dc.contributor.author | Choquet, Marvin | |
dc.contributor.author | Smolina, Irina | |
dc.contributor.author | Dhanasiri, Anusha K. S. | |
dc.contributor.author | Blanco-Bercial, Leocadio | |
dc.contributor.author | Kopp, Martina | |
dc.contributor.author | Jueterbock, Alexander | |
dc.contributor.author | Sundaram, Arvind Y. M. | |
dc.contributor.author | Hoarau, Galice | |
dc.date.accessioned | 2019-08-10T18:39:18Z | |
dc.date.available | 2019-08-10T18:39:18Z | |
dc.date.issued | 2019 | |
dc.identifier.citation | Choquet, M.; Smolina, I.; Dhanasiri, A.K.S.; Blanco-Bercial, L.; Kopp, M.; Jueterbock, A.; Sundaram, A.Y.M. and Hoarau, G. (2019) Towards population genomics in non-model
species with large genomes: a case study of the
marine zooplankton Calanus finmarchicus. Royal Society Open Science. 6: 180608, 14pp. DOI: http://dx.doi.org/10.1098/rsos.180608 | en_US |
dc.identifier.uri | http://hdl.handle.net/11329/1017 | |
dc.identifier.uri | http://dx.doi.org/10.25607/OBP-549 | |
dc.description.abstract | Advances in next-generation sequencing technologies and the
development of genome-reduced representation protocols have
opened the way to genome-wide population studies in non-model
species. However, species with large genomes remain
challenging, hampering the development of genomic resources
for a number of taxa including marine arthropods. Here, we
developed a genome-reduced representation method for the
ecologically important marine copepod Calanus finmarchicus
(haploid genome size of 6.34 Gbp). We optimized a capture
enrichment-based protocol based on 2656 single-copy genes,
yielding a total of 154 087 high-quality SNPs in C. finmarchicus
including 62 372 in common among the three locations tested.
The set of capture probes was also successfully applied to the
congeneric C. glacialis. Preliminary analyses of these markers
revealed similar levels of genetic diversity between the two
Calanus species, while populations of C. glacialis showed
stronger genetic structure compared to C. finmarchicus. Using
this powerful set of markers, we did not detect any evidence of
hybridization between C. finmarchicus and C. glacialis. Finally,
we propose a shortened version of our protocol, offering a
promising solution for population genomics studies in
non-model species with large genomes. | en_US |
dc.language.iso | en | en_US |
dc.rights | Attribution 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject.other | Genome reduced-representation | en_US |
dc.subject.other | Sequence capture enrichment | en_US |
dc.subject.other | Calanus spp | en_US |
dc.title | Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus. | en_US |
dc.type | Journal Contribution | en_US |
dc.description.refereed | Refereed | en_US |
dc.format.pagerange | 14pp. | en_US |
dc.identifier.doi | http://dx.doi.org/10.1098/rsos.180608 | |
dc.subject.parameterDiscipline | Parameter Discipline::Biological oceanography::Other biological measurements | en_US |
dc.bibliographicCitation.title | Royal Society Oen Science | en_US |
dc.bibliographicCitation.volume | 6 | en_US |
dc.bibliographicCitation.issue | Article 180608 | en_US |
dc.description.sdg | 14 | en_US |
dc.description.maturitylevel | Pilot or Demonstrated: Methodologies are being demonstrated and validated; limited consensus exists on widespread use or in any given situation (TRL 4-6); | en_US |
dc.description.bptype | Guide | en_US |
obps.contact.contactname | Marvin Choquet | |
obps.contact.contactemail | marvin.choquet@nord.no | |
obps.resourceurl.publisher | https://royalsocietypublishing.org/doi/10.1098/rsos.180608 | en_US |