Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation

Abstract

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can “jump” and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10−6% to 5.63 × 10−2% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.

Impact of Repetitive DNA Elements on Snake Genome Biology and Evolution

“…Kimura divergence analysis of repeat landscaping showed that TEs in snakes were older compared with those of anole lizard TEs [ 25 , 123 ]. Nevertheless, some young elements have also experienced recent expansion in snake genomes, e.g., snake1, CR1, LINEs, and BovB [ 40 , 78 , 125 ]. The CR1 element has also expanded in the crocodilian lineage, constituting around 10% of the total genome.…”

“…These TEs are important phylogenetic markers in studies investigating the diversity of snake lineages. Recent exploration of a retroelement termed Bov-B LINE shed light on the diversity of snake lineages [ 125 ]. Sequence variability of Bov-B LINE resolved the complex phylogenetic framework among eight diverse snake lineages, including Henophidian (Cylindrophidae, Boidae, and Pythonidae) and Caenophidian (Acrochordidae, Viperidae, Homalopsidae, Elapidae, and Colubridae) snakes.…”

Genome sequences of fourIxodesspecies expands understanding of tick evolution

“…Our analysis of transposable elements (TEs) shows that they constitute a large proportion of the genomes in four Ixodes tick species, which is typical of large eukaryotic genomes. Interestingly, we identified Bov-B LINEs in the genome of I. ricinus , a subclass of retrotransposons abundant in vertebrates, which have also been found in the genomes of reptile ticks, with evidence of horizontal gene transfer between vertebrates and ticks (Walsh et al 2013; Puinongpo et al 2020). The presence of Bov-B LINE sequences in several species of Ixodes could therefore reflect independent acquisitions of transposons from vertebrate hosts.…”

RPA-CRISPR/Cas12a-LFA combined with a digital visualization instrument to detect Toxoplasma gondii in stray dogs and cats in Zhejiang province, China

“…3C ); however, there was no difference in fluorescence intensity between the plasmid at 10 −8 ng and the negative control group. The results showed that the lower limit of detection was 31 copies/μL, and the plasmid copy number was calculated using the equation: DNA (copy number) = [(6.023 × 1,023) × (copy number/mol) × DNA amount (g)]/[DNA length (bp) × 660 × (g/mol/bp)], where the base number of recombinant plasmid pMD-19T- B1 was 4,907 bp ( 34 ). The sensitivity of RPA-CRISPR/Cas12a to detect pMD-19T- B1 was 10 times greater than the sensitivity of qPCR ( Fig.…”