Methylation data from Pseudotaxus chienii obtained using methylation-dependent restriction-site associated DNA sequencing

Pseudotaxus chienii is an endangered coniferous plant that is endemic to China. Because P. chienii is sessile and has a long life cycle, its options for responding to drastic or rapid changes in climate are limited. To survive locally, P. chienii must be able to adapt, and the species shows variations in leaf size along an environmental gradient from east to west. It is important to determine whether this phenotypic variation is driven by DNA methylation. Therefore, we performed a preliminarily survey using methylation-dependent restriction-site associated DNA sequencing (MethylRAD) to investigate the methylation status of three P. chienii individuals from heterogeneous ecological niches. In total, 372,611 CCGG tags and 726,332 CCHGG tags were obtained. The rate of high quality methylation tags for a specific site in the genome varied from 42.31% (Gxdms3-4) to 50.01% (Jxbj3-4) and 50.18% (Zjdxg3-6). The level of CCHGG methylation (16.63%) was higher than that of CCGG (13.60%), which may be why P. chienii has low levels of phenotypic variation. The methylation data can be accessed using the Sequence Read Archive (SRA) database (SRP128155).


a b s t r a c t
Pseudotaxus chienii is an endangered coniferous plant that is endemic to China. Because P. chienii is sessile and has a long life cycle, its options for responding to drastic or rapid changes in climate are limited. To survive locally, P. chienii must be able to adapt, and the species shows variations in leaf size along an environmental gradient from east to west. It is important to determine whether this phenotypic variation is driven by DNA methylation. Therefore, we performed a preliminarily survey using methylation-dependent restriction-site associated DNA sequencing (MethylRAD) to investigate the methylation status of three P. chienii individuals from heterogeneous ecological niches. In total, 372,611 CCGG tags and 726,332 CCHGG tags were obtained. The rate of high quality methylation tags for a specific site in the genome varied from 42.31% (Gxdms3-4) to 50.01% (Jxbj3-4) and 50.18% (Zjdxg3-6). The level of CCHGG methylation (16.63%) was higher than that of CCGG (13.60%), which may be why P. chienii has low levels of phenotypic variation. The methylation data can be accessed using the Sequence Read Archive (SRA) database (SRP128155

Data accessibility
The Methylation data have been deposited and made accessible via Bio-Project ID: PRJNA419098; BioSample accessions: SAMN08048873, SAMN08048874, and SAMN08048875; and the SRA database (SRP128155).

Value of the data
This dataset provides valuable information that could help predict epigenetic adaptations to future changes in climate.
These data enhance our understanding of the mechanisms of natural phenotypic variation and may be used to provide guidance for the management of genetic resources and species conservation.

Data
This article provides methylation data for three Pseudotaxus chienii individuals from heterogeneous ecological niches. The clean data were deposited in the National Center for Biotechnology Information SRA database (SRP128155).

DNA samples and digestion
In this study, we selected one P. chienii individual from Daxiagu in Zhejiang Province (Zjdxg3-6), one from Bijiashan in Jiangxi Province (Jxbj3-4), and one from Damingshan in Guangxi Zhuang Autonomous Region (Gxdms3-4). P. chienii individuals across these regions possess high genetic diversity and show strong local adaptations to rapid environmental changes, which are suitable for methylation analysis [1]. Young and healthy leaves at the same developmental stage and from the same climate conditions were sampled. We extracted genomic DNA using a modified cetyltrimethylammonium bromide method [2]. Each genomic sample (200 ng) was digested separately with FspEI (New England BioLabs, cat. no. R0662L) at 37°C for 45 min together with control DNA [3].

Barcoding and library pooling
Sample barcodes were introduced using PCR. Each 85-mL PCR reaction mix contained 5 Â High-Fidelity DNA Polymerase Buffer, 10 mM dNTPs, 10 mM Primer3, 10 mM Index Primer, 1.6 U Phusion High-Fidelity DNA polymerase (New England Biolabs, cat. no. M0530, Ipswich, MA, USA), and 50 ng of gel-extracted PCR product. A total of 1-16 cycles of PCR were performed as described above, and following purification, the PCR products were subjected to single-end sequencing (100-150 bp) using an Illumina Hiseq X Ten sequencer (Illumina Inc., San Diego, California, USA) (Tables 1 and 2).