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

The Baboon Genome Analysis Consortium

    Research output: Contribution to journalArticle

    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 languageEnglish (US)
    Article number10
    JournalMobile DNA
    Volume9
    Issue number1
    DOIs
    StatePublished - Mar 19 2018

    Fingerprint

    Papio anubis
    Papio
    Alu Elements
    Genome
    Primates
    Retroelements
    Gene Frequency
    Polymerase Chain Reaction

    Keywords

    • Alu
    • Baboon
    • Papio
    • Subfamily

    ASJC Scopus subject areas

    • Molecular Biology

    Cite this

    Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. / The Baboon Genome Analysis Consortium.

    In: Mobile DNA, Vol. 9, No. 1, 10, 19.03.2018.

    Research output: Contribution to journalArticle

    The Baboon Genome Analysis Consortium. / Analysis of lineage-specific Alu subfamilies in the genome of the olive baboon, Papio anubis. In: Mobile DNA. 2018 ; Vol. 9, No. 1.
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    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.",
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    author = "{The Baboon Genome Analysis Consortium} and 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 Karen Rice and Mason, {Christopher E.} and Todd Disotell",
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    AU - The Baboon Genome Analysis Consortium

    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 - Rice, Karen

    AU - Mason, Christopher E.

    AU - Disotell, Todd

    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

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    JF - Mobile DNA

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