Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Adam T. McLain; Glenn W. Carman; Mitchell L. Fullerton; Thomas O. Beckstrom; William Gensler; Thomas J. Meyer; Christopher Faulk; Mark A. Batzer

doi:10.1186/1759-8753-4-26

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Adam T. McLain, Glenn W. Carman, Mitchell L. Fullerton, Thomas O. Beckstrom, William Gensler, Thomas J. Meyer, Christopher Faulk, Mark A. Batzer

Animal Science

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

Abstract

Background: Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results: Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions: The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.

Original language	English (US)
Article number	26
Journal	Mobile DNA
Volume	4
Issue number	1
DOIs	https://doi.org/10.1186/1759-8753-4-26
State	Published - Nov 22 2013

Bibliographical note

Funding Information:
The authors wish to thank G. Cook, J.A. Walker, S. Herke, and M.K. Konkel for all of their helpful advice during the course of this project. Special thanks go to Sydney Szot (szot@tigers.lsu.edu) for the primate illustrations. We thank the American Type Culture Collection, The Coriell Institute for Medical Research, the Integrated Primate Biomaterials and Information Resource, and Dr. Lucia Carbone (http://carbonelab.com) for providing the DNA samples used in this study. This research was supported by National Institutes of Health Grant RO1 GM59290 (MAB). ATM was supported in part by a Louisiana Board of Regents Graduate Fellowship and the Louisiana State University Graduate School Dissertation Fellowship. MLF was supported by the Louisiana Biomedical Research Network with funding from the National Center for Research Resources (Grant Number P20GM103424), and by the Louisiana Board of Regents Support Fund.

Keywords

Gorilla
Mobile elements
Primate
Retrotransposon
SINE

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1186/1759-8753-4-26

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title = "Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats",

abstract = "Background: Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results: Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions: The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.",

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author = "McLain, {Adam T.} and Carman, {Glenn W.} and Fullerton, {Mitchell L.} and Beckstrom, {Thomas O.} and William Gensler and Meyer, {Thomas J.} and Christopher Faulk and Batzer, {Mark A.}",

note = "Funding Information: The authors wish to thank G. Cook, J.A. Walker, S. Herke, and M.K. Konkel for all of their helpful advice during the course of this project. Special thanks go to Sydney Szot (szot@tigers.lsu.edu) for the primate illustrations. We thank the American Type Culture Collection, The Coriell Institute for Medical Research, the Integrated Primate Biomaterials and Information Resource, and Dr. Lucia Carbone (http://carbonelab.com) for providing the DNA samples used in this study. This research was supported by National Institutes of Health Grant RO1 GM59290 (MAB). ATM was supported in part by a Louisiana Board of Regents Graduate Fellowship and the Louisiana State University Graduate School Dissertation Fellowship. MLF was supported by the Louisiana Biomedical Research Network with funding from the National Center for Research Resources (Grant Number P20GM103424), and by the Louisiana Board of Regents Support Fund.",

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AU - Meyer, Thomas J.

AU - Faulk, Christopher

AU - Batzer, Mark A.

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N2 - Background: Research into great ape genomes has revealed widely divergent activity levels over time for Alu elements. However, the diversity of this mobile element family in the genome of the western lowland gorilla has previously been uncharacterized. Alu elements are primate-specific short interspersed elements that have been used as phylogenetic and population genetic markers for more than two decades. Alu elements are present at high copy number in the genomes of all primates surveyed thus far. The AluY subfamily and its derivatives have been recognized as the evolutionarily youngest Alu subfamily in the Old World primate lineage. Results: Here we use a combination of computational and wet-bench laboratory methods to assess and catalog AluY subfamily activity level and composition in the western lowland gorilla genome (gorGor3.1). A total of 1,075 independent AluY insertions were identified and computationally divided into 10 subfamilies, with the largest number of gorilla-specific elements assigned to the canonical AluY subfamily. Conclusions: The retrotransposition activity level appears to be significantly lower than that seen in the human and chimpanzee lineages, while higher than that seen in orangutan genomes, indicative of differential Alu amplification in the western lowland gorilla lineage as compared to other Homininae.

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Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Abstract

Bibliographical note

Keywords

UN SDGs

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