Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats
The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, which usually comprises around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian g...
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| Format: | Online |
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Oxford University Press
2012
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342881/ |
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pubmed-33428812012-05-04 Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats Pagán, Heidi J. T. Macas, Jiří Novák, Petr McCulloch, Eve S. Stevens, Richard D. Ray, David A. Research Articles The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, which usually comprises around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes exhibit a precipitous decline in Class II activity beginning roughly 40 Ma. The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus, and are reflected by higher genome content (∼5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3–4%) was observed in all five vesper bats, while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammalian species, revealing genome-scale differences in TE content within a single family. Oxford University Press 2012 2012-04-04 /pmc/articles/PMC3342881/ /pubmed/22491057 http://dx.doi.org/10.1093/gbe/evs038 Text en © The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Pagán, Heidi J. T. Macas, Jiří Novák, Petr McCulloch, Eve S. Stevens, Richard D. Ray, David A. |
| spellingShingle |
Pagán, Heidi J. T. Macas, Jiří Novák, Petr McCulloch, Eve S. Stevens, Richard D. Ray, David A. Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| author_facet |
Pagán, Heidi J. T. Macas, Jiří Novák, Petr McCulloch, Eve S. Stevens, Richard D. Ray, David A. |
| author_sort |
Pagán, Heidi J. T. |
| title |
Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| title_short |
Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| title_full |
Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| title_fullStr |
Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| title_full_unstemmed |
Survey Sequencing Reveals Elevated DNA Transposon Activity, Novel Elements, and Variation in Repetitive Landscapes among Vesper Bats |
| title_sort |
survey sequencing reveals elevated dna transposon activity, novel elements, and variation in repetitive landscapes among vesper bats |
| description |
The repetitive landscapes of mammalian genomes typically display high Class I (retrotransposon) transposable element (TE) content, which usually comprises around half of the genome. In contrast, the Class II (DNA transposon) contribution is typically small (<3% in model mammals). Most mammalian genomes exhibit a precipitous decline in Class II activity beginning roughly 40 Ma. The first signs of more recently active mammalian Class II TEs were obtained from the little brown bat, Myotis lucifugus, and are reflected by higher genome content (∼5%). To aid in determining taxonomic limits and potential impacts of this elevated Class II activity, we performed 454 survey sequencing of a second Myotis species as well as four additional taxa within the family Vespertilionidae and an outgroup species from Phyllostomidae. Graph-based clustering methods were used to reconstruct the major repeat families present in each species and novel elements were identified in several taxa. Retrotransposons remained the dominant group with regard to overall genome mass. Elevated Class II TE composition (3–4%) was observed in all five vesper bats, while less than 0.5% of the phyllostomid reads were identified as Class II derived. Differences in satellite DNA and Class I TE content are also described among vespertilionid taxa. These analyses present the first cohesive description of TE evolution across closely related mammalian species, revealing genome-scale differences in TE content within a single family. |
| publisher |
Oxford University Press |
| publishDate |
2012 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342881/ |
| _version_ |
1611526736298639360 |