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.

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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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