Helitrons and Retrotransposons Are Co-localized in Bos taurus Genomes

Abstract

Background: DNA transposons helitrons are mobile genetic elements responsible for major movements of the genetic material within and across different genomes. This ability makes helitrons suitable candidate elements for the development of new approaches of multilocus genotyping of live-stock animals, along with the well-known microsatellite loci.Objective: We aimed to estimate the informativeness of helitron and microsatellite markers in assessing the consolidation and the “gene pool” standards of two commercial dairy cattle breeds (Ayrshire breed and holsteinized Black-and-White cattle) and one local breed of Kalmyk cattle, and to reveal any inter-breed difference in the organization of genomic regions flanked by helitrons in the studied cattle breeds.Method: We used the combination of two highly-polymorphic genomic elements – helitrons and trinu-cleotide microsatellites (AGC)6G and (GAG)6C, respectively – for genome scanning of the sampled groups of cattle. Also, we pyrosequenced the genomic regions flanked by the inverted repeats of 3'-end of Heligloria family of helitron fragments.Results: Generally, the both combinations of markers generated polymorphic spectra, based on which certain interbreed differentiation could be observed. The analysis of the identified interspersed repeats suggests that in factory and local cattle the genomic regions flanked by helitron fragments are shaped differently and contain different superfamilies of transposable elements, especially retrotransposons.Conclusion: Despite the well-known fact of retrotransposon-dependent microsatellite expansion, our data suggest that, in the cattle genome, the DNA transposons and microsatellites can also be found in close neighbourhood, and that helitrons and retrotransposons may form domains of increased variability – targets for factors of artificial selection.

Taming transposable elements in livestock and poultry: a review of their roles and applications

“…For example, the L1_BT sequence is used as a primer in polymerase chain reactions (PCR) for multi-site genotyping, and is a convenient marker for genetic differentiation between breeds [ 73 ]. The Heligloria family of DNA transposons was genotyped using the ISSR-PCR-like method to study the co-localization of DNA transposons (Helitron) and retrotransposons in the genomes of three cattle breeds [ 74 ]. Han et al used NGS data and the droplet digital PCR platform to quantitatively detect Hanwoo-specific structural variations (SV) generated by TE-associated deletion events, and then used these TE to distinguish different cattle breeds (e.g., Hanwoo vs. Holstein) [ 75 , 76 ].…”

CELLULAR AND EXTRACELLULAR LEVELS OF RETROVIRUS—HOST INTERACTIONS ON THE EXAMPLE OF THE BOVINE LEUKOSE VI-RUS. 2. CRITICAL STAGES — MULTIPLICITY AND VERSATILITY (review)

“…Обнаружено также, что у инфицированных BLV животных во фрагментах геномной ДНК, фланкированных инвертированным повтором идентификационной последовательности ДНК транспозона Helitron, частота встречаемости суперсемейства NonLTR/SINE/SINE2 в 5 раз больше, чем у коров, свободных от инфекции. В целом в секвенированных фрагментах плотность мобильных генетических элементов (в частности, ретротранспозонов) у инфицированных BLV животных оказалась выше, чем у свободных от инфекции (106)(107)(108).…”