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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: To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis.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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Sequence statistics per Ves insertion. (A) After approximately 5 million reads, the number of Ves insertions identified tended to stabilize so that more sequencing did not identify additional insertions, proportionally. (B) The average coverage of each Ves insertion is directly related to the number of read pairs.
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evv099-F3: Sequence statistics per Ves insertion. (A) After approximately 5 million reads, the number of Ves insertions identified tended to stabilize so that more sequencing did not identify additional insertions, proportionally. (B) The average coverage of each Ves insertion is directly related to the number of read pairs.

Mentions: On average, each Ves insertion was sequenced to 129.6 × coverage. Although M. auriculus was sequenced 2.5 × (13.6 million read pairs) more frequently than M. simus, the difference in number of Ves insertions identified was less than 17,800 insertions. Assuming these two taxa that diverged approximately 10 Ma (Stadelmann et al. 2007) have similar numbers of Ves insertions, this suggests that a saturation point is reached where more sequencing does not significantly increase the number of unique insertions discovered (fig. 3A). Our results indicate that after approximately 5 million read pairs, most Ves insertion sequences are represented. Additionally, when the number of reads pair is compared with the number of reads per Ves insertion, a strong linear relationship is recovered (R2 = 0.975; fig. 3B).Fig. 3.—


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)

Sequence statistics per Ves insertion. (A) After approximately 5 million reads, the number of Ves insertions identified tended to stabilize so that more sequencing did not identify additional insertions, proportionally. (B) The average coverage of each Ves insertion is directly related to the number of read pairs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv099-F3: Sequence statistics per Ves insertion. (A) After approximately 5 million reads, the number of Ves insertions identified tended to stabilize so that more sequencing did not identify additional insertions, proportionally. (B) The average coverage of each Ves insertion is directly related to the number of read pairs.
Mentions: On average, each Ves insertion was sequenced to 129.6 × coverage. Although M. auriculus was sequenced 2.5 × (13.6 million read pairs) more frequently than M. simus, the difference in number of Ves insertions identified was less than 17,800 insertions. Assuming these two taxa that diverged approximately 10 Ma (Stadelmann et al. 2007) have similar numbers of Ves insertions, this suggests that a saturation point is reached where more sequencing does not significantly increase the number of unique insertions discovered (fig. 3A). Our results indicate that after approximately 5 million read pairs, most Ves insertion sequences are represented. Additionally, when the number of reads pair is compared with the number of reads per Ves insertion, a strong linear relationship is recovered (R2 = 0.975; fig. 3B).Fig. 3.—

Bottom Line: To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis.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