publication . Article . Other literature type . 2019

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale.

Krehenwinkel, Henrik; Pomerantz, Aaron; Henderson, James B; Kennedy, Susan R; Lim, Jun Ying; Swamy, Varun; Shoobridge, Juan Diego; Graham, Natalie; Patel, Nipam H; Gillespie, Rosemary G; ...
Open Access
  • Published: 01 May 2019 Journal: GigaScience, volume 8 (eissn: 2047-217X, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
Abstract Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) a...
Subjects
free text keywords: Research, biodiversity, ribosomal, eukaryotes, long DNA barcodes, Oxford Nanopore Technologies, MinION, metabarcoding
79 references, page 1 of 6

1.Sala OE, Chapin FS, Armesto JJ, et al.Global biodiversity scenarios for the year 2100. Science. 2000;287:1770–4.10710299 [PubMed]

2.Pimm SL, Jenkins CN, Abell R, et al.The biodiversity of species and their rates of extinction, distribution, and protection. Science. 2014;344:1246752.24876501 [OpenAIRE] [PubMed]

3.Rominger A, Goodman K, Lim J, et al.Community assembly on isolated islands: macroecology meets evolution. Global Ecol Biogeogr. 2016;25:769–80.

4.Hebert PD, Ratnasingham S, de Waard JR Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci. 2003;270:S96–9.12952648 [OpenAIRE] [PubMed]

5.Schoch CL, Seifert KA, Huhndorf S, et al.Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci. 2012;109:6241–6.22454494 [OpenAIRE] [PubMed]

6.Li D-Z, Gao L-M China Plant BOL Group; et al.; China Plant BOL Group Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci. 2011;108:19641–6.22100737 [OpenAIRE] [PubMed]

7.Shokralla S, Porter TM, Gibson JF, et al.Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep. 2015;5:9687.25884109 [OpenAIRE] [PubMed]

8.Yu DW, Ji Y, Emerson BC, et al.Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol. 2012;3:613–23.

9.Graham CH, Fine PV Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett. 2008;11:1265–77.19046358 [PubMed]

10.Krehenwinkel H, Graze M, Rödder D, et al.A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna. J Biogeogr. 2016;43:1583–94. [OpenAIRE]

11.Hurst GD, Jiggins FM Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proc Biol Sci. 2005;272:1525–34.16048766 [OpenAIRE] [PubMed]

12.Bernatchez L, Glémet H, Wilson CC, et al.Introgression and fixation of Arctic char (Salvelinus alpinus) mitochondrial genome in an allopatric population of brook trout (Salvelinus fontinalis). Can J Fish AquatSci. 1995;52:179–85. [OpenAIRE]

13.Melo‐Ferreira J, Boursot P, Suchentrunk F, et al.Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Mol Ecol. 2005;14:2459–64.15969727 [OpenAIRE] [PubMed]

14.Soltis PS, Soltis DE Molecular evolution of 18S rDNA in angiosperms: implications for character weighting in phylogenetic analysis. In: Molecular systematics of plants II. Springer; 1998 pp. 188–210.

15.Hillis DM, Dixon MT Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991;66:411–53.1784710 [OpenAIRE] [PubMed]

79 references, page 1 of 6
Abstract
Abstract Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) a...
Subjects
free text keywords: Research, biodiversity, ribosomal, eukaryotes, long DNA barcodes, Oxford Nanopore Technologies, MinION, metabarcoding
79 references, page 1 of 6

1.Sala OE, Chapin FS, Armesto JJ, et al.Global biodiversity scenarios for the year 2100. Science. 2000;287:1770–4.10710299 [PubMed]

2.Pimm SL, Jenkins CN, Abell R, et al.The biodiversity of species and their rates of extinction, distribution, and protection. Science. 2014;344:1246752.24876501 [OpenAIRE] [PubMed]

3.Rominger A, Goodman K, Lim J, et al.Community assembly on isolated islands: macroecology meets evolution. Global Ecol Biogeogr. 2016;25:769–80.

4.Hebert PD, Ratnasingham S, de Waard JR Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Biol Sci. 2003;270:S96–9.12952648 [OpenAIRE] [PubMed]

5.Schoch CL, Seifert KA, Huhndorf S, et al.Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci. 2012;109:6241–6.22454494 [OpenAIRE] [PubMed]

6.Li D-Z, Gao L-M China Plant BOL Group; et al.; China Plant BOL Group Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc Natl Acad Sci. 2011;108:19641–6.22100737 [OpenAIRE] [PubMed]

7.Shokralla S, Porter TM, Gibson JF, et al.Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform. Sci Rep. 2015;5:9687.25884109 [OpenAIRE] [PubMed]

8.Yu DW, Ji Y, Emerson BC, et al.Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods Ecol Evol. 2012;3:613–23.

9.Graham CH, Fine PV Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time. Ecol Lett. 2008;11:1265–77.19046358 [PubMed]

10.Krehenwinkel H, Graze M, Rödder D, et al.A phylogeographical survey of a highly dispersive spider reveals eastern Asia as a major glacial refugium for Palaearctic fauna. J Biogeogr. 2016;43:1583–94. [OpenAIRE]

11.Hurst GD, Jiggins FM Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proc Biol Sci. 2005;272:1525–34.16048766 [OpenAIRE] [PubMed]

12.Bernatchez L, Glémet H, Wilson CC, et al.Introgression and fixation of Arctic char (Salvelinus alpinus) mitochondrial genome in an allopatric population of brook trout (Salvelinus fontinalis). Can J Fish AquatSci. 1995;52:179–85. [OpenAIRE]

13.Melo‐Ferreira J, Boursot P, Suchentrunk F, et al.Invasion from the cold past: extensive introgression of mountain hare (Lepus timidus) mitochondrial DNA into three other hare species in northern Iberia. Mol Ecol. 2005;14:2459–64.15969727 [OpenAIRE] [PubMed]

14.Soltis PS, Soltis DE Molecular evolution of 18S rDNA in angiosperms: implications for character weighting in phylogenetic analysis. In: Molecular systematics of plants II. Springer; 1998 pp. 188–210.

15.Hillis DM, Dixon MT Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol. 1991;66:411–53.1784710 [OpenAIRE] [PubMed]

79 references, page 1 of 6
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