Towards population genomics in non-model species with large genomes: a case study of the marine zooplankton Calanus finmarchicus.

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Date
2019Author
Choquet, Marvin
Smolina, Irina
Dhanasiri, Anusha K. S.
Blanco-Bercial, Leocadio
Kopp, Martina
Jueterbock, Alexander
Sundaram, Arvind Y. M.
Hoarau, Galice
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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 .....
Journal
Royal Society Oen ScienceVolume
6Issue
Article 180608Page Range
14pp.Document Language
enSustainable Development Goals (SDG)
14Maturity Level
Pilot or Demonstrated: Methodologies are being demonstrated and validated; limited consensus exists on widespread use or in any given situation (TRL 4-6);Best Practice Type
GuideDOI Original
http://dx.doi.org/10.1098/rsos.180608Citation
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.180608Collections
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