The Mitochondrial Genome of the Leaf-Cutter Ant Atta laevigata: A Mitogenome with a Large Number of Intergenic Spacers

Abstract

In this paper we describe the nearly complete mitochondrial genome of the leaf-cutter ant Atta laevigata, assembled using transcriptomic libraries from Sanger and Illumina next generation sequencing (NGS), and PCR products. This mitogenome was found to be very large (18,729 bp), given the presence of 30 non-coding intergenic spacers (IGS) spanning 3,808 bp. A portion of the putative control region remained unsequenced. The gene content and organization correspond to that inferred for the ancestral pancrustacea, except for two tRNA gene rearrangements that have been described previously in other ants. The IGS were highly variable in length and dispersed through the mitogenome. This pattern was also found for the other hymenopterans in particular for the monophyletic Apocrita. These spacers with unknown function may be valuable for characterizing genome evolution and distinguishing closely related species and individuals. NGS provided better coverage than Sanger sequencing, especially for tRNA and ribosomal subunit genes, thus facilitating efforts to fill in sequence gaps. The results obtained showed that data from transcriptomic libraries contain valuable information for assembling mitogenomes. The present data also provide a source of molecular markers that will be very important for improving our understanding of genomic evolutionary processes and phylogenetic relationships among hymenopterans.

Two nearly complete mitogenomes of wheat stem borers, Cephus pygmeus (L.) and Cephus sareptanus Dovnar-Zapolskij (Hymenoptera: Cephidae): An unusual elongation of rrnS gene

“…Moreover, most of intergenic nucleotides are reduced to the point of overlap, especially in the highly efficient mitogenomes (Sheffield et al, 2008). Cephus mitogenomes similarly exhibit high coding density (Table 1) and more so than in some other hymenopteran mitogenomes (Cha et al, 2007;Crozier and Crozier, 1993;Rodovalho et al, 2014;Silvestre et al, 2008;Wu et al, 2014). The total length of the intergenic nucleotides ranges from 202 bp (C. cinctus) to 208 bp (C. pygmeus) placed in 18 locations with size of 1-56 bp (Table 1).…”

The complete mitochondrial genomes of two globally invasive ants, the Argentine ant Linepithema humile and the little fire ant Wasmannia auropunctata

“…The mitochondrial genomes were assembled using the Assembly by Reduced Complexity (ARC) pipeline (http://ibest.github.io/ARC/) (Hunter et al 2015), with that of Solenopsis invicta (GenBank: HQ215538) (Gotzek et al 2010) as the reference. The resultant genomes were annotated by using the MITOS Web Server (Bernt et al 2013) and by aligning with other available formicid mitochondrial genomes (Babbucci et al 2014;Berman et al 2014;Gotzek et al 2010;Hasegawa et al 2011;Kim et al 2016;Liu et al 2016;Rodovalho et al 2014;Yang et al 2016). 2).…”

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

“…Our data also corroborates this, as 12 out of 14 Pseudomyrmecinae species presents an AT content value that is equal or superior to 90% in the intergenic region between rrnS and trn-M that contains the D-loop (Table 1). Also, this region has already been proved to be particularly difficult to sequence in hymenopterans (Castro & Dowton, 2005;Dowton et al, 2009;Rodovalho et al, 2014). The difficulties to obtain the complete mitogenomes for ants could be the reason why there are so few mitochondrial genomes available for this group despite the availability of public data.…”