A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

doi:10.1016/j.pld.2018.04.001

Plant Diversity ›› 2018, Vol. 40 ›› Issue (03): 106-116.DOI: 10.1016/j.pld.2018.04.001

A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

Ying Guo^a,b, Guo-Qian Yang^a,b, Yun-Mei Chen^a,b, De-Zhu Li^a, Zhen-Hua Guo^a

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
b University of Chinese Academy of Sciences, Beijing 100049, China

收稿日期:2018-03-09 修回日期:2018-04-17 出版日期:2018-06-25 发布日期:2018-07-13
通讯作者: De-Zhu Li, Zhen-Hua Guo
基金资助:
This work was supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011).

A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

Ying Guo^a,b, Guo-Qian Yang^a,b, Yun-Mei Chen^a,b, De-Zhu Li^a, Zhen-Hua Guo^a

a Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
b University of Chinese Academy of Sciences, Beijing 100049, China

Received:2018-03-09 Revised:2018-04-17 Online:2018-06-25 Published:2018-07-13
Contact: De-Zhu Li, Zhen-Hua Guo
Supported by:
This work was supported by the National Natural Science Foundation of China (Grant No. 31470322 and 31430011).

摘要/Abstract

摘要：

Obtaining high-quality plant materials for experiments is challenging for many research projects. Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on ddRADseq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species (Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the ddRAD-seq technique (MiddRAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA, regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The ddRAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by ddRAD-seq.

关键词: Molecular materials, DNA extraction and preservation, DNA quality, ddRAD-seq, Bamboo, Phylogeny

Abstract:

Key words: Molecular materials, DNA extraction and preservation, DNA quality, ddRAD-seq, Bamboo, Phylogeny

Ying Guo, Guo-Qian Yang, Yun-Mei Chen, De-Zhu Li, Zhen-Hua Guo. A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing[J]. Plant Diversity, 2018, 40(03): 106-116.

参考文献

Akinlabi, E.T., Anane-Fenin, K., Akwada, D.R., 2017. Bamboo taxonomy and distribution across the globe. In:Akinlabi, E.T., Anane-Fenin, K., Akwada, D.R. (Eds.), Bamboo:the Multipurpose Plant. Springer International Publishing, Cham, pp. 1-37.
Andrews, K.R., Good, J.M., Miller, M.R., Luikart, G., Hohenlohe, P.A., 2016. Harnessing the power of RADseq for ecological and evolutionary genomics. Nat. Rev. Genet. 17 (2), 81-92.
Andrews, S., 2014. FastQC:a Quality Control Tool for High Throughput Sequence Data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Baird, N.A., Etter, P.D., Atwood, T.S., Currey, M.C., Shiver, A.L., Lewis, Z.A., Selker, E.U., Cresko, W.A., Johnson, E.A., 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3 (10).
Bamboo Phylogeny Group (BPG), 2012. An updated tribal and subtribal classification of the bamboos (Poaceae:Bambusoideae). J. Am. Bamboo Soc. 24 (1), 1-10.
Cariou, M., Duret, L., Charlat, S., 2013. Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization. Ecol. Evol. 3 (4), 846-852.
Catchen, J., Hohenlohe, P.A., Bassham, S., Amores, A., Cresko, W.A., 2013. Stacks:an analysis tool set for population genomics. Mol. Ecol. 22 (11), 3124-3140.
Catchen, J.M., Amores, A., Hohenlohe, P., Cresko, W., Postlethwait, J.H., 2011. Stacks:building and genotyping loci de novo from short-read sequences. G3 Genes Genomes Genet. 1 (3), 171-182.
Cruaud, A., Gautier, M., Galan, M., Foucaud, J., Sauné, L., Genson, G., Dubois, E., Nidelet, S., Deuve, T., Rasplus, J.-Y., 2014. Empirical assessment of RAD sequencing for interspecific phylogeny. Mol. Biol. Evol. 31 (5), 1272-1274.
Dillon, N., Austin, A.D., Bartowsky, E., 1996. Comparison of preservation techniques for DNA extraction from hymenopterous insects. Insect Mol. Biol. 5 (1), 21-24.
Doyle, J.J., Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11-15.
Doyle, J.J., Dickson, E.E., 1987. Preservation of plant-samples for DNA restriction endonuclease analysis. Taxon 36 (4), 715-722.
Friar, E., Kochert, G., 1994. A study of genetic variation and evolution of Phyllostachys, (Bambusoideae:Poaceae) using nuclear restriction fragment length polymorphisms. Theor. Appl. Genet. 89, 265-270.
Graham, C.F., Glenn, T.C., McArthur, A.G., Boreham, D.R., Kieran, T., Lance, S., Manzon, R.G., Martino, J.A., Pierson, T., Rogers, S.M., 2015. Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq). Mol. Ecol. Res. 15, 1304-1315.
Gray, M.A., Zoe, A.P., Kellogg, C.A., 2013. Comparison of DNA preservation methods for environmental bacterial community samples. FEMS Microbiol. Ecol. 83 (2), 468-477.
Hodkinson, T.R., Renvoize, S.A., Chonghaile, G.N., Stapleton, C.M., Chase, M.W., 2000. A comparison of its nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae). J. Plant Res. 113 (3), 259-269.
Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9 (4), 357.
Ledoux, J.B., Aurelle, D., Feral, J.P., Garrabou, J., 2013. Molecular forensics in the precious Mediterranean red coral, Corallium rubrum:testing DNA extraction and microsatellite genotyping using dried colonies. Conserv. Genet. 5 (2), 327-330.
Li, D.Z., Wang, Z.P., Zhu, Z.D., Xia, N.H., Jia, L.Z., Guo, Z.H., Yang, G.Y., Stapleton, C.M.A., 2006. Flora of China Vol. 22 (Poaceae, Tribe Bambuseae). Science Press, Beijing.
Liang, H., Fu, M., Yang, G., Chen, J., Yang, X., 2016. Effects of different preservation methods on yield and quality of total genomic DNA of Tamarix chinensis. Genom. Appl. Biol. 35 (8), 2168-2172.
Maxine, P.P., Andrea, C.T., 2003. Extensive evaluation of faecal preservation and DNA extraction methods in Australian native and introduced species. Aust. J. Zool. 51(4), 341-355.
Mitchell, K.R., Takacs-Vesbach, C.D., 2008. A comparison of methods for total community DNA preservation and extraction from various thermal environments. J. Ind. Microbiol. Biotechnol. 35 (10), 1139.
Peterson, B.K., Weber, J.N., Kay, E.H., Fisher, H.S., Hoekstra, H.E., 2012. Double digest RADseq:an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7 (5), e37135.
Poland, J.A., Brown, P.J., Sorrells, M.E., Jannink, J.-L., 2012. Development of highdensity genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7 (2), e32253.
Prugh, L.R., Ritland, C.E., Arthur, S.M., Krebs, C.J., 2005. Monitoring coyote population dynamics by genotyping faeces. Mol. Ecol. 14 (5), 1585-1596.
Puritz, J.B., Matz, M.V., Toonen, R.J., Weber, J.N., Bolnick, D.I., Bird, C.E., 2014. Demystifying the RAD fad. Mol. Ecol. 23 (24), 5937-5942.
Qin, H.T., Yang, G.Q., Provan, J., Liu, J., Gao, L.M., 2017. Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species. Plant Divers. 39 (5), 294-299.
Rubin, B.E.R., Ree, R.H., Moreau, C.S., 2012. Inferring phylogenies from RAD sequence data. PLoS One 7 (4), e33394.
Scandura, M., Capitani, C., Iacolina, L., Marco, A., 2006. An empirical approach for reliable microsatellite genotyping of wolf DNA from multiple noninvasive sources. Conserv. Genet. 7 (6), 813-823.
Stamatakis, A., 2014. RAxML version 8:a tool for phylogenetic analysis and postanalysis of large phylogenies. Bioinformatics 30 (9), 1312-1313.
Suzuki, S., 1978. Index to Japanese Bambusaceae.
Takahashi, T., Nagata, N., Sota, T., 2014. Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock. Mol. Phylogenet. Evol. 80, 137-144.
Tin, M.M., Economo, E.P., Mikheyev, A.S., 2014. Sequencing degraded DNA from nondestructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics. PLoS One 9 (5), e96793.
Tin, M.M.Y., Rheindt, F.E., Cros, E., Mikheyev, A.S., 2015. Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype calling accuracy. Mol. Ecol. Res. 15 (2), 329-336.
Triplett, J.K., Clark, L.G., Fisher, A.E., Wen, J., 2014. Independent allopolyploidization events preceded speciation in the temperate and tropical woody bamboos. New Phytol. 204 (1), 66-73.
Wang, X.Q., Ye, X.Y., Zhao, L., Li, D.Z., Guo, Z.H., Zhuang, H.F., 2017. Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae:Bambusoideae). Sci. Rep. 7.
Wang, X.Q., Zhao, L., Eaton, D.A.R., Li, D.Z., Guo, Z.H., 2013. Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae:Bambusoideae) using RAD sequencing. Mol. Ecol. Res. 13 (5), 938-945.
Wysocki, W.P., Ruiz-Sanchez, E., Yin, Y., Duvall, M.R., 2016. The floral transcriptomes of four bamboo species (Bambusoideae; Poaceae):support for common ancestry among woody bamboos. BMC Genom. 17 (1), 384.
Yang, G.Q., Chen, Y.M., Wang, J.P., Guo, C., Zhao, L., Wang, X.Y., Guo, Y., Li, L., Li, D.Z., Guo, Z.H., 2016. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Meth. 12.
Zhang, X.Z., Zeng, C.X., Ma, P.F., Haevermans, T., Zhang, Y.X., Zhang, L.N., Guo, Z.H., Li, D.Z., 2016. Multi-locus plastid phylogenetic biogeography supports the Asian hypothesis of the temperate woody bamboos (Poaceae:Bambusoideae). Mol.Phylogenet. Evol. 96, 118-129.
Zhang, Y.X., Zeng, C.X., Li, D.Z., 2012. Complex evolution in Arundinarieae (Poaceae:Bambusoideae):incongruence between plastid and nuclear GBSSI gene phylogenies. Mol. Phylogenet. Evol. 63 (3), 777-797.
Zhao, H.S., Peng, Z.H., Fei, B.H., Li, L.B., Hu, T., Gao, Z.M., Jiang, Z.H., 2014. BambooGDB:a bamboo genome database with functional annotation and an analysis platform. Database J. Biol. Databases Curation. 10.

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A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing

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