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Sequencing and Annotation of Mitochondrial Genomes from Individual Parasitic Helminths

  • Aaron R. Jex
  • D. Timothy Littlewood
  • Robin B. GasserEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1201)

Abstract

Mitochondrial (mt) genomics has significant implications in a range of fundamental areas of parasitology, including evolution, systematics, and population genetics as well as explorations of mt biochemistry, physiology, and function. Mt genomes also provide a rich source of markers to aid molecular epidemiological and ecological studies of key parasites. However, there is still a paucity of information on mt genomes for many metazoan organisms, particularly parasitic helminths, which has often related to challenges linked to sequencing from tiny amounts of material. The advent of next-generation sequencing (NGS) technologies has paved the way for low cost, high-throughput mt genomic research, but there have been obstacles, particularly in relation to post-sequencing assembly and analyses of large datasets. In this chapter, we describe protocols for the efficient amplification and sequencing of mt genomes from small portions of individual helminths, and highlight the utility of NGS platforms to expedite mt genomics. In addition, we recommend approaches for manual or semi-automated bioinformatic annotation and analyses to overcome the bioinformatic “bottleneck” to research in this area. Taken together, these approaches have demonstrated applicability to a range of parasites and provide prospects for using complete mt genomic sequence datasets for large-scale molecular systematic and epidemiological studies. In addition, these methods have broader utility and might be readily adapted to a range of other medium-sized molecular regions (i.e., 10–100 kb), including large genomic operons, and other organellar (e.g., plastid) and viral genomes.

Keywords

Parasitic Helminth Complete Mitochondrial Genome Molecular Size Marker Ethylenediaminetetraacetic Acid Disodium Salt Individual Nematode 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Notes

Acknowledgements

Our research has been supported largely through grants from the Australian Research Council (ARC) and the National Health and Medical Research Council. Other support from the Alexander von Humboldt Foundation, Australian Academy of Science, the Fulbright Commission, Melbourne Water Corporation, the Victorian Life Sciences Computation Initiative (VLSCI), and the IBM Collaboratory is gratefully acknowledged.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Aaron R. Jex
    • 1
  • D. Timothy Littlewood
    • 2
  • Robin B. Gasser
    • 1
    Email author
  1. 1.Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleAustralia
  2. 2.Department of Life SciencesNatural History MuseumLondonUK

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