Book contents
- Frontmatter
- Contents
- List of contributors
- Introduction: studying diversity in an era of ubiquitous genomics
- Part I Next Generation Phylogenetics
- 1 Perspective: Challenges in assembling the ‘next generation’ Tree of Life
- 2 The role of next generation sequencing technologies in shaping the future of insect molecular systematics
- 3 Phylogenomics of Nematoda
- 4 High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
- 5 Investigating bacterial microevolution through next generation sequencing
- Part II Next Generation Biodiversity Science
- Part III Next Generation Challenges and Questions
- Index
- Systematics Association Special Volumes
- Plate section
- References
4 - High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
from Part I - Next Generation Phylogenetics
Published online by Cambridge University Press: 05 June 2016
Book contents
- Frontmatter
- Contents
- List of contributors
- Introduction: studying diversity in an era of ubiquitous genomics
- Part I Next Generation Phylogenetics
- 1 Perspective: Challenges in assembling the ‘next generation’ Tree of Life
- 2 The role of next generation sequencing technologies in shaping the future of insect molecular systematics
- 3 Phylogenomics of Nematoda
- 4 High-throughput multiplexed mitogenomics for Metazoa: prospects and limitations
- 5 Investigating bacterial microevolution through next generation sequencing
- Part II Next Generation Biodiversity Science
- Part III Next Generation Challenges and Questions
- Index
- Systematics Association Special Volumes
- Plate section
- References
Summary
Introduction
Mitochondrial gene markers have been used in molecular systematics for well over 25 years and they have an established role in resolving phylogenetic and ecological patterns in a multitude of phyla and across a range of taxonomic levels (Randi 2000; Avise 2004). However, there are some problems and limitations in their use; in-depth studies over the last three decades have shown that mitochondrial DNA (mtDNA) is not always inherited clonally through the maternal line, nor is it evolving neutrally (Ballard and Whitlock 2004; Galtier et al. 2009). Also, PCR-based approaches can inadvertently amplify nuclear copies of mitochondrial genes (NUMTs) thus introducing non-homologous signal to datasets (Bensasson et al. 2001). However, for the molecular taxonomist and systematist ‘mtDNA is the most convenient and cheapest solution when a new species has to be genetically explored in the wild’ (Galtier et al. 2009, p. 4541).
Meanwhile, the use of entire mitochondrial genomes (mitogenomes) in systematics has had a varied history since they became available as a tractable source of phylogenetic data. Often met with either enthusiasm or hostility it is clear that their reliability as accurate estimators of species trees has been dependent upon our knowledge of the mitogenomes themselves and how to model the evolutionary signal contained within while accounting for lineage-specific differences in rate heterogeneity and nucleotide composition. Only through denser taxonomic sampling across the Metazoa have mitogenomes become better understood, easier to characterize, and more attractive as a source of homologous markers across multiple levels of organization; from nucleotides to amino acids, from gene content to genetic code and gene order. In order to expand on the known mitogenomes, NGS techniques offer a diversity of methods for fast characterization of novel mitogenomes but, depending on the starting material and the NGS platform, there remain barriers as to which techniques might be most cost-effective and reliable. Here we review recent published studies, report on unpublished work of our own, provide empirical evidence from simulations and cast a critical eye over the prospects and limitations we currently see for reliable use of NGS and high-throughput mitogenome sequencing in the context of systematics and biodiversity studies.
- Type
- Chapter
- Information
- Next Generation Systematics , pp. 84 - 100Publisher: Cambridge University PressPrint publication year: 2016
References
, and (2007). MtArt, a new model of amino acid replacement for Arthropoda. Molecular Biology and Evolution, 24, 1–5.Google ScholarPubMed
and (2003). Evolution of mitochondrial gene content, gene loss and transfer to the nucleus. Molecular Phylogenetics and Evolution, 29, 380–95.CrossRefGoogle ScholarPubMed
, , , et al. (2002). Mammalian mitogenomic relationships and the root of the eutherian tree. Proceedings of the National Academy of Sciences of the United States of America, 99, 8151–6.CrossRefGoogle ScholarPubMed
(2004). Molecular Markers, Natural History, and Evolution, edn. Sunderland, MA, Sinauer Associates.Google Scholar
and (2004). The incomplete natural history of mitochondria. Molecular Ecology, 13, 729–44.CrossRefGoogle ScholarPubMed
, , , and (2010). Characteristics of 454 pyrosequencing data: enabling realistic simulation with flowsim. Bioinformatics, 26, i420–5.CrossRefGoogle ScholarPubMed
, , and (2001). Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends in Ecology and Evolution, 16, 314–21.CrossRefGoogle ScholarPubMed
, , and (2013). Genetic aspects of mitochondrial genome evolution. Molecular Phylogenetics and Evolution, 69, 328–38.CrossRefGoogle ScholarPubMed
, , , et al. (2012). MITOS, Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69, 313–9.Google ScholarPubMed
, , , et al. (2007). CREx, inferring genomic rearrangements based on common intervals. Bioinformatics, 23, 2957–8.CrossRefGoogle ScholarPubMed
, and (1999). Gene order breakpoint evidence in animal mitochondrial phylogeny. Journal of Molecular Evoution, 49, 193–203.Google ScholarPubMed
(2006). The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology and Evolution, 21, 439–46.CrossRefGoogle ScholarPubMed
and (1998). Big trees from little genomes, mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development, 8, 668–74.CrossRefGoogle ScholarPubMed
, and (2010). Characterization of a mitochondrial ORF from the gender-associated mtDNAs of Mytilus spp. (Bivalvia, Mytilidae), identification of the missing ATPase 8 gene. Marine Genomics, 3, 11–18.CrossRefGoogle Scholar
, , , et al. (2009). Targeted retrieval and analysis of five neandertal mtDNA genomes. Science, 325, 318–21.CrossRefGoogle ScholarPubMed
, , , et al. (2009). BLAST+, architecture and applications. BMC Bioinformatics, 10, 421.CrossRefGoogle ScholarPubMed
, , , and (2011). Mitochondrial genome deletions and mini-circles are common in lice (Insecta, Phthiraptera). BMC Genomics, 12, 394.CrossRefGoogle Scholar
, and (1999). Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology, Proceedings of the German Conference on Bioinformatics (GCB), 99, 45–56.Google Scholar
and (2013). The seven deadly sins of DNA barcoding. Molecular Ecology Resources, 13, 969–75.Google ScholarPubMed
, , , et al. (2008). Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology. Nucleic Acids Research, 36, e122.CrossRefGoogle ScholarPubMed
, , , et al. (2012). MitoZoa 2.0, a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. Nucleic Acids Research, 40, D1168–D1172.Google Scholar
, , and (2013). Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices. PLoS One, 8, e55816.CrossRefGoogle ScholarPubMed
, and (1997). Nucleotide composition bias affects amino acid content in proteins coded by animal mitochondria. Journal of Molecular Evolution, 44, 282–8.CrossRefGoogle ScholarPubMed
, , and (2009). Mitochondrial DNA as a marker of molecular diversity, a reappraisal. Molecular Ecology, 18, 4541–50.CrossRefGoogle ScholarPubMed
, , and (2012). The complete mitogenome of Cylindrus obtusus (Helicidae, Ariantinae) using Illumina next generation sequencing. BMC Genomics, 13, 114.CrossRefGoogle ScholarPubMed
, , , et al. (2013). Targeted multiplex next-generation sequencing: advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics. Molecular Ecology Resources, 13, 254–68.CrossRefGoogle ScholarPubMed
, and (2013). Mitogenome sequences stabilize the phylogenetics of weevils (Curculionoidea) and establish the monophyly of larval ectophagy. Molecular Phylogenetics and Evolution, 67, 156–66.CrossRefGoogle ScholarPubMed
, , and (2007). Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing. Nature Protocols, 2, 2339–44.CrossRefGoogle ScholarPubMed
and (1999). CAP3, A DNA sequence assembly program. Genome Research, 9, 868–77.CrossRefGoogle ScholarPubMed
, , , et al. (2013). MitoFish and MitoAnnotator, a mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Molecular Biology and Evolution, 30, 2531–40.CrossRefGoogle ScholarPubMed
, , and (2010a). An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Research, 38, 522–33.CrossRefGoogle ScholarPubMed
, , , and (2008). Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics, 9, 11.CrossRefGoogle Scholar
, and (2010b). Toward next-generation sequencing of mitochondrial genomes: focus on parasitic worms of animals and biotechnological implications. Biotechnology Advances, 28, 151–9.Google ScholarPubMed
, , , et al. (2010). Complete mitochondrial genomes of Taenia multiceps, T. hydatigena and T. pisiformis, additional molecular markers for a tapeworm genus of human and animal health significance. BMC Genomics, 11, 447.CrossRefGoogle Scholar
, , , et al. (2012). Mitochondrial genes and genomes support a cryptic species of tapeworm within Taenia taeniaeformis. Acta Tropica, 123, 154–63.CrossRefGoogle ScholarPubMed
, and (2012). Multiple rearrangements in mitochondrial genomes of Isopoda and phylogenetic implications. Molecular Phylogenetics and Evolution, 64, 106–17.CrossRefGoogle ScholarPubMed
and (2005). Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. Systematic Biology, 54, 651–9.CrossRefGoogle ScholarPubMed
, , , et al. (2000). Phylogenies inferred from mitochondrial gene orders: a cautionary tale from the parasitic flatworms. Molecular Biology and Evolution, 17, 1123–5.CrossRefGoogle ScholarPubMed
, , and (2012). Next generation sequencing and comparative analyses of Xenopus mitogenomes. BMC Genomics, 13, 496.CrossRefGoogle ScholarPubMed
, , , et al. (2010). MitoZoa, a curated mitochondrial genome database of metazoans for comparative genomics studies. Mitochondrion, 10, 192–9.CrossRefGoogle ScholarPubMed
, , , et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–80.CrossRefGoogle ScholarPubMed
, and (2010). Multiplexed DNA sequence capture of mitochondrial genomes using PCR products. PLoS One, 5, e14004.CrossRefGoogle ScholarPubMed
and (2005). DNA barcoding, error rates based on comprehensive sampling. PLoS Biol, 3, e422.CrossRefGoogle ScholarPubMed
, , , et al. (2007). Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research, 35, e97.CrossRefGoogle ScholarPubMed
, , , et al. (2009). Application of full mitochondrial genome sequencing using 454 GS FLX pyrosequencing. Forensic Science International Genetics Supplement Series, 2, 518–19.CrossRefGoogle Scholar
and (1999). Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile (Teleostei, Stomiiformes): first example of transfer RNA gene rearrangements in bony fishes. Marine Biotechnology, 1, 41626.CrossRefGoogle ScholarPubMed
, , , et al. (2003). Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 26, 121–38.CrossRefGoogle ScholarPubMed
and (2013). Sequence assembly demystified. Nature Reviews Genetics, 14, 157–67.CrossRefGoogle ScholarPubMed
, , , et al. (2011). Evolution of modern birds revealed by mitogenomics, timing the radiation and origin of major orders. Molecular Biology and Evolution, 28, 1927–42.CrossRefGoogle ScholarPubMed
, , and (2013). The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny. Molecular Phylogenetics and Evolution, 66, 898–905.CrossRefGoogle ScholarPubMed
and (2011). Difficult phylogenetic questions, more data, maybe; better methods, certainly. BMC Biology, 9, 91.CrossRefGoogle ScholarPubMed
, , and (2012). |SE|S|AM|E| Barcode, NGS-oriented software for amplicon characterization: application to species and environmental barcoding. Molecular Ecology Resources, 12, 1151–7.CrossRefGoogle ScholarPubMed
, , , and (2009). Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea. BMC Genomics, 10, 364.CrossRefGoogle ScholarPubMed
, , and (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics, 12, 38.CrossRefGoogle ScholarPubMed
(2000). Mitochondrial DNA. In Molecular Methods in Ecology, ed. . London, Blackwell Science; pp. 136–67.Google Scholar
, and (2009). MtZoa, a general mitochondrial amino acid substitutions model for animal evolutionary studies. Molecular Phylogenetics and Evolution, 52, 268–72.CrossRefGoogle ScholarPubMed
, and (2006). A genomic perspective on the shortcomings of mitochondrial DNA for “barcoding” identification. Journal of Heredity, 97, 581–94.CrossRefGoogle ScholarPubMed
, , , et al. (2013). Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes. Genome Biology and Evolution, 5, 1185–99.CrossRefGoogle ScholarPubMed
, , and (2006). Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): a linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene, 381, 92–101.CrossRefGoogle ScholarPubMed
, and (2013). Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships. Molecular Phylogenetics and Evolution, 66, 776–89.CrossRefGoogle ScholarPubMed
, , , et al. (2012). First complete mitochondrial genome sequence from a box jellyfish reveals a highly fragmented linear architecture and insights into telomere evolution. Genome Biology and Evolution, 4, 52–8.CrossRefGoogle ScholarPubMed
and (2012). Mitogenomics does not resolve deep molluscan relationships (yet?). Molecular Phylogenetics and Evolution, 69, 376–92.Google Scholar
, , , and (2008). Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.Molecular Biology and Evolution, 25, 1129–1137.CrossRefGoogle ScholarPubMed
, , and (2000). Changes in mitochondrial genetic codes as phylogenetic characters, two examples from the flatworms. Proceedings of the National Academy of Sciences of the United States of America, 97, 11359–64.CrossRefGoogle ScholarPubMed
, , , et al. (2010). Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Research, 38, e197–e197.CrossRefGoogle ScholarPubMed
, and (2012). Molecular variability in the Celleporella hyalina (Bryozoa; Cheilostomata) species complex: evidence for cryptic speciation from complete mitochondrial genomes. Molecular Biology Reports, 39, 8601–14.CrossRefGoogle ScholarPubMed
, , and (1999). Mitochondrial genes are found on minicircle DNA molecules in the mesozoan animal Dicyema. Journal of Molecular Biology, 286, 645–50.CrossRefGoogle ScholarPubMed
and (2012). Mitochondrial gene order change in Schistosoma (Platyhelminthes, Digenea, Schistosomatidae). International Journal of Parasitology, 42, 313–21.CrossRefGoogle Scholar
, , and (2012). Platyzoan mitochondrial genomes. Molecular Phylogenetics and Evolution, 69, 365–75.Google ScholarPubMed
, and (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252–5.CrossRefGoogle ScholarPubMed
, , , and (2011). Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm. PLoS One, 6, e17729.CrossRefGoogle ScholarPubMed
, and (1998). Models of amino acid substitution and applications to mitochondrial protein evolution. Molecular Biology and Evolution, 15, 1600–11.CrossRefGoogle ScholarPubMed
, and (2012). Comprehensive one-step molecular analyses of mitochondrial genome by massively parallel sequencing. Clinical Chemistry, 58, 1322–31.CrossRefGoogle ScholarPubMed