Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as l...
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ftunivbergen:oai:bora.uib.no:11250/2737929 2023-05-15T17:35:31+02:00 Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management Maduna, Simo Vivian-Smith, Adam Jónsdóttir, Ólöf Dóra Bartels Imsland, Albert Klutsch, Cornelya Nyman, Tommi Eiken, Hans Geir Hagen, Snorre 2020 application/pdf https://hdl.handle.net/11250/2737929 https://doi.org/10.1038/s41598-019-57071-w eng eng Nature Research Norges forskningsråd: 282460 urn:issn:2045-2322 https://hdl.handle.net/11250/2737929 https://doi.org/10.1038/s41598-019-57071-w cristin:1795527 Scientific Reports. 2020, 10, 559. Navngivelse 4.0 Internasjonal http://creativecommons.org/licenses/by/4.0/deed.no Copyright The Author(s) 2020 559 Scientific Reports 10 Journal article Peer reviewed 2020 ftunivbergen https://doi.org/10.1038/s41598-019-57071-w 2023-03-14T17:44:58Z The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many ... Article in Journal/Newspaper North Atlantic University of Bergen: Bergen Open Research Archive (BORA-UiB) Scientific Reports 10 1 |
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Open Polar |
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University of Bergen: Bergen Open Research Archive (BORA-UiB) |
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ftunivbergen |
language |
English |
description |
The lumpfish Cyclopterus lumpus is commercially exploited in numerous areas of its range in the North Atlantic Ocean, and is important in salmonid aquaculture as a biological agent for controlling sea lice. Despite the economic importance, few genetic resources for downstream applications, such as linkage mapping, parentage analysis, marker-assisted selection (MAS), quantitative trait loci (QTL) analysis, and assessing adaptive genetic diversity are currently available for the species. Here, we identify both genome- and transcriptome-derived microsatellites loci from C. lumpus to facilitate such applications. Across 2,346 genomic contigs, we detected a total of 3,067 microsatellite loci, of which 723 were the most suitable ones for primer design. From 116,555 transcriptomic unigenes, we identified a total of 231,556 microsatellite loci, which may indicate a high coverage of the available STRs. Out of these, primer pairs could only be designed for 6,203 loci. Dinucleotide repeats accounted for 89 percent and 52 percent of the genome- and transcriptome-derived microsatellites, respectively. The genetic composition of the dominant repeat motif types showed differences from other investigated fish species. In the genome-derived microsatellites AC/GT (67.8 percent), followed by AG/CT (15.1 percent) and AT/AT (5.6 percent) were the major motifs. Transcriptome-derived microsatellites showed also most dominantly the AC/GT repeat motif (33 percent), followed by A/T (26.6 percent) and AG/CT (11 percent). Functional annotation of microsatellite-containing transcriptomic sequences showed that the majority of the expressed sequence tags encode proteins involved in cellular and metabolic processes, binding activity and catalytic reactions. Importantly, STRs linked to genes involved in immune system process, growth, locomotion and reproduction were discovered in the present study. The extensive genomic marker information reported here will facilitate molecular ecology studies, conservation initiatives and will benefit many ... |
format |
Article in Journal/Newspaper |
author |
Maduna, Simo Vivian-Smith, Adam Jónsdóttir, Ólöf Dóra Bartels Imsland, Albert Klutsch, Cornelya Nyman, Tommi Eiken, Hans Geir Hagen, Snorre |
spellingShingle |
Maduna, Simo Vivian-Smith, Adam Jónsdóttir, Ólöf Dóra Bartels Imsland, Albert Klutsch, Cornelya Nyman, Tommi Eiken, Hans Geir Hagen, Snorre Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
author_facet |
Maduna, Simo Vivian-Smith, Adam Jónsdóttir, Ólöf Dóra Bartels Imsland, Albert Klutsch, Cornelya Nyman, Tommi Eiken, Hans Geir Hagen, Snorre |
author_sort |
Maduna, Simo |
title |
Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
title_short |
Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
title_full |
Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
title_fullStr |
Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
title_full_unstemmed |
Genome- and transcriptomederived microsatellite loci in lumpfsh Cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
title_sort |
genome- and transcriptomederived microsatellite loci in lumpfsh cyclopterus lumpus: molecular tools for aquaculture, conservation and fsheries management |
publisher |
Nature Research |
publishDate |
2020 |
url |
https://hdl.handle.net/11250/2737929 https://doi.org/10.1038/s41598-019-57071-w |
genre |
North Atlantic |
genre_facet |
North Atlantic |
op_source |
559 Scientific Reports 10 |
op_relation |
Norges forskningsråd: 282460 urn:issn:2045-2322 https://hdl.handle.net/11250/2737929 https://doi.org/10.1038/s41598-019-57071-w cristin:1795527 Scientific Reports. 2020, 10, 559. |
op_rights |
Navngivelse 4.0 Internasjonal http://creativecommons.org/licenses/by/4.0/deed.no Copyright The Author(s) 2020 |
op_doi |
https://doi.org/10.1038/s41598-019-57071-w |
container_title |
Scientific Reports |
container_volume |
10 |
container_issue |
1 |
_version_ |
1766134714910900224 |