Comprehensive primer design for analysis of population genetics in non-sequenced organisms.
Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design c...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3289539?pdf=render |
| _version_ | 1811195578109919232 |
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| author | Ayumi Tezuka Noe Matsushima Yoriko Nemoto Hiroshi D Akashi Masakado Kawata Takashi Makino |
| author_facet | Ayumi Tezuka Noe Matsushima Yoriko Nemoto Hiroshi D Akashi Masakado Kawata Takashi Makino |
| author_sort | Ayumi Tezuka |
| collection | DOAJ |
| description | Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation. |
| first_indexed | 2024-04-12T00:45:32Z |
| format | Article |
| id | doaj.art-ead1cc571f334d10873a3078403ad290 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T00:45:32Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ead1cc571f334d10873a3078403ad2902022-12-22T03:54:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0172e3231410.1371/journal.pone.0032314Comprehensive primer design for analysis of population genetics in non-sequenced organisms.Ayumi TezukaNoe MatsushimaYoriko NemotoHiroshi D AkashiMasakado KawataTakashi MakinoNuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris), anole lizard (Anolis sagrei), guppy (Poecilia reticulata), and fruit fly (Drosophila melanogaster), for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.http://europepmc.org/articles/PMC3289539?pdf=render |
| spellingShingle | Ayumi Tezuka Noe Matsushima Yoriko Nemoto Hiroshi D Akashi Masakado Kawata Takashi Makino Comprehensive primer design for analysis of population genetics in non-sequenced organisms. PLoS ONE |
| title | Comprehensive primer design for analysis of population genetics in non-sequenced organisms. |
| title_full | Comprehensive primer design for analysis of population genetics in non-sequenced organisms. |
| title_fullStr | Comprehensive primer design for analysis of population genetics in non-sequenced organisms. |
| title_full_unstemmed | Comprehensive primer design for analysis of population genetics in non-sequenced organisms. |
| title_short | Comprehensive primer design for analysis of population genetics in non-sequenced organisms. |
| title_sort | comprehensive primer design for analysis of population genetics in non sequenced organisms |
| url | http://europepmc.org/articles/PMC3289539?pdf=render |
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