Application of Next-Generation Transcriptomic Tools for Non-Model Organisms: Gene Discovery and Marker DevelopmentWithin Plecoptera (Insecta)
Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction soft...
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| Format: | Others |
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BYU ScholarsArchive
2013
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| Online Access: | https://scholarsarchive.byu.edu/etd/4265 https://scholarsarchive.byu.edu/cgi/viewcontent.cgi?article=5264&context=etd |
| Summary: | Phylogenetic research on non-model organisms has been hindered by limited marker availability. Next generation sequencing techniques are eliminating that barrier. Using Illumina sequencing technology, Trinity assembly software, custom Perl reciprocal BLAST scripts, and Primer3 primer prediction software, we produced and analyzed 7 Plecopteran transcriptomes, representing 7 of the 16 total families, in an attempt to identify and develop conserved orthologous genetic markers. The transcriptomes were used to reconstruct a gene content phylogeny using a simple distance matrix generated from reciprocal blastn data. By producing and filtering a reciprocal blast network we identified and aligned over 450 putative orthologs. Out of these, 25 primer pairs were selected that showed 100% conserved primer sites across all the transcripts from which they were created. Of those 25, 3 loci (PlecSK1, Perl534, and PvC2190) show very positive phylogenetic potential. These 3 markers may also be suitable and even highly useful in population genetic studies in which the populations have had sufficient time to develop significant genetic separation. The rapid and affordable nature of this study demonstrates the ease by which non-model organism phylogenetics can be expanded and made more robust. |
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