<script type="text/javascript">
<!--
document.write('<div id="oa_widget"></div>');
document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=undefined&type=result"></script>');
-->
</script>

COPY SCRIPT

For further information contact us at helpdesk@openaire.eu

The Genome Sequence of the Octocoral Paramuricea clavata – A Key Resource To Study the Impact of Climate Change in the Mediterranean

descriptionPublicationkeyboard_double_arrow_right Article 01 Sep 2020 Spain, Spain, Croatia, France Publisher:Oxford University Press (OUP)Journal:G3 Genes|Genomes|Genetics, volume 10, pages 2,941-2,952 (eissn: 2160-1836,

Authors: Jean-Baptiste Ledoux; Fernando Cruz; Jèssica Gómez-Garrido; Regina Antoni; Julie Blanc; Daniel Gómez-Gras; Silvija Kipson; +6 Authors

doi: 10.1534/g3.120.401371

pmc: PMC7467007

pmid: 32660973

handle: 10230/45630 , 10261/219096

The Genome Sequence of the Octocoral Paramuricea clavata – A Key Resource To Study the Impact of Climate Change in the Mediterranean

- Summary
- Subjects
- References
  (58)
- Related research
  (1)
- Metrics

Abstract

The octocoral, Paramuricea clavata, is a habitat-forming anthozoan with a key ecological role in rocky benthic and biodiversity-rich communities in the Mediterranean and Eastern Atlantic. Shallow populations of P. clavata in the North-Western Mediterranean are severely affected by warming-induced mass mortality events (MMEs). These MMEs have differentially impacted individuals and populations of P. clavata (i.e., varied levels of tissue necrosis and mortality rates) over thousands of kilometers of coastal areas. The eco-evolutionary processes, including genetic factors, contributing to these differential responses remain to be characterized. Here, we sequenced a P. clavata individual with short and long read technologies, producing 169.98 Gb of Illumina paired-end and 3.55 Gb of Oxford Nanopore Technologies (ONT) reads. We obtained a de novo genome assembly accounting for 607 Mb in 64,145 scaffolds. The contig and scaffold N50s are 19.15 Kb and 23.92 Kb, respectively. Despite of the low contiguity of the assembly, its gene completeness is relatively high, including 75.8% complete and 9.4% fragmented genes out of the 978 metazoan genes contained in the metazoa_odb9 database. A total of 62,652 protein-coding genes have been annotated. This assembly is one of the few octocoral genomes currently available. This is undoubtedly a valuable resource for characterizing the genetic bases of the differential responses to thermal stress and for the identification of thermo-resistant individuals and populations. Overall, having the genome of P. clavata will facilitate studies of various aspects of its evolutionary ecology and elaboration of effective conservation plans such as active restoration to overcome the threats of global change

We acknowledge the funding support of the European Union’s Horizon 2020 research and innovation program under grant agreement No 689518 (MERCES) and the Strategic Funding UID/Multi/04423/2013 through national funds provided by FCT – Foundation for Science and Technology and European Regional Development Fund (ERDF), in the framework of the programme PT2020. JBL is funded by an assistant researcher contract framework of the RD Unit - UID/Multi/04423/2019 - Interdisciplinary Centre of Marine and Environmental Research – financed by the European Regional Development Fund (ERDF) through COMPETE2020 - Operational Program for Competitiveness and Internationalisation (POCI) and national funds through FCT/MCTES (PIDDAC). AA was partially supported by the FCT project PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017). DGG was supported by an FPU grant (FPU15/05457) from the Spanish Ministry of Education. We acknowledge support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme / Generalitat de Catalunya, the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement, and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program. JBL and JG planned and granted the funding to start the project

With the funding support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S), of the Spanish Research Agency (AEI)

12 pages, 5 figures, 6 tables, supplemental material https://doi.org/10.25387/g3.12640691

Peer reviewed

Countries

Spain, Spain, Croatia, France

Related Organizations

View all View all

Subjects by Vocabulary

Microsoft Academic Graph classification: ved/biology.organism_classification_rank.species Sequence assembly Biology Genome Gene Whole genome sequencing Contig ved/biology Genome project Evolutionary biology Evolutionary ecology Paramuricea clavata

Keywords

genome annotation, Climate Change, Paramuricea clavata, QH426-470, de novo assembly, global warming, octocoral, Genetics, Animals, Humans, Molecular Biology, Ecosystem, Genetics (clinical), [SDU.OCEAN]Sciences of the Universe [physics]/Ocean, Atmosphere, Oxford Nanopore Technologies, whole genome sequencing, Genome, long read sequencing, Paramuricea clavata ; octocoral ; temperate habitat-forming anthozoan ; mass mortality events ; global warming ; whole genome sequencing ; de novo assembly ; genome 30 annotation ; Oxford Nanopore Technologies ; long read sequencing, High-Throughput Nucleotide Sequencing, temperate habitat-forming anthozoan, Anthozoa, Genome Report, mass mortality events

58 references, page 1 of 6

Adachi, K., H. Miyake, T. Kuramochi, K. Mizusawa, and S. Okumura, 2017 Genome size distribution in phylum Cnidaria. Fish. Sci. 83: 107-112. https://doi.org/10.1007/s12562-016-1050-4

Alexa, A., J. Rahnenfuhrer, and T. Lengauer, 2006 Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607. https://doi.org/10.1093/bioinformatics/btl140 [OpenAIRE]

Altschul, S. F., T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang et al., 1997 Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402. https:// doi.org/10.1093/nar/25.17.3389

Arizmendi-Mejía, R., C. Linares, J. Garrabou, A. Antunes, E. Ballesteros et al., 2015a Combining genetic and demographic data for the conservation of a mediterranean marine habitat-forming species. PLoS One 10: e0119585. https://doi.org/10.1371/journal.pone.0119585

Arizmendi-Mejía, R., J.-B. Ledoux, S. Civit, A. Antunes, Z. Thanopoulou et al., 2015b Demographic responses to warming: reproductive maturity and sex influence vulnerability in an octocoral. Coral Reefs 34: 1207-1216. https://doi.org/10.1007/s00338-015-1332-9

Van der Auwera, G. A., M. O. Carneiro, C. Hartl, R. Poplin, G. del Angel et al., 2013 From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline, pp. 11.10.1-11.10.33 in Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Hoboken, NJ.

Ballesteros E., 2006 Mediterranean coralligenous assemblages: A synthesis of present knowledge. Oceanogr. Mar. Biol. 44: 123-195. https://doi.org/ 10.1201/9781420006391.ch4

Boavida, J., J. Assis, I. Silva, and E. A. Serrão, 2016 Overlooked habitat of a vulnerable gorgonian revealed in the Mediterranean and Eastern Atlantic by ecological niche modelling. Sci. Rep. 6: 36460. https://doi.org/10.1038/ srep36460

Coma, R., M. Ribes, E. Serrano, E. Jiménez, J. Salat et al., 2009 Global warming-enhanced stratification and mass mortality events in the Mediterranean. Proc. Natl. Acad. Sci. USA 106: 6176-6181. https://doi.org/ 10.1073/pnas.0805801106

Conesa, A., S. Gotz, J. M. Garcia-Gomez, J. Terol, M. Talon et al., 2005 Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21: 3674-3676. https://doi.org/10.1093/bioinformatics/bti610

chevron_left
1
2
3
4
5
chevron_right

1 Research products, page 1 of 1

Supplemental Material for Ledoux et al., 2020
2020IsSupplementedBy

Impact byBIP!

	citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	6
	popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.	Top 10%
	influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	Average
	impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.	Average

Usage byUsageCounts

visibility	views	20
download	downloads	109

	citations This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	6
	popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.	Top 10%
	influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	Average
	impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.	Average