Genome‐ and transcriptome‐assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

• Published in: Molecular ecology resources Vol. 14; no. 5; pp. 1072 - 1079
• Main Authors: Smolina, I, Kollias, S, Poortvliet, M, Nielsen, T. G, Lindeque, P, Castellani, C, Møller, E. F, Blanco‐Bercial, L, Hoarau, G
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.09.2014; Wiley Subscription Services, Inc
• Subjects: Animals; Calanoida; Calanus finmarchicus; Calanus glacialis; Calanus marshallae; Copepoda - classification; Copepoda - genetics; Evolution; gene deletion; Genetic Markers; Genome; Genomes; hybrids; InDels; insertional mutagenesis; Ion Torrent; marine ecosystems; marker design; Molecular Sequence Data; Mutagenesis, Insertional; next-generation sequencing; nuclear genome; sequence analysis; Sequence Analysis, DNA; Sequence Deletion; sibling species; species delimitation; species identification; Transcriptome; zooplankton; species delimitation; Ion Torrent; next-generation sequencing; InDels; marker design; zooplankton
• ISSN: 1755-098X; 1755-0998
• DOI: 10.1111/1755-0998.12241

Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers to efficiently identify parental species and hybrids. Using next‐generation sequencing analysis of both the genome and transcriptome from two sibling species, Calanus finmarchicus and Calanus glacialis, we developed a panel of 12 nuclear insertion/deletion markers. All the markers showed species‐specific amplicon length. Furthermore, most of the markers were successfully amplified in other Calanus species, allowing the molecular identification of Calanus helgolandicus, Calanus hyperboreus and Calanus marshallae.