First Application of the SINE (Short Interspersed Repetitive Element) Method to Infer Phylogenetic Relationships in Reptiles: An Example from the Turtle Superfamily Testudinoidea

Abstract

Although turtles (order Testudines) constitute one of the major reptile groups, their phylogenetic relationships remain largely unresolved. Hence, we attempted to elucidate their phylogeny using the SINE (short interspersed repetitive element) method, in which the sharing of a SINE at orthologous loci is indicative of synapomorphy. First, a detailed characterization of the tortoise polIII/SINE was conducted using 10 species from eight families of hidden-necked turtles (suborder Cryptodira). Our analysis of 382 SINE sequences newly isolated in the present study revealed two subgroups, namely Cry I and Cry II, which were distinguishable according to diagnostic nucleotides in the 3' region. Furthermore, four (IA-ID) and five (IIA-IIE) different SINE types were identified within Cry I and Cry II subgroups, respectively, based on features of insertions/deletions located in the middle of the SINE sequences. The relative frequency of occurrence of the subgroups and the types of SINEs in this family were highly variable among different lineages of turtles, suggesting active differential retroposition in each lineage. Further application of the SINE method using the most retrotranspositionally active types, namely IB and IC, challenged the established phylogenetic relationships of Bataguridae and its related families. The data for 11 orthologous loci demonstrated a close relationship between Bataguridae and Testudinidae, as well as the presence of the three clades within Bataguridae. Although the SINE method has been used to infer the phylogenies of a number of vertebrate groups, it has never been applied to reptiles. The present study represents the first application of this method to a phylogenetic analysis of this class of vertebrates, and it provides detailed information on the SINE subgroups and types. This information may be applied to the phylogenetic resolution of relevant turtle lineages.

Transposable Elements in Reptilian and Avian (Sauropsida) Genomes

“…In sauropsids, the most intensively investigated TEs have been non-LTR retrotransposons (LINEs or retroposons), such as RTE clade (including Bov-B LINEs) [Zupunski et al, 2001;Gogolevsky et al, 2008;Novick et al, 2009;Piskurek et al, 2009], L2 clade [Lovsin et al, 2001;Novick et al, 2009;Piskurek et al, 2009], L1 clade [Kordis et al, 2006;Novick et al, 2009;Piskurek et al, 2009], R4 clade [Volff et al, 2001a;Novick et al, 2009;Piskurek et al, 2009], CR1 clade [Fantaccione et al, 2004;International Chicken Genome Sequencing Consortium, 2004;Wicker et al, 2005;Shedlock, 2006;Kaiser et al, 2007;Kriegs et al, 2007;Shedlock et al, 2007;Abrusan et al, 2008;Chapus and Edwards, 2009;Liu et al, 2009;Novick et al, 2009;Piskurek et al, 2009;Shan et al, 2009] and R2 clade [Kojima and Fujiwara, 2005]. Much research in sauropsids has been focused on SINEs, such as on the CR1 LINE/SINE pair in a lizard [Fantaccione et al, 2004], LF SINEs [Bejerano et al, 2006], AmnSINE1s [Nishihara et al, 2006;Hirakawa et al, 2009], Sauria SINEs [Piskurek et al, 2006[Piskurek et al, , 2009Piskurek and Okada, 2007;Gogolevsky et al, 2008;Kosushkin et al, 2008], polIII/SINE in turtles …”

“…Short interspersed elements (SINEs) are one of the major types of mobile elements in vertebrate genomes and are generally lineage-specific [Ohshima and Okada, 2005]. SINEs are among the first retroposons to be very extensively studied in sauropsid genomes [Endoh and Okada, 1986;Endoh et al, 1990;Smit and Riggs, 1995;Ohshima et al, 1996;Okada et al, 1997;Terai et al, 1998;Gilbert and Labuda, 1999;Fantaccione et al, 2004;Sasaki et al, 2004;Bejerano et al, 2006;Kosushkin et al, 2006Kosushkin et al, , 2008Nishihara et al, 2006;Piskurek et al, 2006Piskurek et al, , 2009Sasaki et al, 2006;Piskurek and Okada, 2007;Shedlock et al, 2007;Gogolevsky et al, 2008;Hirakawa et al, 2009]. The first sauropsid SINE to be discovered was polIII/SINE in turtles [Endoh and Okada, 1986;Endoh et al, 1990], and its LINE partner is CR1 LINE [Ohshima et al, 1996;Kajikawa et al, 1997].…”

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

“…The turtle and alligator species investigated here have environmental as opposed to genetic sex determination, and sex determination in Anolis is inferred to be genetic based on some karyological evidence (11). Several retroelement lineages have been characterized in turtles and other reptiles (12)(13)(14)(15). Projects in progress will produce genome sequences for another bird, the Zebra Finch, Taeniopygia guttata, and a lizard, Anolis carolinensis.…”

SINEs and LINEs: symbionts of eukaryotic genomes with a common tail

“…We defined sequences that contain internal promoters for RNA polymerase III and are subject to multiple rounds of retroposition as SINEs. Almost all the SINEs re- Endoh and Okada, 1986;Endoh et al, 1990;Ohshima et al, 1996;Sasaki et al, 2004 tRNA ( Kido et al, 1991;Gilbert and Labuda, 1999 tRNA RSg-1 CORE-SINEs (AvaIII) All Salmonids, Salmonidae Kido et al, 1994;Gilbert and Labuda, 1999 tRNA nd CORE-SINEs (AFC/ROn-1) Cichlid fishes (AFC)…”

“…Second, flying lemur CYN/t-SINE and Mosquito Twin SINE are almost entirely composed of tDNA, and therefore do not comprise LINE-related 3) sequences (Table 1). Finally, three tRNA-derived SINE families of Arabidopsis tha- (Sasaki et al, 2004) and the PsCR1 LINE from turtle (Kajikawa et al, 1997). Identical nucleotides are indicated by asterisks.…”