SoEM: a novel PCR-free biodiversity assessment method based on small-organelles enriched metagenomics |
Jo, Jihoon
(School of Biological Sciences and Technology, College of Natural Sciences, Chonnam National University)
Lee, Hyun-Gwan (Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center) Kim, Kwang Young (Marine Ecosystem Disturbing and Harmful Organisms (MEDHO) Research Center) Park, Chungoo (School of Biological Sciences and Technology, College of Natural Sciences, Chonnam National University) |
1 | Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J. & Glockner, F. O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41(Database issue):D590-D596. |
2 | Roy, K. & Foote, M. 1997. Morphological approaches to measuring biodiversity. Trends Ecol. Evol. 12:277-281. |
3 | Saunders, G. W. & McDevit, D. C. 2012. Methods for DNA barcoding photosynthetic protists emphasizing the macroalgae and diatoms. Methods Mol. Biol. 858:207-222. DOI |
4 | Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., Sahl, J. W., Stres, B., Thallinger, G. G., Van Horn, D. J. & Weber, C. F. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75:7537-7541. DOI |
5 | Schuster, S. C. 2007. Next-generation sequencing transforms today's biology. Nat. Methods 5:16-18. DOI |
6 | Scotland, R. W., Olmstead, R. G. & Bennett, J. R. 2003. Phylogeny reconstruction: the role of morphology. Syst. Biol. 52:539-548. DOI |
7 | Straub, S. C., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C. & Liston, A. 2012. Navigating the tip of the genomic iceberg: next-generation sequencing for plant systematics. Am. J. Bot. 99:349-364. DOI |
8 | Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C. & Willerslev, E. 2012. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21:2045-2050. DOI |
9 | Tang, M., Tan, M., Meng, G., Yang, S., Su, X., Liu, S., Song, W., Li, Y., Wu, Q., Zhang, A. & Zhou, X. 2014. Multiplex sequencing of pooled mitochondrial genomes: a crucial step toward biodiversity analysis using mito-metagenomics. Nucleic Acids Res. 42:e166. DOI |
10 | Walker, B. H. 1992. Biodiversity and ecological redundancy. Conserv. Biol. 6:18-23. DOI |
11 | Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. 2014. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics 30:614-620. DOI |
12 | Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P. & Kauserud, H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol. 10:189. DOI |
13 | Zhou, J., Bruns, M. A. & Tiedje, J. M. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316-322. DOI |
14 | Zhou, X., Adamowicz, S. J., Jacobus, L. M., Dewalt, R. E. & Hebert, P. D. N. 2009. Towards a comprehensive barcode library for arctic life: Ephemeroptera, Plecoptera, and Trichoptera of Churchill, Manitoba, Canada. Front. Zool. 6:30. DOI |
15 | 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. DOI |
16 | Andujar, C., Arribas, P., Ruzicka, F., Crampton-Platt, A., Timmermans, M. J. T. N. & Vogler, A. P. 2015. Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics. Mol. Ecol. 24:3603-3617. DOI |
17 | Andujar, C., Arribas, P., Yu, D. W., Vogler, A. P. & Emerson, B. C. 2018. Why the COI barcode should be the community DNA metabarcode for the metazoa. Mol. Ecol. 27:3968-3975. DOI |
18 | Ansorge, W. J. 2009. Next-generation DNA sequencing techniques. N. Biotechnol. 25:195-203. DOI |
19 | Appeltans, W., Ahyong, S. T., Anderson, G., Angel, M. V., Artois, T., Bailly, N., Bamber, R., Barber, A., Bartsch, I., Berta, A., Blazewicz-Paszkowycz, M., Bock, P., Boxshall, G., Boyko, C. B., Brandāo, S. N., Bray, R. A., Bruce, N. L., Cairns, S. D., Chan, T. -Y., Cheng, L., Collins, A. G., Cribb, T., Curini-Galletti, M., Dahdouh-Guebas, F., Davie, P. J. F., Dawson, M. N., De Clerck, O., Decock, W., De Grave, S., de Voogd, N. J., Domning, D. P., Emig, C. C., Erseus, C., Eschmeyer, W., Fauchald, K., Fautin, D. G., Feist, S. W., Fransen, C. H. J. M., Furuya, H., Garcia-Alvarez, O., Gerken, S., Gibson, D., Gittenberger, A., Gofas, S., Gomez-Daglio, L., Gordon, D. P., Guiry, M. D., Hernandez, F., Hoeksema, B. W., Hopcroft, R. R., Jaume, D., Kirk, P., Koedam, N., Koenemann, S., Kolb, J. B., Kristensen, R. M., Kroh, A., Lambert, G., Lazarus, D. B., Lemaitre, R., Longshaw, M., Lowry, J., Macpherson, E., Madin, L. P., Mah, C., Mapstone, G., McLaughlin, P. A., Mees, J., Meland, K., Messing, C. G., Mills, C. E., Molodtsova, T. N., Mooi, R., Neuhaus, B., Ng, P. K. L., Nielsen, C., Norenburg, J., Opresko, D. M., Osawa, M., Paulay, G., Perrin, W., Pilger, J. F., Poore, G. C. B., Pugh, P., Read, G. B., Reimer, J. D., Rius, M., Rocha, R. M., Saiz-Salinas, J. I., Scarabino, V., Schierwater, B., Schmidt-Rhaesa, A., Schnabel, K. E., Schotte, M., Schuchert, P., Schwabe, E., Segers, H., Self-Sullivan, C., Shenkar, N., Siegel, V., Sterrer, W., Stohr, S., Swalla, B., Tasker, M. L., Thuesen, E. V., Timm, T., Todaro, M. A., Turon, X., Tyler, S., Uetz, P., van der Land, J., Vanhoorne, B., van Ofwegen, L. P., van Soest, R. W. M., Vanaverbeke, J., Walker-Smith, G., Walter, T. C., Warren, A., Williams, G. C., Wilson, S. P. & Costello, M. J. 2012. The magnitude of global marine species diversity. Curr. Biol. 22:2189-2202. DOI |
20 | Bik, H. M., Fournier, D., Sung, W., Bergeron, R. D. & Thomas, W. K. 2013. Intra-genomic variation in the ribosomal repeats of nematodes. PLoS ONE 8:e78230. DOI |
21 | Chamberlain, S. A. & Szocs, E. 2013. taxize: taxonomic search and retrieval in R. F1000Res 2:191. DOI |
22 | Bolger, A. M., Lohse, M. & Usadel, B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-2120. DOI |
23 | Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Pena, A. G., Goodrich, J. K., Gordon, J. I., Huttley, G. A., Kelley, S. T., Knights, D., Koenig, J. E., Ley, R. E., Lozupone, C. A., McDonald, D., Muegge, B. D., Pirrung, M., Reeder, J., Sevinsky, J. R., Turnbaugh, P. J., Walters, W. A., Widmann, J., Yatsunenko, T., Zaneveld, J. & Knight, R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336. DOI |
24 | Cha, R. S. & Thilly, W. G. 1993. Specificity, efficiency, and fidelity of PCR. PCR Methods Appl. 3:S18-S29. DOI |
25 | Crampton-Platt, A., Timmermans, M. J., Gimmel, M. L., Kutty, S. N., Cockerill, T. D., Vun Khen, C. & Vogler, A. P. 2015. Soup to tree: the phylogeny of beetles inferred by mitochondrial metagenomics of a Bornean rainforest sample. Mol. Biol. Evol. 32:2302-2316. DOI |
26 | Crampton-Platt, A., Yu, D. W., Zhou, X. & Vogler, A. P. 2016. Mitochondrial metagenomics: letting the genes out of the bottle. Gigascience 5:15. DOI |
27 | Davenport, C. F. & Tümmler, B. 2013. Advances in computational analysis of metagenome sequences. Environ. Microbiol. 15:1-5. DOI |
28 | Decelle, J., Probert, I., Bittner, L., Desdevises, Y., Colin, S., de Vargas, C., Galí, M., Simo, R. & Not, F. 2012. An original mode of symbiosis in open ocean plankton. Proc. Natl. Acad. Sci. U. S. A. 109:18000-18005. DOI |
29 | Dodsworth, S. 2015. Genome skimming for next-generation biodiversity analysis. Trends Plant Sci. 20:525-527. DOI |
30 | Drummond, A. J., Newcomb, R. D., Buckley, T. R., Xie, D., Dopheide, A., Potter, B. C. M., Heled, J., Ross, H. A., Tooman, L., Grosser, S., Park, D., Demetras, N. J., Stevens, M. I., Russell, J. C., Anderson, S. H., Carter, A. & Nelson, N. 2015. Evaluating a multigene environmental DNA approach for biodiversity assessment. Gigascience 4:46. DOI |
31 | Eberhardt, U. 2012. Methods for DNA barcoding of fungi. Methods Mol. Biol. 858:183-205. DOI |
32 | Edgar, R. C. 2013. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat. Methods 10:996-998. DOI |
33 | 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. DOI |
34 | Federhen, S. 2012. The NCBI Taxonomy database. Nucleic Acids Res. 40(Database issue):D136-D143. DOI |
35 | Fenchel, T. 1988. Marine plankton food chains. Annu. Rev. Ecol. Syst. 19:19-38. DOI |
36 | Fontaneto, D., Kaya, M., Herniou, E. A. & Barraclough, T. G. 2009. Extreme levels of hidden diversity in microscopic animals (Rotifera) revealed by DNA taxonomy. Mol. Phylogenet. Evol. 53:182-189. DOI |
37 | Greshake, B., Zehr, S., Dal Grande, F., Meiser, A., Schmitt, I. & Ebersberger, I. 2016. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens. Mol. Ecol. Resour. 16:511-523. DOI |
38 | Haider, B., Ahn, T. -H., Bushnell, B., Chai, J., Copeland, A. & Pan, C. 2014. Omega: an overlap-graph de novo assembler for metagenomics. Bioinformatics 30:2717-2722. DOI |
39 | Hays, G. C., Richardson, A. J. & Robinson, C. 2005. Climate change and marine plankton. Trends Ecol. Evol. 20:337-344. DOI |
40 | Hajibabaei, M., Shokralla, S., Zhou, X., Singer, G. A. C. & Baird, D. J. 2011. Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6:e17497. DOI |
41 | Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. 2003a. Biological identifications through DNA barcodes. Proc. Biol. Sci. 270:313-321. DOI |
42 | Hebert, P. D. N., Penton, E. H., Burns, J. M., Janzen, D. H. & Hallwachs, W. 2004. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. U. S. A. 101:14812-14817. DOI |
43 | Hebert, P. D. N., Ratnasingham, S. & deWaard, J. R. 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. Biol. Sci. 270(Suppl. 1):S96-S99. |
44 | Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R. & Knights, D. 2018. Evaluating the information content of shallow shotgun metagenomics. mSystems 3:e00069-18. |
45 | Huson, D. H., Mitra, S., Ruscheweyh, H. -J., Weber, N. & Schuster, S. C. 2011. Integrative analysis of environmental sequences using MEGAN4. Genome Res. 21:1552-1560. DOI |
46 | Krehenwinkel, H., Wolf, M., Lim, J. Y., Rominger, A. J., Simison, W. B. & Gillespie, R. G. 2017. Estimating and mitigating amplification bias in qualitative and quantitative arthropod metabarcoding. Sci. Rep. 7:17668. DOI |
47 | Kress, W. J. & Erickson, D. L. 2008. DNA barcodes: genes, genomics, and bioinformatics. Proc. Natl. Acad. Sci. U. S. A. 105:2761-2762. DOI |
48 | Leasi, F. & Todaro, M. A. 2009. Meiofaunal cryptic species revealed by confocal microscopy: the case of Xenotrichula intermedia (Gastrotricha). Mar. Biol. 156:1335-1346. DOI |
49 | Kress, W. J., Garcia-Robledo, C., Uriarte, M. & Erickson, D. L. 2015. DNA barcodes for ecology, evolution, and conservation. Trends Ecol. Evol. 30:25-35. DOI |
50 | Kroger, N. & Poulsen, N. 2008. Diatoms-from cell wall biogenesis to nanotechnology. Annu. Rev. Genet. 42:83-107. DOI |
51 | Lee, H. -G., Kim, H. M., Min, J., Kim, K., Park, M. G., Jeong, H. J. & Kim, K. Y. 2017. An advanced tool, droplet digital PCR (ddPCR), for absolute quantification of the red-tide dinoflagellate, Cochlodinium polykrikoides Margalef (Dinophyceae). Algae 32:189-197. DOI |
52 | Linard, B., Crampton-Platt, A., Gillett, C. P., Timmermans, M. J. & Vogler, A. P. 2015. Metagenome skimming of insect specimen pools: potential for comparative genomics. Genome Biol. Evol. 7:1474-1489. DOI |
53 | Liu, S., Wang, X., Xie, L., Tan, M., Li, Z., Su, X., Zhang, H., Misof, B., Kjer, K. M., Tang, M., Niehuis, O., Jiang, H. & Zhou, X. 2016. Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomics biodiversity analysis. Mol. Ecol. Resour. 16:470-479. DOI |
54 | Losos, J. B. 2010. Adaptive radiation, ecological opportunity, and evolutionary determinism. American Society of Naturalists E. O. Wilson award address. Am. Nat. 175:623-639. DOI |
55 | Pawlowski, J., Audic, S., Adl, S., Bass, D., Belbahri, L., Berney, C., Bowser, S. S., Cepicka, I., Decelle, J., Dunthorn, M., Fiore-Donno, A. M., Gile, G. H., Holzmann, M., Jahn, R., Jirku, M., Keeling, P. J., Kostka, M., Kudryavtsev, A., Lara, E., Lukes, J., Mann, D. G., Mitchell, E. A. D., Nitsche, F., Romeralo, M., Saunders, G. W., Simpson, A. G. B., Smirnov, A. V., Spouge, J. L., Stern, R. F., Stoeck, T., Zim-mermann, J., Schindel, D. & de Vargas, C. 2012. CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10:e1001419. DOI |
56 | Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., Tang, J., Wu, G., Zhang, H., Shi, Y., Liu, Y., Yu, C., Wang, B., Lu, Y., Han, C., Cheung, D. W., Yiu, S. -M., Peng, S., Xiaoqian, Z., Liu, G., Liao, X., Li, Y., Yang, H., Wang, J., Lam, T. -W. & Wang, J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1:18. DOI |
57 | Martin, M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17:10-12. DOI |
58 | Kunin, V., Copeland, A., Lapidus, A., Mavromatis, K. & Hugenholtz, P. 2008. A bioinformatician's guide to metagenomics. Microbiol. Mol. Biol. Rev. 72:557-578. DOI |
59 | McManus, G. B. & Katz, L. A. 2009. Molecular and morphological methods for identifying plankton: what makes a successful marriage? J. Plankton Res. 31:1119-1129. DOI |
60 | Nilakanta, H., Drews, K. L., Firrell, S., Foulkes, M. A. & Jablonski, K. A. 2014. A review of software for analyzing molecular sequences. BMC Res. Notes 7:830. DOI |
61 | Porter, T. M. & Hajibabaei, M. 2018. Scaling up: a guide to high-throughput genomic approaches for biodiversity analysis. Mol. Ecol. 27:313-338. DOI |
62 | Pawluczyk, M., Weiss, J., Links, M. G., Egana Aranguren, M., Wilkinson, M. D. & Egea-Cortines, M. 2015. Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples. Anal. Bioanal. Chem. 407:1841-1848. DOI |
63 | Peng, Y., Leung, H. C., Yiu, S. M. & Chin, F. Y. 2012. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28:1420-1428. DOI |
64 | Porazinska, D. L., Giblin-Davis, R. M., Faller, L., Farmerie, W., Kanzaki, N., Morris, K., Powers, T. O., Tucker, A. E., Sung, W. & Thomas, W. K. 2009. Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity. Mol. Ecol. Resour. 9:1439-1450. DOI |