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As a part of a phylogenetic study, I need to find a nuclear gene that meets the following requirements:

  • Single copy gene;
  • Highly variable gene;
  • Gene longer than 400 bps;
  • Gene that gives information at the species/genus level in Gastropoda.

My candidate genes are the following: 5.8S, 18S, 28S, ACT, APN54, EF-1alpha, endo-1,4-beta-glucanase, GSTM, GSTO, GSTP, H3, ITS1, ITS2, MCP, MYO.

However, I do not know where to find whether or not they are single copy.

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The simple way to do this is to use blast to search the genomes your interested in for sequences similar to your gene. If there's another copy it'll turn up in the blast results (so will orthologous genes - but they'll have lower scores than an actual copy). That relies on the annotation and genome being correct, of course.

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Even simpler: If you are lucky and your target Gastropoda is in Ensembl (http://ensemblgenomes.org/) you can just introduce the gene ID and see if it has any paralogs. A lot of other info is available for each gene.

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