Culture Protocols Generally Available
Gamete Cryopreservation Protocols	Gamete Cryopreservation Protocols Not Available or Not Applicable	Gamete Cryopreservation Protocols Partially Available	Gamete Cryopreservation Protocols Widely Available	Gamete Cryopreservation Protocols Generally Available
Embryonic Cryopreservation Protocols	Embryonic Cryopreservation Protocols Not Available or Not Applicable	Embryonic Cryopreservation Protocols Partially Available	Embryonic Cryopreservation Protocols Widely Available	Embryonic Cryopreservation Protocols Generally Available
In Vitro Reproductive Technologies	In Vitro Reproductive Technologies Not Available or Not Applicable	In Vitro Reproductive Technologies Partially Available	In Vitro Reproductive Technologies Widely Available	In Vitro Reproductive Technologies Generally Available
Surrogate Species for Embryonic / Germ-Line Transfer	Surrogate Species for Embryonic / Germ-Line Transfer Not Available or Not Applicable	Surrogate Species for Embryonic / Germ-Line Transfer Partially Available	Surrogate Species for Embryonic / Germ-Line Transfer Widely Available	Surrogate Species for Embryonic / Germ-Line Transfer Generally Available

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* 14. Identify the value of the following technologies in terms of conservation value to your research area:

	Critical	Very Important	Somewhat Important	Not Important	Not Applicable
Established Immortalized Cell Lines	Established Immortalized Cell Lines Critical	Established Immortalized Cell Lines Very Important	Established Immortalized Cell Lines Somewhat Important	Established Immortalized Cell Lines Not Important	Established Immortalized Cell Lines Not Applicable
Primary Cell Sorting Capabilities	Primary Cell Sorting Capabilities Critical	Primary Cell Sorting Capabilities Very Important	Primary Cell Sorting Capabilities Somewhat Important	Primary Cell Sorting Capabilities Not Important	Primary Cell Sorting Capabilities Not Applicable
Functional Primary Cell Culture Protocols	Functional Primary Cell Culture Protocols Critical	Functional Primary Cell Culture Protocols Very Important	Functional Primary Cell Culture Protocols Somewhat Important	Functional Primary Cell Culture Protocols Not Important	Functional Primary Cell Culture Protocols Not Applicable
Gamete Cryopreservation Protocols	Gamete Cryopreservation Protocols Critical	Gamete Cryopreservation Protocols Very Important	Gamete Cryopreservation Protocols Somewhat Important	Gamete Cryopreservation Protocols Not Important	Gamete Cryopreservation Protocols Not Applicable
Embryonic Cryopreservation Protocols	Embryonic Cryopreservation Protocols Critical	Embryonic Cryopreservation Protocols Very Important	Embryonic Cryopreservation Protocols Somewhat Important	Embryonic Cryopreservation Protocols Not Important	Embryonic Cryopreservation Protocols Not Applicable
In Vitro Reproductive Technologies	In Vitro Reproductive Technologies Critical	In Vitro Reproductive Technologies Very Important	In Vitro Reproductive Technologies Somewhat Important	In Vitro Reproductive Technologies Not Important	In Vitro Reproductive Technologies Not Applicable
Surrogate Species for Embryonic / Germ-Line Transfer	Surrogate Species for Embryonic / Germ-Line Transfer Critical	Surrogate Species for Embryonic / Germ-Line Transfer Very Important	Surrogate Species for Embryonic / Germ-Line Transfer Somewhat Important	Surrogate Species for Embryonic / Germ-Line Transfer Not Important	Surrogate Species for Embryonic / Germ-Line Transfer Not Applicable

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* 15. Cell cultures allow for a variety of research into genetics and molecular biology in vitro, as a substitute to working with live organisms, from basic cell culture to lab-grown organoids. Many questions you may have about your system could have an in vitro research pathway if cell cultures were available.

Rank the following in terms of how cell culture could improve the conservation outcome for your taxon.

	Very Critical	Critical	Somewhat Critical	Not Critical
Genome Annotation	Genome Annotation Very Critical	Genome Annotation Critical	Genome Annotation Somewhat Critical	Genome Annotation Not Critical
Disease Pathology / Host Immunology	Disease Pathology / Host Immunology Very Critical	Disease Pathology / Host Immunology Critical	Disease Pathology / Host Immunology Somewhat Critical	Disease Pathology / Host Immunology Not Critical
Mechanisms of Symbiosis	Mechanisms of Symbiosis Very Critical	Mechanisms of Symbiosis Critical	Mechanisms of Symbiosis Somewhat Critical	Mechanisms of Symbiosis Not Critical
Cellular or Molecular Responses (i.e. gene expression, metabolism, etc.) to Specific Stimuli (i.e. mimicking environmental changes such as ocean acidification)	Cellular or Molecular Responses (i.e. gene expression, metabolism, etc.) to Specific Stimuli (i.e. mimicking environmental changes such as ocean acidification) Very Critical	Cellular or Molecular Responses (i.e. gene expression, metabolism, etc.) to Specific Stimuli (i.e. mimicking environmental changes such as ocean acidification) Critical	Cellular or Molecular Responses (i.e. gene expression, metabolism, etc.) to Specific Stimuli (i.e. mimicking environmental changes such as ocean acidification) Somewhat Critical	Cellular or Molecular Responses (i.e. gene expression, metabolism, etc.) to Specific Stimuli (i.e. mimicking environmental changes such as ocean acidification) Not Critical
Functional Genomic Analyses	Functional Genomic Analyses Very Critical	Functional Genomic Analyses Critical	Functional Genomic Analyses Somewhat Critical	Functional Genomic Analyses Not Critical
Genetic Engineering / Gene Editing	Genetic Engineering / Gene Editing Very Critical	Genetic Engineering / Gene Editing Critical	Genetic Engineering / Gene Editing Somewhat Critical	Genetic Engineering / Gene Editing Not Critical

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* 16. With the right technologies (e.g. cloning, stem cells, etc.), cell cultures can be a resource not simply for conservation insight to develop genetic rescue applications, but they can also be used to directly facilitate conservation goals for threatened populations. For example, preserved cell lines could be used to maintain genetic viability over time, or the information obtained from studying disease pathology could be translated directly into a solution to establish disease resistance.

Rank the following in terms of how cellular-based technologies could improve the conservation outcome of your taxon / system:

	Critical	Very Critical	Somewhat Critical	Not Critical	Not Applicable
Genetic preservation for future recovery and deployment to the wild.	Genetic preservation for future recovery and deployment to the wild. Critical	Genetic preservation for future recovery and deployment to the wild. Very Critical	Genetic preservation for future recovery and deployment to the wild. Somewhat Critical	Genetic preservation for future recovery and deployment to the wild. Not Critical	Genetic preservation for future recovery and deployment to the wild. Not Applicable
Assisted reproduction to spread adaptive alleles.	Assisted reproduction to spread adaptive alleles. Critical	Assisted reproduction to spread adaptive alleles. Very Critical	Assisted reproduction to spread adaptive alleles. Somewhat Critical	Assisted reproduction to spread adaptive alleles. Not Critical	Assisted reproduction to spread adaptive alleles. Not Applicable
Assisted reproduction to increase / restore genetic diversity.	Assisted reproduction to increase / restore genetic diversity. Critical	Assisted reproduction to increase / restore genetic diversity. Very Critical	Assisted reproduction to increase / restore genetic diversity. Somewhat Critical	Assisted reproduction to increase / restore genetic diversity. Not Critical	Assisted reproduction to increase / restore genetic diversity. Not Applicable
Gene-editing organisms to increase genetic diversity.	Gene-editing organisms to increase genetic diversity. Critical	Gene-editing organisms to increase genetic diversity. Very Critical	Gene-editing organisms to increase genetic diversity. Somewhat Critical	Gene-editing organisms to increase genetic diversity. Not Critical	Gene-editing organisms to increase genetic diversity. Not Applicable
Gene-editing organisms for biocontrol (e.g. gene drives).	Gene-editing organisms for biocontrol (e.g. gene drives). Critical	Gene-editing organisms for biocontrol (e.g. gene drives). Very Critical	Gene-editing organisms for biocontrol (e.g. gene drives). Somewhat Critical	Gene-editing organisms for biocontrol (e.g. gene drives). Not Critical	Gene-editing organisms for biocontrol (e.g. gene drives). Not Applicable
Gene-editing organisms to integrate / spread adaptive alleles.	Gene-editing organisms to integrate / spread adaptive alleles. Critical	Gene-editing organisms to integrate / spread adaptive alleles. Very Critical	Gene-editing organisms to integrate / spread adaptive alleles. Somewhat Critical	Gene-editing organisms to integrate / spread adaptive alleles. Not Critical	Gene-editing organisms to integrate / spread adaptive alleles. Not Applicable
Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation).	Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation). Critical	Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation). Very Critical	Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation). Somewhat Critical	Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation). Not Critical	Synthetic Alternatives (e.g. lab-grown bioproducts to reduce overexploitation). Not Applicable

Conclusion

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* 17. Please provide any additional comments with regard to genomic technologies and conservation in marine ecosystems that you feel warrant consideration and were not covered by this survey. (500 characters max.)

Thank you for taking the time to complete this survey. Revive & Restore will use it to refine our research findings on the status of genomics in marine conservation.

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* 18. If you are interested, please add your contact information below to receive the results of the Ocean Genomics Horizon Scan:

Name

Email Address