Characterisation of the complete mitochondrial genome and 13 microsatellite loci through next-generation sequencing for the New Caledonian spider-ant Leptomyrmex pallens

• Published in: Molecular biology reports Vol. 41; no. 3; pp. 1179 - 1187
• Main Authors: Berman, Maïa, Austin, Chris M., Miller, Adam D.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-03-2014; Springer Nature B.V; Springer Verlag
• Subjects: Animal Anatomy; Animal Biochemistry; Animals; Biodiversity; Biodiversity and Ecology; Biomedical and Life Sciences; Botanics; Ecology, environment; Ecosystems; Entomology; Environmental Sciences; Formicidae; Gene loci; Genome, Mitochondrial - genetics; Genomics; High-Throughput Nucleotide Sequencing; Histology; Hymenoptera - genetics; Insects; Life Sciences; Microsatellite Repeats - genetics; Mitochondrial DNA; Morphology; Population genetics; Solenopsis; Systematics, Phylogenetics and taxonomy; Vegetal Biology; Mitogenome characterization; Microsatellites; 454-Pyrosequencing; Population genetics; Formicidae species cross amplification
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-013-2657-5

The complete mitochondrial genome and a set of polymorphic microsatellite markers were identified by 454 pyrosequencing (1/16th of a plate) for the New Caledonian rainforest spider-ant
Leptomyrmex pallens
. De novo genome assembly recovered the entire mitochondrial genome with mean coverage of 8.9-fold (range 1–27). The mitogenome consists of 15,591 base pairs including 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a non-coding AT-rich region. The genome arrangement is typical of insect taxa and very similar to the only other published ant mitogenome from the
Solenopsis
genus, with the main differences consisting of translocations and inversions of tRNAs. A total of 13 polymorphic loci were also characterized using 41 individuals from a single population in the Aoupinié region, corresponding to workers from 21 nests and 16 foraging workers. We observed moderate genetic variation across most loci (mean number of alleles per locus = 4.50; mean expected heterozygosity = 0.53) with evidence of only two loci deviating significantly from Hardy–Weinberg equilibrium due to null alleles. Marker independence was confirmed with tests for linkage disequilibrium. Most loci cross amplified for three additional
Leptomyrmex
species. The annotation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the colony structure, population genetic patterns, and dispersal strategy of
L. pallens
in the context of rainforest fragmentation in New Caledonia. Furthermore, this paper confirms a recent line of evidence that comprehensive mitochondrial data can be obtained relatively easily from small next-generation sequencing analyses. Greater synthesis of next-generation sequencing data will play a significant role in expanding the taxonomic representation of mitochondrial genome sequences.