Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

The Baboon Genome Analysis Consortium

doi:10.1186/s13100-018-0115-6

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

The Baboon Genome Analysis Consortium

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

2 Citations (Scopus)

Abstract

Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions: Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.

Original language	English
Article number	10
Journal	Mobile DNA
Volume	9
Issue	1
ISSN	1383-469X
DOIs	https://doi.org/10.1186/s13100-018-0115-6
Publication status	Published - 19 Mar 2018

Keywords

Alu
Baboon
Papio
Subfamily

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@article{7d4e9fc1e70b4f62b767f513d38c6c66,

title = "Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis",

abstract = "Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions: Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.",

keywords = "Alu, Baboon, Papio, Subfamily",

author = "Steely, {Cody J.} and Baker, {Jasmine N.} and Walker, {Jerilyn A.} and Loupe, {Charles D.} and Batzer, {Mark A.} and Jeffrey Rogers and Harris, {R. Alan} and Muthuswamy Raveendran and Yue Liu and Shwetha Murali and Vilgalys, {Tauras P.} and Walker, {Jerilyn A.} and Konkel, {Miriam K.} and Jordan, {Vallmer E.} and Steely, {Cody J.} and Beckstrom, {Thomas O.} and Thomas, {Gregg W.C.} and Pagel, {Kymberleigh A.} and Vikas Pejaver and Catacchio, {Claudia R.} and Nicoletta Archidiacono and Mario Ventura and Alessia Marra-Campanale and Antonio Palazzo and Oronzo Capozzi and Archana Raja and John Huddleston and Quick, {Veronica Searles} and Anis Karimpour-Fard and Dominik Schrempf and {de Manuel Montero}, Marc and Konstantinos Billis and Martin, {Fergal J.} and Matthieu Muffato and Georgios Athanasiadis and Christina Bergey and Andrew Burrell and Jade Cheng and Laura Cox and James Else and Yi Han and Kopp, {Gisela H.} and Maximilian Kothe and Kalle Lepp{\"a}l{\"a} and Angela Noll and Jera Pecotte and Lenore Pipes and Kasper Munch and Thomas Mailund and Mikkel Schierup and {The Baboon Genome Analysis Consortium}",

year = "2018",

month = mar,

day = "19",

doi = "10.1186/s13100-018-0115-6",

language = "English",

volume = "9",

journal = "Mobile DNA",

issn = "1383-469X",

publisher = "Springer",

number = "1",

}

TY - JOUR

T1 - Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

AU - Steely, Cody J.

AU - Baker, Jasmine N.

AU - Walker, Jerilyn A.

AU - Loupe, Charles D.

AU - Batzer, Mark A.

AU - Rogers, Jeffrey

AU - Harris, R. Alan

AU - Raveendran, Muthuswamy

AU - Liu, Yue

AU - Murali, Shwetha

AU - Vilgalys, Tauras P.

AU - Walker, Jerilyn A.

AU - Konkel, Miriam K.

AU - Jordan, Vallmer E.

AU - Steely, Cody J.

AU - Beckstrom, Thomas O.

AU - Thomas, Gregg W.C.

AU - Pagel, Kymberleigh A.

AU - Pejaver, Vikas

AU - Catacchio, Claudia R.

AU - Archidiacono, Nicoletta

AU - Ventura, Mario

AU - Marra-Campanale, Alessia

AU - Palazzo, Antonio

AU - Capozzi, Oronzo

AU - Raja, Archana

AU - Huddleston, John

AU - Quick, Veronica Searles

AU - Karimpour-Fard, Anis

AU - Schrempf, Dominik

AU - de Manuel Montero, Marc

AU - Billis, Konstantinos

AU - Martin, Fergal J.

AU - Muffato, Matthieu

AU - Athanasiadis, Georgios

AU - Bergey, Christina

AU - Burrell, Andrew

AU - Cheng, Jade

AU - Cox, Laura

AU - Else, James

AU - Han, Yi

AU - Kopp, Gisela H.

AU - Kothe, Maximilian

AU - Leppälä, Kalle

AU - Noll, Angela

AU - Pecotte, Jera

AU - Pipes, Lenore

AU - Munch, Kasper

AU - Mailund, Thomas

AU - Schierup, Mikkel

AU - The Baboon Genome Analysis Consortium

PY - 2018/3/19

Y1 - 2018/3/19

N2 - Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions: Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.

AB - Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage. We analyzed 233 Alu insertions in the genome of the olive baboon using locus specific polymerase chain reaction assays, covering 113 of the 129 subfamilies. The allele frequency data from these insertions show that none of the nine groups of subfamilies are nearing fixation in the lineage. Conclusions: Many subfamilies of Alu elements are actively mobilizing throughout the baboon lineage, with most being specific to the baboon lineage.

KW - Alu

KW - Baboon

KW - Papio

KW - Subfamily

U2 - 10.1186/s13100-018-0115-6

DO - 10.1186/s13100-018-0115-6

M3 - Journal article

C2 - 29560044

AN - SCOPUS:85044182302

SN - 1383-469X

VL - 9

JO - Mobile DNA

JF - Mobile DNA

IS - 1

M1 - 10

ER -

Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis

Abstract

Keywords

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