Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management

Onami, Jun-ichi; Nikaido, Masato; Mannen, Hideyuki; Okada, Norihiro

doi:10.1007/s00335-007-9000-1

Cited by 11 publications

(15 citation statements)

References 38 publications

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“…It was later shown to be widely distributed among other ruminant genomes [ 15 ]. The element is composed of two Bov-A monomers which are joined together by a linker sequence, and ends with a [AGC]n repeat [ 16 , 17 ]. Bov-A2 is usually categorized as a member of the short interspersed nuclear element (SINE) family [ 11 , 14 , 18 ].…”

Section: Introductionmentioning

confidence: 99%

Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency

et al. 2015

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BackgroundIn recent years, the perception of transposable genetic elements has changed from “junk DNA” to a focus of interest when appearing near or inside genes. Bov-A2 is a short interspersed nuclear element (SINE) that was first found in Bovidae and later in other ruminants. This retroposon is mostly used as a marker for phylogenetic analysis.ResultsWe describe insertions of Bov-A2 in the promoter region of TP53, a key tumor suppressor gene that is indispensable for diverse developmental processes, in Antilopinae and Tragelaphini (belonging to the Bovinae subfamily). In Tragelaphini two Bov-A2 elements were inserted sequentially, whereas in 5 tribes of Antilopinae only one Bov-A2 element was inserted, in a different site and reverse orientation. The entrance site in both cases employed short palindromes that can form hairpin secondary structures. Interestingly, mutations that create or disrupt base pairing in the palindrome sequence dictated the presence or absence of Bov-A2, such as in the domestic cow and buffalo, which lack Bov-A2. Transcription factor binding site analysis revealed unique binding sites for STAT3 and NFκB within the Bov-A2 sequence, which together with TP53 itself are known to play a crucial role in mammary involution.ConclusionsThis report demonstrates how short palindromes serve as hot spots for Bov-A2 retroposon insertion into the mammalian genome. The strict correlation between point mutation in the palindromes and the presence/absence of Bov-A2 retroposon insertions, questions the use of singular insertion events as valid phylogenetic markers inside families. Bov-A2 insertion into the TP53 promoter in Antilopinae and Tragelaphini may not only provide a genetic network that regulates mammary involution, but can also answer the need for rapid mammary involution in Savanna antelopes after weaning, partially in response to predation stress. The absence of Bov-A2 in domestic bovids may constitute the molecular background for greater lactation persistency.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1235-8) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency

et al. 2015

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“…The low percentage of shared loci in the cervid data sets might be associated with the variable levels of DNA degradation and the distribution of the targeted TE in cervid genomes. BOV2A, the TE targeted in the cervid data set, is a SINE element that is widely distributed in the genomes of ruminants (e.g., deer) (Nilsson et al, ; Onami, Nikaido, Mannen, & Okada, ). The high abundance of the element combined with the reduced effort on sequencing could be driving the allelic dropout.…”

Section: Discussionmentioning

confidence: 99%

MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements

Rey‐Iglesia

Gopalakrishan

Carøe

et al. 2019

Molecular Ecology Resources

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In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome‐scale studies to characterize both model and non‐model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome‐wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site‐associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms—enabling the exploration of diverse evolutionary and conservation questions.

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“…Our survey-sequencing and comparative TE analysis indicate that BOVA2 has been highly prolific in lesser kudu (Tragelaphini), and that the BOVA2 expansion is restricted to Bovinae (cow, lesser kudu) ( Table 2). The BOVA2 is the most recently proliferating SINE in the cow genome and can be found in cow breeds in different repeat unit numbers, which occur by unequal crossing over (Onami et al, 2007). The lesser kudu (Tragelaphini) separated from Bovini (cow, bison, buffalo) 13.9-17 mya (Hassanin et al, 2012;Bibi, 2013).…”

Section: Bova2 and Bovb Expansion In The Lesser Kudu And Bovini Genomementioning

confidence: 99%

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

Gallus

Kumar

Bertelsen

et al. 2015

Gene

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Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management

Cited by 11 publications

References 38 publications

Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency

Dispersal of an ancient retroposon in the TP53 promoter of Bovidae: phylogeny, novel mechanisms, and potential implications for cow milk persistency

MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements

A genome survey sequencing of the Java mouse deer (Tragulus javanicus) adds new aspects to the evolution of lineage specific retrotransposons in Ruminantia (Cetartiodactyla)

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