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

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Abstract

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.

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Acknowledgments

This work has been partly funded by a competitive funding grant from Charles Darwin University to MB as part as her PhD thesis, and by the Agence Nationale de la Recherche BDIV-07-008, project ‘Incendies Nouvelle Calédonie’. We are very grateful to the New Caledonian Gohapin tribe who has allowed us to access and sample on their land, and to Jasmin Packer, Quentin Auriac, Barbara Pianu and Viviane Degret for their help in the field. We thank Alan Andersen for providing the Leptomyrmex nigriventris specimen from the CSIRO-TERC collection.

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Authors and Affiliations

  1. CSIRO Ecosystem Sciences, PMB 44, Winnellie, NT, 0822, Australia

    Maïa Berman

  2. Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT, Australia

    Maïa Berman & Chris M. Austin

  3. Université de Montpellier II, UMR AMAP, Montpellier, France

    Maïa Berman

  4. Monash University Sunway Campus, Jalan Lagoon Selatan, Bandar Sunway, 46150, Petaling Jaya, Selangor, Malaysia

    Chris M. Austin

  5. Department of Zoology, The University of Melbourne, Parkville, VIC, 3010, Australia

    Adam D. Miller

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Berman, M., Austin, C.M. & Miller, A.D. Characterisation of the complete mitochondrial genome and 13 microsatellite loci through next-generation sequencing for the New Caledonian spider-ant Leptomyrmex pallens . Mol Biol Rep 41, 1179–1187 (2014). https://doi.org/10.1007/s11033-013-2657-5

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