Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management |
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Authors: | Jun-ichi Onami Masato Nikaido Hideyuki Mannen Norihiro Okada |
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Institution: | (1) Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan;(2) Faculty of Agriculture, Kobe University, Kobe, Japan;(3) Department of Speciation, National Institute for Basic Biology, Okazaki, Japan;(4) Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21 Nagatsuta-cho, Midori-ku Yokohama, 226-8501, Japan |
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Abstract: | Bov-A2 is a retroposon that is widely distributed among the genomes of ruminants (e.g., cow, deer, giraffe, pronghorn, musk
deer, and chevrotain). This retroposon is composed of two monomers, called Bov-A units, which are joined by a linker sequence.
The structure and origin of Bov-A2 has been well characterized but a genome-level exploration of this retroposon has not been
implemented. In this study we performed an extensive search for Bov-A2 using all available genome sequence data on Bos taurus. We found unique Bov-A2-derived sequences that were longer than Bov-A2 due to amplification of three to six Bov-A units arranged
in tandem. Detailed analysis of these elongated Bov-A2-derived sequences revealed that they originated through unequal crossing-over
of Bov-A2. We found a large number of these elongated Bov-A2-derived sequences in cattle genomes, indicating that unequal
crossing-over of Bov-A2 occurred very frequently. We found that this type of elongation is not observed in wild bovine and
is therefore specific to the domesticated cattle genome. Furthermore, at specific loci, the number of Bov-A units was also
polymorphic between alleles, implying that the elongation of Bov-A units might have occurred very recently. For these reasons,
we speculate that genomic instability in bovine genomes can lead to extensive unequal crossing-over of Bov-A2 and levels of
polymorphism might be generated in part by repeated outbreeding. |
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