Transposons are present as dynamic elements in all eukaryotic genomes. Their ability to ‘jump’ around the genome and amplify offers potential for significant genomic change resulting in segment duplication, chromosomal rearrangement and sex chromosome differentiation. Long interspersed nuclear elements (LINEs) accumulate in snakes on Z or W sex chromosomes in several lineages. Partial sequences of the reverse transcriptase gene of BovB LINE non-LTR retrotransposon were sequenced and characterized from males and females of 24 snake species to better understand LINE dynamics and organization in snake genomes. Phylogenetic analysis showed four BovB LINE subfamilies with most BovB element sequences grouped among respective species. Most caenophidian snakes were clustered together in the same subfamily, except for Acrochordus javanicus which was grouped with boid and xenopeltid snakes. Three of four subfamilies contained dispersed henophidian snakes and other squamate reptiles as outgroups. This phylogenetic topology differed from the tree based on functional nuclear and mitochondrial gene sequences, suggesting that horizontal transfer events occurred in snake lineages. Average Ka/Ks approached 1, suggesting that after retrotransposition the BovB element was influenced by pseudogene-like evolution. Quantitative real-time polymerase chain reaction (qPCR) was applied to measure BovB element copy number. Variation was demonstrated between sexes with males showing higher copy number than females in eight species (Cylindrophis ruffus, Python bivittatus, Daboia siamensis, Homolopsis buccata, Naja kaouthia, Naja siamensis, Ahaetulla prasina and Ptyas mucosa), whereas females proved higher than males in two species (Python regius, Coelognathus radiata). This suggests that sex-biased copy number of the BovB element occurred independently in snake lineages, possibly by preferred accumulation of transposons on Z or W sex chromosomes.
Transposons are present as dynamic elements in all eukaryotic genomes. Their ability to ‘jump’ around the genome and amplify offers potential for significant genomic change resulting in segment duplication, chromosomal rearrangement and sex chromosome differentiation. Long interspersed nuclear elements (LINEs) accumulate in snakes on Z or W sex chromosomes in several lineages. Partial sequences of the reverse transcriptase gene of BovB LINE non-LTR retrotransposon were sequenced and characterized from males and females of 24 snake species to better understand LINE dynamics and organization in snake genomes. Phylogenetic analysis showed four BovB LINE subfamilies with most BovB element sequences grouped among respective species. Most caenophidian snakes were clustered together in the same subfamily, except for Acrochordus javanicus which was grouped with boid and xenopeltid snakes. Three of four subfamilies contained dispersed henophidian snakes and other squamate reptiles as outgroups. This phylogenetic topology differed from the tree based on functional nuclear and mitochondrial gene sequences, suggesting that horizontal transfer events occurred in snake lineages. Average Ka/Ks approached 1, suggesting that after retrotransposition the BovB element was influenced by pseudogene-like evolution. Quantitative real-time polymerase chain reaction (qPCR) was applied to measure BovB element copy number. Variation was demonstrated between sexes with males showing higher copy number than females in eight species (Cylindrophis ruffus, Python bivittatus, Daboia siamensis, Homolopsis buccata, Naja kaouthia, Naja siamensis, Ahaetulla prasina and Ptyas mucos ...
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