Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

Abstract

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Short interspersed nuclear elements (SINEs) are repetitive genomic sequences, members of class 1 transposable elements (retrotransposons), that are present in most eukaryotic organisms (Wicker et al. 2007), including monotreme, marsupial, and eutherian mammals, (Nishihara et al. 2006; Gu et al. 2007; Munemasa et al. 2008). Characterized by unique features in structure, proliferation, and genome distribution, SINEs are chimeras of transcribed RNA genes and simple repeats that proliferate via reverse transcription using the enzymatic machinery of autonomous elements, which recognize internal polymerase III promoter sequences (Collier and Largaespada 2007). Approximately 40 (transfer RNA) tRNA, 7SL RNA, and 5S ribosomal RNA derived SINE families have been described in mammals thus far, many of which are present in more than 10⁴ copies (Miyamoto 1999; Gu et al. 2007). As a source of insertional mutagenesis, SINEs have been linked to unequal recombination events (Callinan et al. 2005) and genetic diseases (Deininger and Batzer 1999) as well as proven to be informative evolutionary markers across genomes. With the publication of whole-genome sequences from domestic dog (Canis familiaris) (Lindblad-Toh et al. 2005), domestic cat (Felis catus) (Pontius et al. 2007), and most recently giant panda (Ailuropoda melanoleuca) (Li et al. 2010), new insights are possible on the family of SINEs unique to the Carnivora order termed Can-SINEs. Here, we review the structural, functional, and evolutionary impact of Can-SINEs on carnivore genomes.

Discovery and Characterization of Can-SINEs

Can-SINEs were first described in the early 1990s when an interspersed repetitive element was discovered on the X chromosome of the American mink (Mustela vison) that shared 55% sequence similarity with tRNA-lysine derived rodent B2 SINEs (Lawrence et al. 1985; Lavrentieva et al. 1991). Subsequent studies of other caniform suborder species including harbor seal (Phoca vitulina concolor), dog (C. familiaris), wolf (C. lupus), coyote (C. latrans), and mink (M. vision) affirmed the presence of these sequences in high copy number (Coltman and Wright 1994). Initially not observed in the feliform suborder representative, F. catus, this newly characterized SINE family appeared caniform specific and therefore was named Can-SINE (Coltman and Wright 1994). However, subsequent hybridization studies with F. catus (van der Vlugt and Lenstra 1995; Vassetzky and Kramerov 2002) as well as a sequence study of 3 Y-chromosome genes among all members of the Felis genus, the bobcat (Lynx rufus), C. familiaris, and several bear species (Pecon-Slattery et al. 2000) conclusively demonstrated that Can-SINEs are ubiquitous across Carnivora.

Can-SINEs are defined by a tRNA-related region, which includes A and B promoter boxes, followed by a (CT)_n microsatellite and terminate with a poly-A/T tail containing the polyadenylation signal AATAAA (Figure 1) (Lavrentieva et al. 1991). The tRNA-related region has primary sequence similarity of 70–79% to lysine-tRNAs (Vassetzky and Kramerov 2002), and most inserts are between 150 and 300 base pairs (bp) in length, depending on the size of the (CT)n and poly A/T regions (Vassetzky and Kramerov 2002; Pecon-Slattery et al. 2004). Each Can-SINE locus is flanked by target site duplications of 8–15 bp generated during retrotransposition. The number of SINE repeats within carnivore genomes, based on estimates of the C. familiaris genome, range from 1.1 × 10⁶ (Lindblad-Toh et al. 2005) to 1.3 × 10⁶ (Coltman and Wright 1994) copies.

Figure 1.

Alignment and minimum evolution phylogeny of Repbase Can-SINE voucher sequences. All Can-SINE vouchers begin with the designation “SINEC,” followed by species of first discovery where “Fc” = Felis catus, “CF” = Canis familiaris, “Ame” = Ailuropoda melanoleuca, and “Pv” = Phoca vitulina. (A) The initial global alignment of lysine-tRNA derived segments was estimated using the Geneious alignment module (Drummond et al. 2010) and refined by hand. Lines indicate RNA polymerase III promoter boxes A and B. (B) The neighbor-joining clustering algorithm was used to estimate phylogeny with the Tamura–Nei distance model, and branch support approximated using 1000 bootstrap replications. Feliform SINEs form a distinct clade.

Can-SINE Amplification

Although the specific retrotransposition mechanism has yet to be fully described, comparative evidence indicates that Can-SINEs proliferate in a manner similar to other mammalian SINEs (Gentles et al. 2005). In general, SINE amplification occurs through a “copy and paste” mechanism known as target-primed reverse transcription wherein a few SINE master or source copies are transcribed in high copy number (Cordaux et al. 2004; Tong et al. 2010). Lacking functional coding regions, SINE amplification, and integration is dependent on enzymes derived from the host genome and long interspersed nuclear elements (LINEs) (Kajikawa and Okada 2002). Proliferation is initiated by recognition of the promoter boxes residing in the RNA-related region by host-derived RNA-polymerase III and followed by cleavage of the genomic DNA at TTAAAA motifs between the T’s and A’s by LINE-derived enzymes (Gentles et al. 2005; Cordaux and Batzer 2009). This process allows the poly-A/T tail of the SINE transcript to bind to the single-stranded genomic DNA, creating a primer for LINE-derived reverse transcriptase to synthesize complementary SINE DNA (Christensen et al. 2006; Kurzynska-Kokorniak et al. 2007). A subsequent nick in the opposite genomic strand 6–10 bp downstream from the initial cut site results in a novel SINE insert flanked by target site duplications (Jurka 1997; Christensen et al. 2006) (Figure 2).

Figure 2.

Retrotransposition of mammalian SINE insertions. (A) The master SINE copy is transcribed by RNA polymerase III. (B) LINE-derived enzyme nicks a chromosome strand at the motif AATTTT. (C) The poly-A tail of a transcribed SINE binds to the free TTTT and acts as a primer for LINE-derived reverse transcriptase. A nick on the opposite strand frees the complementary target site duplication sequence. (D) Reverse transcriptase synthesizes complementary strands. (E) A new SINE insertion with characteristic target site duplications. Adapted from (Cordaux and Batzer 2009). (This figure appears in color in the online version of Journal of Heredity.)

The involvement of LINEs in SINE proliferation has been attributed to structural similarities between the 3′ portions (microsatellite and poly A/T regions) of each transposable element. For example, monotreme Mon-1 and marsupial Ther-2 SINE families share 3′ end sequences with LINEs of the same genome, which are believed to facilitate SINE retrotransposition (Ohshima and Okada 2005). Conversely, the endogenous L1 family LINEs that facilitate rodent and primate 7SL-derived SINE proliferation do not share primary sequence homology (Ohshima and Okada 2005). Whole-genome analyses of C. familiaris and F. catus reveal that at least 19% and 8% of the genome are comprised of LINE sequences respectively, derived from the L1 and L2 families (Lindblad-Toh et al. 2005; Pontius et al. 2007). In addition, complete open reading frames may be found amongst carnivore L1s, indicating recent retrotransposition activity of this LINE family (Pontius et al. 2007). However, further comparative genomic analyses are essential in clarifying the functional and evolutionary associations between carnivore-specific SINEs and LINEs.

Can-SINE Voucher Sequences and Subfamilies

At any given time, only a few SINE insertions will act as the source of novel SINE transcripts during amplification (Cordaux et al. 2004). Gradual accumulation of mutations will eventually inhibit transcription of a given master copy, which then becomes dormant and is replaced by an alternate copy. This process results in SINE subfamilies with diagnostic nucleotide sequence that are classified into phylogenetic lineages (Ray et al. 2006). The 16 Can-SINE voucher sequences described within the Repbase library and RepeatMasker software to date (Jurka et al. 2005; Smit and Green 2005) serve as prototypes for subfamily classification schemes. Can-SINE sequences are collectively designated “SINEC” followed by putative subfamily and species of first discovery identifiers (Figure 1). For example, the first Can-SINE insertion sequence found in the A. melanoleuca genome is designated SINEC1_AMe (Li et al. 2010).

Phylogenetic analysis of existing Can-SINE voucher sequences defines 2 evolutionary lineages concordant with genome origin as either caniform or feliform (Figure 1). Amongst the caniform SINEs, divergent lineages represented by A. melanoeuca (family Ursidae) and P. vitulina (family Phocidae) are interspersed with putative Canis (family Canidae) specific sequences. This structure, unrelated to carnivore taxonomy, suggests SINE master copies that originated early in caniforms have remained active sources of SINE proliferation within independent lineages (Figure 1). Future comparative research will fully characterize the Can-SINE subfamilies and provide further insight to the carnivore genome diversity.

Biomedical Effects of Can-SINEs

Transposable elements, including SINEs, contribute broadly to the functional diversity of mammalian genomes. Although the vast majority of novel insertions that manage to evade purifying selection and genetic drift are functionally benign, a few confer neutral or deleterious phenotypic variants (Belancio et al. 2008). SINE insertions may be co-opted by host genomes as sites for nonhomologous genome rearrangement, as sources for coding sequence, and as regulatory elements. Numerous transposable element insertions have been implicated in human disease (Deininger and Batzer 1999; Batzer and Deininger 2002), and transgenic mice engineered for over expression of the transposable element type known as “Sleeping Beauty” experienced increased cancer development (Dupuy et al. 2005). Relative to primates and rodents, the phenotypic consequences of SINE insertions among Carnivores are less thoroughly documented. However, an increasing number of SINE-derived variants have been found amongst the domestic dog breeds, which provide well-defined populations ideal for studying morphological variation and disease susceptibility.

The merle coat pattern of C. familiaris is an incompletely dominant inherited phenotype noted by marbled coat pigmentation that is sometimes accompanied by symptoms analogous to those associated with human Waardenburg syndrome including auditory, visual, skeletal, cardiac, and reproductive impairments (Clark et al. 2006). This phenotype, common in the Corgi, Dachshund, Australian Shepard, and other domestic breeds, segregates with a region of the C. familiaris genome that includes the silver” gene, SILV, which is responsible for coat pigment in multiple mammalian species including mouse and horse (Kwon et al. 1995; Theos et al. 2005). In merle canines, the SILV gene harbors a Can-SINE insertion in reverse orientation at the boundary of intron 10 and exon 11, which causes alternate splicing of exon 11 and ultimately results in the merle phenotype (Clark et al. 2006).

The autosomal recessive version of spontaneous centronuclear myopathy (CNM), a muscular disorder that affects multiple mammalian species including humans, occurs in Labrador retrievers. The disease is characterized by muscle weakness, muscular atrophy, and other afflictions attributed to compromised muscle fibers (Hu et al. 1996; Laporte et al. 1996). Disease associated genotypes were mapped to the canine autosomal protein tyrosine phosphatase-like member A gene (PTPLA), the mouse and human homologs of which are expressed in myogenic precursors during embryogenesis and in adult skeletal muscles (Uwanogho et al. 1999; Breen et al. 2004). Characterization of canine PTPLA revealed a Can-SINE insertion in the reverse orientation within exon 2 that segregates with CNM disease. The disorder conforms to a recessive model of inheritance in which unaffected carriers are heterozygous, whereas affected individuals are homozygous for the insertion. Can-SINE presence results in 7 transcript isoforms of which only 2 are identical to wild-type PTPLA, whereas the remaining 5 are presumably ineffective or toxic (Pelé et al. 2005).

Narcolepsy is a sleep disorder that affects humans and other mammals including domestic dogs. A mutation within the hypocretin receptor 2 gene (HCRTR2) is among the multiple genetic causes of human early onset narcolepsy (Peyron et al. 2000). Doberman Pinschers with narcolepsy also have an HCRTR2 mutation in the form of a Can-SINE insertion prior to the fourth exon that results in inefficient pre- (messenger RNA) mRNA splicing. Other domestic dog breeds with increased incidence of narcolepsy, however, do not have the HCRTR2 insertion, and thus, similar to the human disease, there may be multiple causes of canine narcolepsy (Lin et al. 1999).

Domestic dogs are characterized by profound body size diversity, ranging from 2 kg Chihuahuas to 82 kg Mastiffs. Recent efforts to unveil genetic factors influencing canine body size have uncovered multiple Can-SINE insertion variants in linkage disequilibrium with size determining genes. Within the second intron of the insulin-like growth factor 1 (IGF1) gene, an SNP and Can-SINE segregate with a wide variety of small breeds (Sutter et al. 2007). Although SINE insertions are demonstrated factors in gene expression (Hasler and Strub 2006; Lin et al. 2008), the causative mutation in IGF1 has yet to be determined. From an evolutionary perspective, although the “small” haplotype is not observed in the domestic dog forbearer, the gray wolf (C. lupus), overall genetic similarity to the homologous locus in Middle Eastern wolves suggests a Middle Eastern origin for a small dog variant that occurred after the initial domestication (Gray et al. 2010).

Retrogenes are derived from processed mRNAs sequences that have been retrotransposed into the genome via reverse transcription and are usually not expressed due to the absence of regulatory elements (Brosius 1999a). However, in rare instances, retrogenes can employ the internal promoters of nearby LINEs or SINEs for transcription and expression (Brosius 1999b; Esnault et al. 2000). Chondrodysplasia (shortened limbs) is a feature of several domestic dog breeds linked to the fibroblast-growth-factor receptor 4 retrogene (fgfr4). This retrogene has been inserted into a LINE sequence that is in close proximity to multiple Can-SINE insertions suggesting that these elements provide promoter sequences that allow expression of the fgfr4 at critical time points in development (Parker et al. 2009).

The Can-SINE induced phenotypes described above, associated with dog domestication and breed development, serve as models for the role of SINEs in gene function and complex genetic diseases in natural populations. Increased genomic data and advances in bioinformatics tools will further elucidate the interplay between Can-SINEs, coding sequences, and regulatory regions (Spady and Ostrander 2008).

Evolutionary Insights

SINEs have been used as synapomorphic markers in the reconstruction of several mammalian phylogenies including the afrotherian, cetacean, and artiodactyls lineages (Nikaido et al. 1999, 2001; Nishihara et al. 2005, 2006). However, very few studies have investigated the utility of Can-SINEs in carnivore systematics. Prior to the availability of carnivore whole-genome sequences, Can-SINEs were primarily characterized as a by-product of other genetic studies. For example, a survey of microsatellite loci inadvertently uncovered a species-specific SINE insertion in the Mel08 locus of American mink (M. vison) (Lopez-Giraldez et al. 2006) that was subsequently used in conservation efforts to distinguish invasive M. vison from the ecologically imperiled European mink (M. lutreola) (Lopez-Giraldez et al. 2005) (Table 1). Similarly, sequence analysis of the transthyretin gene revealed an orthologous Can-SINE locus that is a synapomorphy amongst caniforms (Zehr et al. 2001). Comparative studies of the feliform species bay cat (Profelis temminckii) and Pallas cat (Otocolobus manul), as well as the caniform gray wolf (C. lupus), red wolf (C. rufus), otter (Lutra lutra), and striped skunk (Mephitis mephitis) unveiled multiple, independently-derived Can-SINE insertions in the ß-fibrinogen gene (Yu and Zhang 2005). Moreover, the M. mephitis insert is a chimera, illustrating the tendency for SINEs to be incorporated within or adjacent to existing SINEs (Yu et al. 2004, 2008). (Table 1).

Table 1.

Clade and species-specific Can-SINE insertion sites published in previous evolutionary studies.

Taxonomic group	Locus name	Publication
Suborder
Caniformia	Ttr intron 1	Zehr et al. (2001)/Yu et al. (2011)
Caniformia	CF_L002d	Schröder et al. (2009)
Caniformia	CF_L003c	Schröder et al. (2009)
Caniformia	CF_L006a	Schröder et al. (2009)
Caniformia	CF_L010	Schröder et al. (2009)
Caniformia	CF_L013	Schröder et al. (2009)
Superfamily
Arctiodea	CF_L003b	Schröder et al. (2009)
Musteloidea	CF_L002b	Schröder et al. (2009)
Musteloidea	Ccng2 intron 2	Yu et al. (2011)
Pinnipedia (2)	Ssr1 intron 5	Yu et al. (2011)
Pinnipedia	Wasf1 intron 3	Yu et al. (2011)
Family
Ursidae	Zfy	Pecon-Slattery et al. (2000)
Canidae	CF_L001	Schröder et al. (2009)
Canidae*	CF_L003a	Schröder et al. (2009)
Canidae	CF_L004	Schröder et al. (2009)
Canidae	CF_L007a	Schröder et al. (2009)
Canidae	CF_L007b	Schröder et al. (2009)
Canidae	CF_L008	Schröder et al. (2009)
Canidae	CF_L011	Schröder et al. (2009)
Canidae	CF_L014	Schröder et al. (2009)
Canidae	CF_L015	Schröder et al. (2009)
Odobenidae/Otariidae	CF_L006b	Schröder et al. (2009)
Mustelidae (except Meles)	CF_L004b	Schröder et al. (2009)
Canidae*	CF_L016	Schröder et al. (2009)
Mustelidae	Ccng2 intron 2	Yu et al. (2011)
Otaeiidae	Ccng2 intron 2	Yu et al. (2011)
Ursidae	Cidea1	Yu et al. (2011)
Mustelidae	Cidea1	Yu et al. (2011)
Mustelidae (2)	Impa1 intron 6	Yu et al. (2011)
Procyonidae	Plod2 intron 14	Yu et al. (2011)
Subfamily
Caninae	CF_L002e	Schröder et al. (2009)
Caninae*	CF_L009b	Schröder et al. (2009)
Genus
Felis	Zfy	Pecon-Slattery et al. (2000)
Canis	ß-fibrinogen intron 7	Yu and Zhang (2005)
Ursus	Coro1c intron 5	Yu et al. (2011)
Ursus	Impa1 intron 6	Yu et al. (2011)
Species
Mustela vison	Mel08 locus	Lopez-Giraldez et al. (2005)
Otocolobus manul	Ube1y	Pecon-Slattery et al. (2000)
O. manul	ß-fibrinogen intron 7	Yu and Zhang (2005)
Profelis temminckii	ß-fibrinogen intron 7	Yu and Zhang (2005)
M. erminea	Zfy	Yamada and Masuda (2010)
Meles anakuma	Zfy	Yamada and Masuda (2010)
Mephitis mephitis	ß-fibrinogen intron 7	Yu and Zhang (2008)
Lutra lutra	ß-fibrinogen intron 4	Yu and Zhang (2008)
Ursus arctos	Smcy	Pecon-Slattery et al. (2000)
Lynx rufus	Smcy	Pecon-Slattery et al. (2004)
Felis margarita/silvestris	Smcy	Pecon-Slattery et al. (2004)
Ursus arctos*	CF_L002a	Schröder et al. (2009)
Mep. mephitis*	CF_L002c	Schröder et al. (2009)
Mep. mephitis*	CF_L008a	Schröder et al. (2009)
Canis familiaris*	CF_L005	Schröder et al. (2009)
C. familiaris*	CF_L012	Schröder et al. (2009)
Procyon lotor*	CF_L009a	Schröder et al. (2009)
Zalophus californianus	CF_L017	Schröder et al. (2009)
U. arctos*	CF_L018	Schröder et al. (2009)
Proc. lotor*	CF_L021	Schröder et al. (2009)
C. familiaris/lupus*	Atp5d intron 2	Yu et al. (2011)
C. familiaris/lupus*	Fgb7	Yu et al.(2011)
C. familiaris/lupus* (2)	Ssr1 intron 5	Yu et al. (2011)
Arctonyx collaris*	Cidea1	Yu et al. (2011)
Proc. lotor* (2)	Ccng2 intron 6	Yu et al. (2011)
Mep. mephitis*	Cidea1	Yu et al. (2011)
Mep. mephitis*	Impa1 intron 6	Yu et al. (2011)
M. kathiah*	Impa1 intron 6	Yu et al. (2011)
Mep. mephitis* (2)	Fgb7	Yu et al. (2011)
Ailuropoda melanoleuca*	Guca1b intron 3	Yu et al. (2011)
A. melanoleuca*	Impa1 intron 6	Yu et al. (2011)
A. melanoleuca*	Ssr1 intron 5	Yu et al. (2011)
Mep. mephitis*	Tbk1 intron 8	Yu et al. (2011)
Martes flavigula*	Ociad1 intron 4	Yu et al. (2011)

*Phylogenetic range is not yet conclusive as data is not available from all related taxa. Numbers in parentheses indicate adjacent independent insertions within the same taxa.

The Y chromosome is described as a “sink” for transposable elements where SINEs can accumulate in the nonrecombining region (Krzywinskia et al. 2004; Jurka et al. 2007). Can-SINE insertions have been found within the Zfy gene of the Felis genus, the bear (Ursidae) family, the Japanese badger (Meles anakuma), and the stoat (M. erminea) (Pecon-Slattery et al. 2000; Yamada and Masuda 2010). The Smcy gene hosts an orthologous insertion in the sand cat (F. margarita) and the wildcat (F. silvestris) species complex. Species-specific insertions are also found in the Smcy gene of Ursus arctos and Ly. rufus (Pecon-Slattery et al. 2004). Otocolobus manul has a species-specific insertion in the Ube1y gene (Pecon-Slattery et al. 2000). (Table 1).

As with all mammalian SINEs, Can-SINE insertion distributions are generally congruent with existing hypotheses of speciation (Ray et al. 2006). However, the intronic insertions found in all Felis species and L. rufus (described above) occur at identical genomic coordinates (Pecon-Slattery et al. 2000, 2004), which if interpreted as a single synapomorphy, would unite distantly related species. However, phylogenetic reconstruction with sequences adjacent to the insertion site and differences in the poly A/T tails indicate that the 2 insertions are the result of independent SINE integration events at identical loci that occurred after the divergence of the major cat lineages (Pecon-Slattery et al. 2004; Johnson et al. 2006).

Comparative Genomics Fosters Can-SINEs Analyses

Whole-genome sequencing technologies enable inclusion of SINEs and other transposable elements in comparative analyses. Computational tools for analysis of noncoding regions littered with SINE insertions are becoming more accessible while sequences from model organisms provide a point of reference for the pursuit of informative SINEs in closely related and divergent taxa Wang et al. 2006; Liu et al. 2009; Schröder et al. 2009).

Whole-genome sequences derived from a Standard Poodle and Boxer indicate Can-SINEs account for approximately 8% of the C. familiaris genome (Kirkness et al. 2003; Lindblad-Toh et al. 2005). Nearly, all Can-SINE sequences that most closely align to the SINEC_Cf2 voucher sequence are homozygous and conserved between the 2 individuals, indicating that this subfamily is inactive. However, approximately 7% of sequences that most closely resemble the SINEC_Cf voucher sequence are unfixed, either within or between the 2 canines, which suggests recent proliferation of the corresponding subfamily (Kirkness et al. 2003). In contrast, recently acquired insertions account for only 0.5% of the Alu content in the human genome of which only 25% are unfixed (Batzer and Deininger 2002). Approximately 7.9% of the giant panda (A. melanoleuca) genome is comprised of SINE insertions that are <10% diverged from Repbase voucher sequences (Li et al. 2010). Further, de novo characterization of transposable elements identified an additional 0.1% of sequence belonging to SINE elements that were not yet identified in the Repbase, which suggests the presence of panda-specific subfamilies (Li et al. 2010). Initial estimates of the transposable element content in F. catus found that 11% of the genome is comprised of Can-SINEs similar to SINEC_FC1, SINEC_FC2, and SINEC_C1 voucher sequences and mammalian-wide MIR SINEs. However, novel Can-SINE sequences were also identified (Pontius et al. 2007), suggesting feliform-specific subfamilies in addition to those in Repbase.

Whole-genome sequences may be used as references for comparative analyses, allowing large-scale identification of Can-SINE insertion sites in both coding and noncoding regions that are population, species, or lineage specific. Within C. familiaris, 64 unfixed SINEC_Cf insertions have been localized that segregate with breed (Wang and Kirkness 2005). In addition, 17 intronic parsimony informative Can-SINE loci, distributed among a collection of anonymous introns, were located among 21 caniform species, all of which are congruent with other molecular data (Schröder et al. 2009). Whole-genome sequencing also facilitated identification of 31 diagnostic Can-SINE insertions amongst 14 intronic regions (Yu et al. 2011). Within Feliformia, comparative genomics analysis resulted in the identification of over 90 informative loci that can discern suborder, familial, and species relationships (Walters-Conte KB, unpublished data).

Conclusions

Our understanding of mammalian transposable elements has accelerated in the last 20 years as a consequence of advances in sequencing and computational technologies. Through these advances, we find that carnivore-specific Can-SINEs have a significant impact on genome content and gene function. These abundant retroelement insertions can directly alter phenotypes by becoming incorporated into coding regions and by providing promoter sequences that disrupt the transcriptional regulation of adjacent genes. As sources of genetic diversity, Can-SINEs have proven to be highly informative markers to differentiate protected and invasive species. In addition, Can-SINEs can define domestic dog breeds as well as diagnose species, genus, familial, and suborder relationships throughout Carnivora. Whole-genome sequences provide references to investigate the plethora of Can-SINEs that are clustered within intergenic regions. Future advancements in sequencing and bioinformatics technologies will provide further insights into Can-SINE biology, which will add to our general knowledge of the function and evolution of mammalian SINEs.

Funding

This project has been supported in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract N01-CO-12400. The Robert Weintraub Program in Systematics and Evolution administered by The George Washington University also provided financial support.