OpenLB
Open Library of Bioscience
Advanced Search
Methods in molecular biology (Clifton, N.J.)
2021;2369 27-40.

Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data.

Nikola Palevich, Paul Haydon Maclean
Author Information
  1. Nikola Palevich: AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand. nik.palevich@agresearch.co.nz.
  2. Paul Haydon Maclean: AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
PMID: 34313982 DOI: 10.1007/978-1-0716-1681-9_3

Abstract

We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing multiple species and subsequent specific assembly of specific mitochondrial genomes.

Keywords

DNA extraction Genomics Helminth Mitochondrial genome Parasite

References

  1. Huyse T, Plaisance L, Webster B et al (2007) The mitochondrial genome of Gyrodactylus salaris (Platyhelminthes: Monogenea), a pathogen of Atlantic salmon (Salmo salar). Parasitology 134:739 [PMID: 17156582]
  2. Plaisance L, Huyse T, Littlewood D et al (2007) The complete mitochondrial DNA sequence of the monogenean Gyrodactylus thymalli (Platyhelminthes: Monogenea), a parasite of grayling (Thymallus thymallus). Mol Biochem Parasitol 154:190–194 [PMID: 17559954]
  3. Jex AR, Waeschenbach A, Littlewood DTJ et al (2008) The mitochondrial genome of Toxocara canis. PLoS Negl Trop Dis 2:e273 [PMID: 18682828]
  4. Liu G-H, Lin R-Q, Li M-W et al (2011) The complete mitochondrial genomes of three cestode species of Taenia infecting animals and humans. Mol Biol Rep 38:2249–2256 [PMID: 20922482]
  5. Jia W-Z, Yan H-B, Guo A-J 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 [PMID: 20649981]
  6. Hajibabaei M, Singer GA, Hebert PD et al (2007) DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends Genet. 23:167–172 [PMID: 17316886]
  7. Avise JC, Arnold J, Ball RM et al (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Evol Syst 18:489–522 [DOI: 10.1146/annurev.es.18.110187.002421]
  8. Jex AR, Hall RS, Littlewood DTJ et al (2009) An integrated pipeline for next-generation sequencing and annotation of mitochondrial genomes. Nucleic Acids Res 38:522–533 [PMID: 19892826]
  9. Jex AR, Hu M, Littlewood DTJ et al (2008) Using 454 technology for long-PCR based sequencing of the complete mitochondrial genome from single Haemonchus contortus (Nematoda). BMC Genomics 9:11 [PMID: 18190685]
  10. Hu M, Jex AR, Campbell BE et al (2007) Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing. Nat Prot 2:2339 [DOI: 10.1038/nprot.2007.358]
  11. Jex AR, Littlewood DT, Gasser RB (2015) Sequencing and annotation of mitochondrial genomes from individual parasitic helminths. In: Parasite genomics protocols. Springer, pp 51–63 [DOI: 10.1007/978-1-4939-1438-8_3]
  12. Yoshimura J, Ichikawa K, Shoura MJ et al (2019) Recompleting the Caenorhabditis elegans genome. Genome Res 29:1009–1022 [PMID: 31123080]
  13. Belser C, Istace B, Denis E et al (2018) Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat Plants 4:879–887 [PMID: 30390080]
  14. Michael TP, Vanburen R (2020) Building near-complete plant genomes. Curr Opin Plant Biol 54:26–33 [PMID: 31981929]
  15. Palevich N, Maclean PH, Baten A et al (2019) The genome sequence of the anthelmintic-susceptible New Zealand Haemonchus contortus. Genome Biol Evol 11:1965–1970 [PMID: 31263885]
  16. Seshadri R, Leahy SC, Attwood GT et al (2018) Cultivation and sequencing of rumen microbiome members from the Hungate1000 collection. Nat Biotechnol 36:359–367 [PMID: 29553575]
  17. Palevich N, Kelly WJ, Leahy SC et al (2019) Comparative genomics of rumen Butyrivibrio spp. uncovers a continuum of polysaccharide-degrading capabilities. Appl Environ Microbiol 86:e01993–e01919 [PMID: 31653790]
  18. Nicholls SM, Quick JC, Tang S et al (2019) Ultra-deep, long-read nanopore sequencing of mock microbial community standards. Gigascience 8:giz043 [PMID: 31089679]
  19. Hu M, Gasser RB (2006) Mitochondrial genomes of parasitic nematodes–progress and perspectives. Trends Parasitol 22:78–84 [PMID: 16377245]
  20. Hu M, Chilton NB, Gasser RB (2004) The mitochondrial genomics of parasitic nematodes of socio-economic importance: recent progress, and implications for population genetics and systematics. Adv Parasitol 56:134–213
  21. Lunt DH, Whipple LE, Hyman BC (1998) Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Mol Ecol 7:1441–1455 [PMID: 9819900]
  22. Wetzel J, Kingsford C, Pop M (2011) Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. BMC Bioinformatics 12:95 [PMID: 21486487]
  23. Sahlin K, Chikhi R, Arvestad L (2016) Assembly scaffolding with PE-contaminated mate-pair libraries. Bioinformatics 32:1925–1932 [PMID: 27153683]
  24. Weirather JL, De Cesare M, Wang Y et al (2017) Comprehensive comparison of Pacific biosciences and Oxford nanopore technologies and their applications to transcriptome analysis. F1000Res 6:100 [PMID: 28868132]
  25. Ekblom R, Wolf JB (2014) A field guide to whole-genome sequencing, assembly and annotation. Evol Appl 7:1026–1042 [PMID: 25553065]
  26. Shi H, Xing Y, Mao X (2017) The little brown bat nuclear genome contains an entire mitochondrial genome: real or artifact? Gene 629:64–67 [PMID: 28754635]
  27. Chatre L, Ricchetti M (2011) Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae. PLoS One 6:e17235 [PMID: 21408151]
  28. Zhou X, Rokas A (2014) Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol 23:1679–1700 [PMID: 24471475]
  29. Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. In: Babraham bioinformatics. Babraham Institute, Cambridge
  30. Cox MP, Peterson DA, Biggs PJ (2010) SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11:485 [PMID: 20875133]
  31. Hansen KD, Brenner SE, Dudoit S (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res 38:e131 [PMID: 20395217]
  32. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 [PMID: 24695404]
  33. Dodt M, Roehr JT, Ahmed R et al (2012) FLEXBAR-flexible barcode and adapter processing for next-generation sequencing platforms. Biology 1:895–905 [PMID: 24832523]
  34. Robin ED, Wong R (1988) Mitochondrial DNA molecules and virtual number of mitochondria per cell in mammalian cells. J Cell Physiol 136:507–513 [PMID: 3170646]
  35. Al-Nakeeb K, Petersen TN, Sicheritz-Pontén T (2017) Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data. BMC Bioinformatics 18:1–7 [DOI: 10.1186/s12859-017-1927-y]
  36. Wang X, Cheng F, Rohlsen D et al (2018) Organellar genome assembly methods and comparative analysis of horticultural plants. Hortic Res 5:1–13 [PMID: 29423231]
  37. Dierckxsens N, Mardulyn P, Smits G (2016) NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res 45:e18 [>PMCID: ]
  38. Machado D, Lyra M, Grant T (2016) Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs. Mol Ecol Resour 16:686–693 [PMID: 26607054]
  39. Sloan DB, Wu Z, Sharbrough J (2018) Correction of persistent errors in Arabidopsis reference mitochondrial genomes. Plant Cell 30:525–527 [PMID: 29519893]
  40. Scheunert A, Dorfner M, Lingl T et al (2020) Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS One 15:e0226234 [PMID: 32208422]
  41. Lischer HE, Shimizu KK (2017) Reference-guided de novo assembly approach improves genome reconstruction for related species. BMC Bioinformatics 18:1–12 [DOI: 10.1186/s12859-017-1911-6]
  42. Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760 [PMID: 2705234]
  43. Bushnell B (2014) BBMap: a fast, accurate, splice-aware aligner. Lawrence Berkeley National Lab (LBNL), Berkeley
  44. Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079 [PMID: 2723002]
  45. Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192 [PMID: 22517427]
  46. Kearse M, Moir R, Wilson A et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649 [PMID: 3371832]
  47. Allen C, Mehler DM (2019) Open science challenges, benefits and tips in early career and beyond. PLoS Biol 17:e3000246 [PMID: 31042704]
  48. Leinonen R, Sugawara H, Shumway M et al (2010) The sequence read archive. Nucleic Acids Res 39:D19–D21 [PMID: 21062823]
  49. Hothorn T, Leisch F (2011) Case studies in reproducibility. Brief Bioinform 12:288–300 [PMID: 21278369]
  50. Dabbish L, Stuart C, Tsay J et al (2012) Social coding in GitHub: transparency and collaboration in an open software repository. In: Proceedings of the ACM 2012 conference on computer supported cooperative work, pp 1277–1286
  51. Palevich N, Maclean P, Baten A et al (2019) The complete mitochondrial genome of the New Zealand parasitic roundworm Haemonchus contortus (Trichostrongyloidea: Haemonchidae) field strain NZ_Hco_NP. Mitochondrial DNA B 4:2208–2210 [DOI: 10.1080/23802359.2019.1624634]
  52. Palevich N, Maclean PH, Mitreva M et al (2019) The complete mitochondrial genome of the New Zealand parasitic roundworm Teladorsagia circumcincta (Trichostrongyloidea: Haemonchidae) field strain NZ_Teci_NP. Mitochondrial DNA B 4:2869–2871 [DOI: 10.1080/23802359.2019.1660241]
  53. Palevich N, Maclean PH, Choi Y-J et al (2020) Characterization of the complete mitochondrial genomes of two sibling species of parasitic roundworms, Haemonchus contortus and Teladorsagia circumcincta. Front Genet 11:573395 [PMID: 33133162]
  54. Palevich N, Carvalho L, Maclean PH (2020) Characterization of the complete mitochondrial genome of the New Zealand parasitic blowfly Calliphora vicina (Insecta: Diptera: Calliphoridae). Mitochondrial DNA Part B 6:1270-1272
  55. Palevich N, Carvalho L, Maclean PH (2020) The complete mitochondrial genome of the New Zealand parasitic blowfly Lucilia sericata (Insecta: Diptera: Calliphoridae). Mitochondrial DNA Part B 6:1267–1269
  56. Singh J, Hanson J, Paliwal K et al (2019) RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning. Nat Commun 10:1–13 [DOI: 10.1038/s41467-018-07882-8]
  57. Lorenz R, Bernhart SH, Zu Siederdissen CH et al (2011) ViennaRNA package 20. Algorithms Mol Biol 6:26 [PMID: 22115189]
  58. Darty K, Denise A, Ponty Y (2009) VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics 25:1974 [PMID: 19398448]
  59. Morgulis A, Gertz EM, Schäffer AA et al (2006) A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J Comput Biol 13:1028–1040 [PMID: 16796549]
  60. Benson DA, Cavanaugh M, Clark K et al (2017) GenBank. Nucleic Acids Res 45:D37 [PMID: 27899564]
  61. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning. Cold Spring Harbor Laboratory Press, New York
  62. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359 [PMID: 22388286]

MeSH Term

Animals
Genome, Helminth
Genome, Mitochondrial
Genomics
Helminths
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
Journal Article Research Support, Non-U.S. Gov't
Article has an altmetric score of 3

Word Cloud

Created with Highcharts 10.0.0DNAmitochondrialsequencinggenomesextractiongenomicsilicoapproachdescribedspeciesspecificSequencingHelminthMitochondrialpresentdetailedmethodhigh-molecularweightsuitablenumerousapplicationsstraightforwardreconstructingnovelmtdirectlytotalextractsderivednext-generationNGSdatasetspost-sequencingpipelinefastaccuratehighlyefficientmodestmemoryrequirementscanperformedusingstandarddesktopcomputerparticularlyeffectiveobtaininglittlesequenceinformationcurrentlyavailableovercomesmanylimitationstraditionalstrategiesmethodologiesalsoapplicablemetagenomicsmixedpooledsamplescontainingmultiplesubsequentassemblyReconstructingGenomesDirectlyGenomicNext-GenerationDataGenomicsgenomeParasite

Similar Articles

Cited By