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Title: A novel SINE family occurs frequently in both genomic DNA and transcribed sequences in ixodid ticks of the arthropod sub-phylum Chelicerata.

Author
item SUNTER, JACK - ILRE, NARIOBI, KENYA
item PATEL, SONAL - ILRE, NARIOBI, KENYA
item SKILTON, ROBERT - ILRE, NARIOBI, KENYA
item GITHAKA, N - ILRE, NARIOBI, KENYA
item Knowles Jr, Donald
item Scoles, Glen
item NENE, VISH - TIGR
item DE VILLIERS, ETIENNE - ILRE, NARIOBI, KENYA
item BISHOP, RICHARD - ILRE, NARIOBI, KENYA

Submitted to: Gene
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/30/2008
Publication Date: 5/31/2008
Citation: Sunter, J.D., Patel, S.P., Skilton, R.A., Githaka, N., Knowles Jr, D.P., Scoles, G.A., Nene, V., De Villiers, E., Bishop, R. 2008. A novel SINE family occurs frequently in both genomic DNA and transcribed sequences in ixodid ticks of the arthropod sub-phylum Chelicerata. Gene. 415(1-2):13-22.

Interpretive Summary: Short interspersed repetitive elements (SINEs) are transposable elements whose ability to move to new locations is based on reverse transcription prior to genomic integration. The transposition of SINEs is not autonomous since these elements do not encode the proteins required for mobility. Due to the irreversible, independent nature of their insertion, SINEs represent a powerful molecular tool for defining phylogeny. SINEs have been reported to occur in insect genomes; for example, several distinct families of SINEs have been described in Aedes aeygpti mosquito. Ticks, arthropods in the sub-phylum Chelicerata (order Acari), have been evolutionarily separated from the Insecta for an estimated 350 million years. Ticks are important vectors of pathogens, including the etiologic agents of Lyme disease in humans and a range of protozoan and rickettsial diseases of livestock. The genome sizes of three species of ixodid ticks, Ambylomma americanum, Boophilus (Rhipicephalus) microplus and Ixodes scapularis have been estimated using reassociation kinetics. These studies show that ticks have genome sizes at the upper end of the spectrum described for arthropods, with a comparatively high content (38-42%) of moderately repetitive DNA. In order to underpin new approaches to understand the molecular basis of disease transmission in ticks and initiate research on arthropod comparative genomics, expressed sequence tag (EST) databases have been assembled and annotated for four ixodid tick species, A. variegatum, R. appendiculatus, R. (B.) microplus and I. scapularis. In this paper we describe construction and initial sample sequencing of a bacterial artificial chromosome (BAC) library of R. appendiculatus and the interfacing of this data with the transcripts sequences in gene indices. Analysis of repetitive sequences within genomic and transcribed DNA reveals the widespread presence of a tRNA-derived SINE, that we have designated Ruka, in ixodid ticks.

Technical Abstract: Reassociation kinetics indicates that ixodid tick genomes are large, relative to most arthropods, containing =(greater than or equal to) 10^9 base pairs, although the molecular basis for this is currently unknown. We have identified a novel small interspersed element with features of a tRNA-derived SINE, designated Ruka, in genomic sequences of Rhipicephalus appendiculatus and Boophilus (Rhipicephalus) microplus ticks. The SINE was also identified in expressed sequence tag (EST) databases derived from several tissues in four species of ixodid ticks, including Amblyomma variegatum and also the more distantly related Ixodes scapularis. Secondary structure predictions indicated that Ruka could adopt a tRNA fold that was, atypically, most similar to a serine tRNA. The frequency of occurrence in the randomly selected BAC clone sequences is consistent with at least fifty thousand copies of Ruka in the R. appendiculatus genome. Several conserved Ruka insertion sites were identified in EST sequences of three ixodid tick species based on the flanking sequences associated with the SINES, indicating that some Ruka transpositions probably occurred prior to speciation within the metastriate sub-family of the Ixodidae. The data strongly suggests that type I transposable elements form a significant component of tick genomes and may at least partially account for the large genome sizes observed.