High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?

References

• Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, et al. 2016. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res. 44:W3–W10.
   PubMed Web of Science ®Google Scholar
• Beng KC, Tomlison KW, Shen XH, Surget-Groba Y, Hughes AC, Corlett RT, Slik JW. 2016. The utility of DNA metabarcoding for studying the response of arthropod diversity and composition to land-use change in the tropics. Sci Rep. 6:24965.
   PubMed Web of Science ®Google Scholar
• Bjørnsgaard Aas A, Davey ML, Kauserud H. 2016. ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities. Mol Ecol Resour. 17:730–741.
   PubMed Web of Science ®Google Scholar
• Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ. 2015. DNA metabarcoding of insects and allies: an evaluation of primers and pipelines. Bull Entomol Res. 105:717–727.
   PubMed Web of Science ®Google Scholar
• Brandon-Mong GJ, Littlefair JE, Sing KW, Gan HM, Lee YP, Clare EL, Wilson JJ. 2018. Temporal changes in arthropod activity in tropical anthropogenic forests. Bull Entomol Res. [accessed 2018 Feb 14]:[8 p.]. DOI:10.1017/S000748531800010X
   PubMed Web of Science ®Google Scholar
• Clare EL, Chain FJJ, Littlefair JE, Cristescu M. 2016. The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data. Genome. 59:981–990.
   PubMed Web of Science ®Google Scholar
• Clare EL, Kerr KR, von Königslöw TE, Wilson JJ, Hebert PD. 2008. Diagnosing mitochondrial DNA diversity: applications of a sentinel gene approach. J Mol Evol. 66:362–367.
   PubMed Web of Science ®Google Scholar
• Clarke LJ, Soubrier J, Weyrich LS, Cooper A. 2014. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Mol Ecol Resour. 14:1160–1170.
   PubMed Web of Science ®Google Scholar
• Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. 2015. Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Mol Biol Evol. 32:2302–2316.
   PubMed Web of Science ®Google Scholar
• Crampton-Platt A, Yu DW, Zhou X, Vogler AP. 2016. Mitochondrial metagenomics: letting the genes out of the bottle. Gigascience. 5:15.
   PubMed Web of Science ®Google Scholar
• Cristescu ME. 2014. From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity. Trends Ecol Evol. 29:566–571.
   PubMed Web of Science ®Google Scholar
• de Waard JR, Levesque-Beaudin V, de Waard SL, Ivanova NV, McKeown JTA, Miskie R, Naik S, Perez K, Ratnasingham S, Sobel SN, et al. 2017. Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding. bioRxiv. DOI:10.1101/192732
   Google Scholar
• Elbrecht V, Leese F. 2015. Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass-sequence relationships with an innovative metabarcoding protocol. PLoS One. 10:e0130324.
   PubMed Web of Science ®Google Scholar
• Elbrecht V, Peinert B, Leese F. 2017. Sorting things out: assessing effects of unequal specimen biomass on DNA metabarcoding. Ecol Evol. 7:6918–6926.
   PubMed Web of Science ®Google Scholar
• Elbrecht V, Taberlet P, Dejean T, Valentini A, Usseglio-Polatera P, Beisel JN, Coissac E, Boyer F, Leese F. 2016. Testing the potential of a ribosomal 16S marker for DNA metabarcoding of insects. PeerJ. 4:e1966.
   PubMed Web of Science ®Google Scholar
• Flynn JM, Brown EA, Chain FJ, MacIsaac HJ, Cristescu ME. 2015. Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol Evol. 5:2252–2266.
   PubMed Web of Science ®Google Scholar
• Gan HM, Schultz MB, Austin CM. 2014. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol. 14:19.
   PubMed Web of Science ®Google Scholar
• Gibson J, Shokralla S, Porter TM, King I, van Konynenburg S, Janzen DH, Hallwachs W, Hajibabaei M. 2014. Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics. Proc Natl Acad Sci USA. 111:8007–8012.
   PubMed Web of Science ®Google Scholar
• Hebert PDN, Braukmann TWA, Prosser SWJ, Ratnasingham S, deWaard JR, Ivanova NV, Janzen DH, Hallwachs W, Naik S, Sones JE, et al. 2017. A sequel to Sanger: amplicon sequencing that scales. bioRxiv. DOI:10.1101/191619
   Google Scholar
• Hebert PDN, Ratnasingham S, de Waard JR. 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B Biol Sci. 270(Suppl. 1):S96–S99.
   PubMed Web of Science ®Google Scholar
• Ji Y, Ashton L, Pedley SM, Edwards DP, Tang Y, Nakamura A, Kitching R, Dolman PM, Woodcock P, Edwards FA, et al. 2013. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett. 16:1245–1257.
   PubMed Web of Science ®Google Scholar
• Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25.
   PubMed Web of Science ®Google Scholar
• Lee PS, Sing KW, Wilson JJ. 2015. Reading mammal diversity from flies: the persistence period of amplifiable mammal mtDNA in blowfly guts (Chrysomya megacephala) and a newDNA mini-barcode target. PLoS One. 10:e0123871.
   PubMed Web of Science ®Google Scholar
• Lim VC, Ramli R, Bhassu S, Wilson JJ. 2018. Pollination implications of the diverse diet of nectar-feeding bats inhabiting an urban cave. PeerJ Preprints. 6:e26470v1. DOI:10.7287/peerj.preprints.26470v1
   Web of Science ®Google Scholar
• Liu S, Wang X, Xie L, Tan M, Li Z, Su X, Zhang H, Misof B, Kjer KM, Tang M, et al. 2016. Mitochondrial capture enriches mito–DNA 100 fold, enabling PCR–free mitogenomics biodiversity analysis. Mol Ecol Resour. 16:470–479.
   PubMed Web of Science ®Google Scholar
• McGrath KC, Thomas-Hall SR, Cheng CT, Leo L, Alexa A, Schmidt S, Schenk PM. 2008. Isolation and analysis of mRNA from environmental microbial communities. J Microbiol Methods. 75:172–176.
   PubMed Web of Science ®Google Scholar
• Palumbi SR. 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis DM, Moritz C, Mable BK, editors. Molecular systematics. Massachusetts: Sinauer & Associates Inc.; p. 205–247.
   Google Scholar
• Piñol J, Mir G, Gomez-Polo P, Agustí N. 2015. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour. 15:819–830.
   PubMed Web of Science ®Google Scholar
• Ratnasingham S, Hebert PDN. 2013. BOLD: the barcode of life data system (http://www.barcodinglife.org)). Mol Ecol Notes. 7:355–364.
   Google Scholar
• Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 4:e2584.
   PubMed Web of Science ®Google Scholar
• Schmieder R, Edwards RA. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 27:863–864.
   PubMed Web of Science ®Google Scholar
• Tang M, Hardman CJ, Ji Y, Meng G, Liu S, Tan M, Yang S, Moss ED, Wang J, Yang C, et al. 2015. High-throughput monitoring of wild bee diversity and abundance via mitogenomics. Methods Ecol Evol. 6:1034–1043.
   PubMed Web of Science ®Google Scholar
• Tang M, Tan M, Meng G, Yang S, Su X, Liu S, Song W, Li Y, Wu Q, Zhang A, et al. 2014. Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res. 42:e166.
   PubMed Web of Science ®Google Scholar
• Triplehorn CA, Johnson NF. 2005. Borror and DeLong’s introduction to the study of insects. 7th ed. California: Thomson Brooks/Cole.
   Google Scholar
• Wilson JJ, Sing KW, Floyd RM, Hebert PDN. 2017. DNA barcodes and insect biodiversity. In: Foottit RG, Adler PH, editors. Insect biodiversity: science and society. 2nd ed. Oxford: Blackwell Publishing Ltd.; p. 575–592.
   Google Scholar
• Wilson JJ, Sing KW, Lee PS, Wee AKS. 2016. Application of DNA barcodes in wildlife conservation in Tropical East Asia. Conserv Biol. 30:982–989.
   PubMed Web of Science ®Google Scholar
• Wilson JJ. 2012. DNA barcodes for insects. In: Kress WJ, Erikson DL, editors. DNA barcodes: methods and protocols. New York: Humana Press; p. 17–45.
   Google Scholar
• Wong MM, Lim CL, Wilson JJ. 2015. DNA barcoding implicates 23 species and four orders as potential pollinators of Chinese knotweed (Persicaria chinensis) in Peninsular Malaysia. Bull Entomol Res. 105:515–520.
   PubMed Web of Science ®Google Scholar
• Yu DW, Ji Y, Emerson BC, Wang XY, Ye CX, Wang CY, Ding ZL. 2012. Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol. 3:613–623.
   Web of Science ®Google Scholar
• Zhou X, Li Y, Liu S, Yang Q, Su X, Zhou L, Tang M, Fu R, Li J, Huang Q. 2013. Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience. 2:4.
   PubMed Web of Science ®Google Scholar