Lack of satellite DNA species-specific homogenization and relationship to chromosomal rearrangements in monitor lizards (Varanidae, Squamata)

Abstract

BackgroundSatellite DNAs (stDNAs) are highly repeated sequences that constitute large portions of any genome. The evolutionary dynamics of stDNA (e.g. copy number, nucleotide sequence, location) can, therefore, provide an insight into genome organization and evolution. We investigated the evolutionary origin of VSAREP stDNA in 17 monitor lizards (seven Asian, five Australian, and five African) at molecular and cytogenetic level.ResultsResults revealed that VSAREP is conserved in the genome of Asian and Australian varanids, but not in African varanids, suggesting that these sequences are either differentiated or lost in the African varanids. Phylogenetic and arrangement network analyses revealed the existence of at least four VSAREP subfamilies. The similarity of each sequence unit within the same VSAREP subfamily from different species was higher than those of other VSAREP subfamilies belonging to the same species. Additionally, all VSAREP subfamilies isolated from the three Australian species (Varanus rosenbergi, V. gouldii, and V. acanthurus) were co-localized near the centromeric or pericentromeric regions of the macrochromosomes, except for chromosomes 3 and 4 in each Australian varanid. However, their chromosomal arrangements were different among species.ConclusionsThe VSAREP stDNA family lack homogenized species-specific nucleotide positions in varanid lineage. Most VSAREP sequences were shared among varanids within the four VSAREP subfamilies. This suggests that nucleotide substitutions in each varanid species accumulated more slowly than homogenization rates in each VSAREP subfamily, resulting in non-species-specific evolution of stDNA profiles. Moreover, changes in location of VSAREP stDNA in each Australian varanid suggests a correlation with chromosomal rearrangements, leading to karyotypic differences among these species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-1044-6) contains supplementary material, which is available to authorized users.

Characterization of a satellite DNA in the genera Lacerta and Timon (Reptilia, Lacertidae) and its role in the differentiation of the W chromosome

“…Therefore, it seems that in these Lacerta species, IMO‐TaqI is involved in the differentiation of the W sex chromosome by heterochromatinization. Despite heterochromatinization is often found in reptilian sex‐heterochromosomes, DNA repeats in the heterochromatin of Y and W chromosomes have been partially characterized in just few species of snakes (Jones & Singh, ; Lee, Hugall, Lawson, & Scanlon, ; O'Meally et al., ; Singh, Purdom, & Jones, ), iguanians (Gamble, Geneva, Glor, & Zarkover, ; Altmanová, Rovatsos, Kratochvíl, & Johnson Pokorná, ), monitor lizards (Matsubara et al., ; Prakhongcheep et al., ), and lacertid lizards (Pokorná et al., ; Srikulnath et al., ). In most cases, these repeats are represented by microsatellites (Altmanová et al., ; Gamble et al., ; Matsubara et al., ; O'Meally et al., ; Pokorná et al., ).…”

“…However, given that more and more scientific evidence has been indicating that vari presence of transcripts of this elements that could help explain this remarkable conservation across the phylogeny of lacertid lizards. Prakhongcheep et al, 2017), and lacertid lizards (Pokorná et al, 2011;Srikulnath et al, 2014). In most cases, these repeats are represented by microsatellites Gamble et al, 2014;Matsubara et al, 2014;O'Meally et al, 2010;Pokorná et al, 2011).…”

“…Several studies on satDNA have been carried out also in squamate reptiles. In this taxon, satDNAs have been isolated and characterized in skinks (Giovannotti, Nisi Cerioni, & CaputoV, , ), snakes (Matsubara et al., ; Singh, Purdom, & Jones, ), monitor lizards (Chaiprasertsri et al., ; Prakhongcheep et al., ), and lacertids (Capriglione, Olmo, Odierna, Smith, & Miller, , , , , ; Ciobanu, Roudykh, Grechko, & Kramerov, , , ; Grechko, Ciobanu, Darevsky, & Kramerov, , ; Giovannotti et al., ; Rojo et al., ), with this latter taxon being the most studied squamates with reference to satDNAs so far.…”

Evolutionary Dynamics of the Repetitive DNA in the Karyotypes of Pipa carvalhoi and Xenopus tropicalis (Anura, Pipidae)

“…In addition to its structural role in the eukaryote chromosome, the repetitive fraction of the genome also plays a central role in the stability of the chromosome, the cell cycle, and the regulation of gene expression and is an important substrate for genome evolution (Foulongne-Oriol et al, 2013;Biscotti et al, 2015;Liu et al, 2019). Macrostructurally, sequences of repetitive DNA are involved directly or indirectly in the chromosomal rearrangement events (i.e., deletions, duplications, inversions, and translocations) that are responsible for the significant karyotypic variation observed during the evolution of many groups of organisms (Kidwell, 2002;Feschotte and Pritham, 2007;Cazaux et al, 2011;González and Petrov, 2012;Prakhongcheep et al, 2017;Supiwong et al, 2019).…”

Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae)

“…In this family, satDNAs were characterized at both molecular and cytogenetic levels in several species (Capriglione, 2000; Capriglione, Cardone, Odierna, & Olmo, 1991, 1994; Capriglione, De Santo, Odierna, & Olmo, 1998; Capriglione, Olmo, Odierna, Smith, & Miller, 1989; Ciobanu, Grechko, & Darevsky, 2003; Ciobanu, Grechko, Darevsky, & Kramerov, 2004; Giovannotti et al, 2014, 2018; Grechko, Ciobanu, Darevsky, & Kramerov, 2005, 2006; Rojo et al, 2015). SatDNAs were studied also in other squamates such as skinks (Giovannotti et al, 2013; Giovannotti, Nisi Cerioni, Caputo, & Olmo, 2009), snakes (Matsubara et al, 2015; Singh, Purdom, & Jones, 1976), and monitor lizards (Chaiprasertsri et al, 2013; Prakhongcheep et al, 2017). In particular, one of the satDNA isolated from lacertids, IMO‐TaqI (see Giovannotti et al, 2018), was found to be widespread and highly conserved in this family (Capriglione et al, 1991; Giovannotti et al, 2014, 2018; Rojo et al, 2015).…”