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  • Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD).

Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD).

PloS one (2019-09-26)
Yuyan You, Chao Bai, Xuefeng Liu, Maohua Xia, Ting Jia, Xiaoguang Li, Chenglin Zhang, Yucun Chen, Sufen Zhao, Liqin Wang, Wei Wang, Yanqiang Yin, Yunfang Xiu, Lili Niu, Jun Zhou, Tao Ma, Yang Du, Yanhui Liu
ABSTRACT

The giant panda (Ailuropoda melanoleuca) is a native species to China. They are rare and endangered and are regarded as the 'national treasure' and 'living fossil' in China. For the time being, there are only about 2500 giant pandas in the world. Therefore, we still have to do much more efforts to protect the giant pandas. In captive wildlife, the cataract incidence of mammalian always increases with age. Currently, in China, the proportion of elderly giant pandas who suffering from cataract has reached 20%. The eye disorder thus has a strong influence on the physical health and life quality of the elderly giant pandas. To discover the genes associated with the pathogenesis of cataract in the elderly giant panda and achieve the goal of early assessment and diagnosis of cataract in giant pandas during aging, we performed whole genome methylation sequencing in 3 giant pandas with cataract and 3 healthy giant pandas using methylation-dependent restriction-site associated DNA sequencing (MethylRAD). In the present study, we obtained 3.62M reads, on average, for each sample, and identified 116 and 242 differentially methylated genes (DMGs) between the two groups under the context of CCGG and CCWGG on genome, respectively. Further KEGG and GO enrichment analyses determined a total of 110 DMGs that are involved in the biological functions associated with pathogenesis of cataract. Among them, 6 DMGs including EEA1, GARS, SLITRK4, GSTM3, CASP3, and EGLN3 have been linked with cataract in old age.

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Phenol/Chloroform/Isoamyl Alcohol, 25:24:1 (v/v), Molecular Biology Grade, A 25:24:1 (v/v) mixture of phenol, chloroform and isoamyl alcohol, pH 6.7. Suitable for DNA and RNA applications.