Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): Structure and phylogenetic significance

Abstract

Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed.

Isolation and Characterization of Interspersed Repeated Sequences in the Common Lizard, Zootoca vivipara, and Their Conservation in Squamata

“…4 ), showing 70.5% identity with a homologous segment of the SINE/tRNA Squam2 non-LTR retrotransposon of Lepidosauria [Grechko et al, 2011].…”

“…Both elements have full-length SINE copies of about 360 bp, are derived from tRNA, and are characterized by internal Box A and Box B for DNA polymerase III [Grechko et al, 2011].…”

“…In this study, we used the primer pair SINE A and SINE B from Grechko et al [2011] as well as a newly designed primer pair to isolate and characterize SINEs from the genome of Z. vivipara , with the aim to evaluate their distribution and conservation in different oviparous and viviparous populations of this species as well as in other squamates.…”

“…Furthermore, to test the conservation of the isolated sequences across squamates, experimental analyses were extended to representatives ( Brookesia sp., Chamaeleo chamaeleon , Podarcis muralis , Ctenophorus pictus , Oplurus cuvieri , Zonosaurus laticaudatus , [Grechko et al, 2011]; green, similarity with non-LTR retrotransposon from the Drosophila willistoni group [Kojima and Jurka, 2012]. The SINE-Zv primers used in the following analyses are double underlined (forward in black; reverse in red).…”

“…PCR amplifications were performed in a reaction volume of 20 μL using primers SINE A (TRGCTCAGTGG) and SINE B (GGRATYGAAC [Y]) [Grechko et al, 2011] according to the conditions reported by Grechko et al [2011]: 5 min at 94 ° C; 36 cycles at 94 ° C for 30 s, 50 ° C for 30 s, and 70 ° C for 45 s; 5 min at 72 ° C. Sequences including a trait with high identity to SINE Squam were selected and used to design an internal primer pair that was employed to analyze flanking regions: SINE-Zv forward 5 ′ -CACA-CCTCTGGGAAGGCAAT-3 ′ ; SINE-Zv reverse; 5 ′ -CAGCAT-CCTTCCAGGGTTTGA-3 ′ . The conditions of PCR amplification with SINE-Zv primers were: 5 min at 94 ° C; 36 cycles at 94 ° C for 30 s, 55 ° C for 30 s, and 72 ° C for 60 s; 7 min at 72 ° C.…”