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

Abstract

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.

Bees diversified in the age of eudicots

“…All genes were separately aligned in the Lasergene DNAStar software package using CLUSTALW. Alignments for 28S and 18S were subsequently adjusted by referring to the secondary structure of these genes proposed for Apis mellifera [59], and those regions that could not be aligned with confidence were excluded from the analysis. Intron regions of opsin and EF1a also could not be aligned unambiguously and were therefore excluded from the phylogenetic analysis.…”

Complete mitochondrial genome sequence of Cheirotonus jansoni (Coleoptera: Scarabaeidae)

“…Protein-coding genes and ribosomal RNA genes were identified by comparing their similarity to published insect mitochondrial sequences using ClustalX 1.8 (Thompson et al, 1997) and MEGA 5.0 (Tamura et al, 2011) softwares. Both the rrnL-and rrnS-predicted secondary structures were drawn according to models proposed for these genes in other insects (Gillespie et al, 2006;Cameron and Whiting, 2008;Chai and Du, 2012). The tRNA genes were identified using tRNAscan-SE Search Server v.1.21 (Lowe and Eddy, 1997).…”

Tubulanus tamias sp. nov. (Nemertea: Palaeonemertea) with Two Different Types of Epidermal Eyes

“…Among the aligned 2252-base sequences, there were 14 variable sites, of which three varied only between the individuals, and 11 varied within and between the individuals. In the holotype, this intra-individual variation was found at positions 705 and 706, and between 1870 and 1878 (the 5′ end of the aligned sequences is site 558 in Table 3), corresponding to the D2 and D7 regions (Gillespie et al, 2006), respectively. In the paratype, intra-individual variation occurred at positions 1851 to 1853 (D7 region).…”

“…PCR amplifications for 16S rRNA, 18S rRNA, H3, and COI genes were performed following the procedure described in Andrade et al (2012). For 28S rRNA gene, about 2500 bp (corresponding roughly to the D1 through D7 regions; Gillespie et al, 2006), was PCR-amplified using the primer pair 28S-01 (Kim et al, 2000) and 28S_3KR (Yamasaki et al, 2013) (Table 1) with a thermal cycler (iCycler, Bio-Rad Laboratories, Tokyo, Japan). PCR cycling conditions were 95°C for 1 min; 35 cycles of 95°C for 30 sec, 50°C for 30 sec, and 72°C for 3 min; and 72°C for 7 min.…”