Characterization of Aphidius ervi (hymenoptera, braconidae) ribosomal genes and identification of site-specific insertion elements belonging to the non-LTR retrotransposon family

Varricchio, Paola; Gargiulo, Giuseppe; Graziani, Franco; Manzi, Andrea; Pennacchio, Francesco; Digilio, M. Cristina; Tremblay, E.; Malva, C.

doi:10.1016/0965-1748(94)00102-n

Cited by 5 publications

(6 citation statements)

References 45 publications

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“…6C). It is surprising that the honey bee does not contain complete and functional R1 elements, given that other hymenopteran insects have been purported to harbour them (Jakubczak et al, 1991;Bigot et al, 1992;Varricchio et al, 1994). According to Jakubczak et al (1991), Nasonia sp., S. speciosus and the carpenter bee, Xylocopa sp., all contain R1 elements, although ORFs have not been determined for any of these species, and only the 3′-junctions with the 28S rDNA were actually sequenced.…”

Section: Igsmentioning

confidence: 99%

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Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

Gillespie¹,

Johnston²,

Cannone³

et al. 2006

Insect Molecular Biology

266

287

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As an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) ribosomal RNA (rRNA)-encoding gene sequences (rDNA) and related internally and externally transcribed spacer regions of Apis mellifera (Insecta: Hymenoptera: Apocrita). Additionally, we predict secondary structures for the mature rRNA molecules based on comparative sequence analyses with other arthropod taxa and reference to recently published crystal structures of the ribosome. In general, the structures of honey bee rRNAs are in agreement with previously predicted rRNA models from other arthropods in core regions of the rRNA, with little additional expansion in non-conserved regions. Our multiple sequence alignments are made available on several public databases and provide a preliminary establishment of a global structural model of all rRNAs from the insects. Additionally, we provide conserved stretches of sequences flanking the rDNA cistrons that comprise the externally transcribed spacer regions (ETS) and part of the intergenic spacer region (IGS), including several repetitive motifs. Finally, we report the occurrence of retrotransposition in the nuclear large subunit rDNA, as R2 elements are present in the usual insertion points found in other arthropods. Interestingly, functional R1 elements usually present in the genomes of insects were not detected in the honey bee rRNA genes. The reverse transcriptase products of the R2 elements are deduced from their putative open reading frames and structurally aligned with those from another hymenopteran insect, the jewel wasp Nasonia (Pteromalidae). Stretches of conserved amino acids shared between Apis and Nasonia are illustrated and serve as potential sites for primer design, as target amplicons within these R2 elements may serve as novel phylogenetic markers for Hymenoptera. Given the impending completion of the sequencing of the Nasonia genome, we expect our report eventually to shed light on the evolution of the hymenopteran genome within higher insects, particularly regarding the relative maintenance of conserved rDNA genes, related variable spacer regions and retrotransposable elements.

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Section: Igsmentioning

confidence: 99%

mentioning

confidence: 99%

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

Gillespie¹,

Johnston²,

Cannone³

et al. 2006

Insect Molecular Biology

266

287

View full text Add to dashboard Cite

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“…To date, there are no published DNA sequences of aphidiines, although RFLPs (Gargiulo et al, 1988) and RAPDs (Roehrdanz et al, 1993) have been used to provide markers for distinguishing species and populations, and some of the retroelements responsible for the RFLPs have been characterized (Varricchio et al, 1995). Indeed, the only molecular systematic studies involving braconids are ones using 16S rRNA to examine superfamily relationships within the order Hymenoptera (Derr et al, 1992a,b;Dowton and Austin, 1994).…”

Section: Introductionmentioning

confidence: 97%

A Molecular Phylogeny of the Aphidiinae (Hymenoptera: Braconidae)

Belshaw

Quicke

1997

Molecular Phylogenetics and Evolution

217

155

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“…Most R1 elements from diverse taxonomic species create TSDs of 14 bp as a result of a 14 bp stagger in the cleavage of the target site (Xiong et al. , 1988; Varricchio et al. , 1995; Feng et al.…”

Section: Discussionmentioning

confidence: 99%

“…Based on this R2 mechanism a number of suggestions can be made concerning the cleavage of the target site and its use in priming the integration of R1 elements. Most R1 elements from diverse taxonomic species create TSDs of 14 bp as a result of a 14 bp stagger in the cleavage of the target site (Xiong et al, 1988;Varricchio et al, 1995;Feng et al, 1998;Maita et al, 2007;Stage & Eickbush, 2009). In Nasonia, R1A, R1B and R1C have TSDs that are also 14 bp length.…”

Section: Mechanisms Of R1 Retrotranspositionmentioning

confidence: 99%

Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia

Stage

Eickbush

2010

Insect Molecular Biology

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Abstracti mb_949 37..48Sequencing reads from the Nasonia genome project were used to study the ribosomal RNA gene loci and the retrotransposons R1 and R2 that insert specifically into the 28S genes. Five highly divergent R1 and five highly divergent R2 families were identified in the three sequenced species, as well as a nonautonomous element that appears to use the retrotransposition machinery of R1. A duplication of the R1 target site within the spacer region of the rDNA units was also found to be extensively utilized by R1 elements. We document numerous instances where the R1 and R2 families appropriated parts of the retrotransposition machinery of other lineages and speculate that this enables rapid adaptation and the maintenance of multiple R1 and R2 families.

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Characterization of Aphidius ervi (hymenoptera, braconidae) ribosomal genes and identification of site-specific insertion elements belonging to the non-LTR retrotransposon family

Cited by 5 publications

References 45 publications

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

Characteristics of the nuclear (18S, 5.8S, 28S and 5S) and mitochondrial (12S and 16S) rRNA genes ofApis mellifera(Insecta: Hymenoptera): structure, organization, and retrotransposable elements

A Molecular Phylogeny of the Aphidiinae (Hymenoptera: Braconidae)

Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia

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