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Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.

Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA - Genome Biol Evol (2015)

Bottom Line: Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa.This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi.These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.

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Results of Ves insertion panel on seven species of Myotis with three different loci. The names of each locus and its location in the M. lucifugus genome (Myoluc2.0: GCA_000147115.1) are given. Loci with a Ves insertion are expected to be approximately 200 bp larger than those lacking an insertion. Loci presented are examples of lineage specific (A), ancestral (B), and polymoprhic (C) insertion patterns. Based on the species analyzed here, only the polymorphic insertion locus is useful for phylogenetic analyses.
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evv099-F4: Results of Ves insertion panel on seven species of Myotis with three different loci. The names of each locus and its location in the M. lucifugus genome (Myoluc2.0: GCA_000147115.1) are given. Loci with a Ves insertion are expected to be approximately 200 bp larger than those lacking an insertion. Loci presented are examples of lineage specific (A), ancestral (B), and polymoprhic (C) insertion patterns. Based on the species analyzed here, only the polymorphic insertion locus is useful for phylogenetic analyses.

Mentions: To verify the presence of Ves insertions identified by Ves reads, 42 loci were amplified in all seven taxa (fig. 4). Filled sites are expected to be approximately 200 bp larger than empty sites. Of the loci tested, 32 of 42 amplified in five or more samples, and 30 of the 32 primer pairs produced amplicons of predicted sizes confirming the expected insertion genotype. After verifying the increase in band size that is expected from a Ves insertion, loci were sequenced using internal Ves primers to confirm the approximately 200 bp insertion was indeed a Ves. For each locus, either one or two taxa were selected for sequencing to verify the presence of the Ves insertion as well as the expected flanking DNA sequence. In each case, the Ves sequence was found as expected.Fig. 4.—


Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis.

Platt RN, Zhang Y, Witherspoon DJ, Xing J, Suh A, Keith MS, Jorde LB, Stevens RD, Ray DA - Genome Biol Evol (2015)

Results of Ves insertion panel on seven species of Myotis with three different loci. The names of each locus and its location in the M. lucifugus genome (Myoluc2.0: GCA_000147115.1) are given. Loci with a Ves insertion are expected to be approximately 200 bp larger than those lacking an insertion. Loci presented are examples of lineage specific (A), ancestral (B), and polymoprhic (C) insertion patterns. Based on the species analyzed here, only the polymorphic insertion locus is useful for phylogenetic analyses.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494050&req=5

evv099-F4: Results of Ves insertion panel on seven species of Myotis with three different loci. The names of each locus and its location in the M. lucifugus genome (Myoluc2.0: GCA_000147115.1) are given. Loci with a Ves insertion are expected to be approximately 200 bp larger than those lacking an insertion. Loci presented are examples of lineage specific (A), ancestral (B), and polymoprhic (C) insertion patterns. Based on the species analyzed here, only the polymorphic insertion locus is useful for phylogenetic analyses.
Mentions: To verify the presence of Ves insertions identified by Ves reads, 42 loci were amplified in all seven taxa (fig. 4). Filled sites are expected to be approximately 200 bp larger than empty sites. Of the loci tested, 32 of 42 amplified in five or more samples, and 30 of the 32 primer pairs produced amplicons of predicted sizes confirming the expected insertion genotype. After verifying the increase in band size that is expected from a Ves insertion, loci were sequenced using internal Ves primers to confirm the approximately 200 bp insertion was indeed a Ves. For each locus, either one or two taxa were selected for sequencing to verify the presence of the Ves insertion as well as the expected flanking DNA sequence. In each case, the Ves sequence was found as expected.Fig. 4.—

Bottom Line: Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa.This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi.These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University Department of Biological Sciences, Texas Tech University.

Show MeSH