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Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD)
- Source :
- PLoS ONE, PLoS ONE, Vol 14, Iss 9, p e0222292 (2019)
- Publication Year :
- 2019
- Publisher :
- Public Library of Science, 2019.
-
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.
- Subjects :
- 0301 basic medicine
Male
Gene Expression
Genome
Biochemistry
0302 clinical medicine
PANDAS
Medicine and Health Sciences
Immune Response
Ailuropoda melanoleuca
Genetics
Mammals
Multidisciplinary
DNA methylation
biology
Giant Pandas
Chemical Reactions
Eukaryota
Chromatin
Nucleic acids
Chemistry
Vertebrates
Physical Sciences
Medicine
Epigenetics
Female
DNA modification
Chromatin modification
Ursidae
Research Article
Chromosome biology
Cell biology
Science
Immunology
Context (language use)
Bears
Methylation
DNA sequencing
Cataract
03 medical and health sciences
biology.animal
DNA-binding proteins
medicine
Animals
Gene Regulation
Genetic Predisposition to Disease
KEGG
Whole Genome Sequencing
Cataracts
Organisms
Biology and Life Sciences
Proteins
DNA
medicine.disease
Ophthalmology
030104 developmental biology
Lens Disorders
Amniotes
030221 ophthalmology & optometry
Eye disorder
Sequence Alignment
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 14
- Issue :
- 9
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....aff2bd3487e848d0b390498c4fdc38f3