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

KIB OpenIR

	A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing.
	Guo, Ying; Yang, GuoQian; Chen, Yunmei; Li, Dezhu; Guo, Zhenhua
	2018
发表期刊	Plant diversity
ISSN	2468-2659
卷号	40 期号:3 页码:106-116
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 ddRAD-seq, 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.
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/64808
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Guo, Ying,Yang, GuoQian,Chen, Yunmei,et al. A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing.[J]. Plant diversity,2018,40(3):106-116.
APA	Guo, Ying,Yang, GuoQian,Chen, Yunmei,Li, Dezhu,&Guo, Zhenhua.(2018).A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing..Plant diversity,40(3),106-116.
MLA	Guo, Ying,et al."A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing.".Plant diversity 40.3(2018):106-116.