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Epigenome-wide DNA methylation analysis reveals differentially methylation patterns in skeletal muscle between Chinese Chenghua and Qingyu pigs 被引量:1
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作者 WANG Kai WU Ping-xian +12 位作者 WANG Shu-jie JI Xiang CHEN Dong JIANG An-an XIAO Wei-hang JIANG Yan-zhi ZHU Li ZENG Yang-shuang XU Xu QIU Xiao-tian LI Ming-zhou LI Xue-wei TANG Guo-qing 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2022年第6期1731-1739,共9页
Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There a... Chenghua(CH)pig and Qingyu(QY)pig are typical Chinese native fatty breeds.CH pig is mainly distributed in Chengdu Plain,while QY pig is widely distributed throughout the mountain areas around the Sichuan Basin.There are significant differences in their phenotypic traits,including body image,growth performance,and meat quality.This study compared several meat quality traits of CH and QY pigs and conducted a genome-wide DNA methylation analysis using reduced representation bisulfite sequencing(RRBS).It was observed that the pH at 45 min(pH_(45min),P=5.22e-13),lightness at 45 min(L^(*)_(45min),P=4.85e-5),and lightness at 24 h(L^(*)_(24h),P=3.57e-5)of CH pigs were higher than those of QY pigs.We detected 10699 differentially methylated cytosines(DMCs)and 2760 differentially methylated genes(DMGs)associated with these DMCs.Functional analysis showed that these DMGs were mainly enriched in the AMPK signaling pathway,Type II diabetes mellitus,Insulin signaling pathway,mTOR signaling pathway,and Insulin resistance.Furthermore,15 DMGs were associated with fat metabolism(ACACA,CAB39,CRADD,CRTC2,FASN,and GCK),muscle development(HK2,IKBKB,MTOR,PIK3CD,PPARGC1A,and RPTOR),or meat quality traits(PCK1,PRKAG2,and SLC2A4).The findings may help to understand further the epigenetic regulation mechanisms of meat quality traits in pigs and provide new basic data for the study of local pigs. 展开更多
关键词 DNA methylation reduced representation bisulfite sequencing(RRBS) Chenghua pig Qingyu pig
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Phylogenomics and the flowering plant tree of life 被引量:10
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作者 Cen Guo Yang Luo +4 位作者 Lian-Ming Gao Ting-Shuang Yi Hong-Tao Li Jun-Bo Yang De-Zhu Li 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2023年第2期299-323,共25页
The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopti... The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era.In the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.This review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower levels.We also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of life.Finally,we discuss promising avenues for future plant phylogenomic studies. 展开更多
关键词 ANGIOSPERMS HYBRIDIZATION incomplete lineage sorting orthology inference phylogenetic conflicts reduced representation sequencing whole-genome sequencing whole-genome duplication
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DNA methylome study of human cerebellar tissues identified genes and pathways possibly involved in essential tremor 被引量:1
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作者 Jennifer L.Paul Khashayar Dashtipour +1 位作者 Zhong Chen Charles Wang 《Precision Clinical Medicine》 2019年第4期221-234,共14页
Background:Essential tremor(ET)is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis.It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of... Background:Essential tremor(ET)is a neurological syndrome of unknown origin with poorly understood etiology and pathogenesis.It is suggested that the cerebellum and its tracts may be involved in the pathophysiology of ET.DNA methylome interrogation of cerebellar tissue may help shine some light on the understanding of the mechanism of the development of ET.Our study used postmortem human cerebellum tissue samples collected from 12 ET patients and 11 matched non-ET controls for DNA methylome study to identify differentially methylated genes in ET.Results:Using Nugen’s Ovation reduced representation bisulfite sequencing(RRBS),we identified 753 genes encompassing 938 CpG sites with significant differences in DNA methylation between the ET and the control group.Identified genes were further analyzed with Ingenuity Pathway Analysis(IPA)by which we identified certain significant pathways,upstream regulators,diseases and functions,and networks associated with ET.Conclusions:Our study provides evidence that there are significant differences in DNA methylation patterns between the ET and control samples,suggesting that the methylation alteration of certain genes in the cerebellum may be associated with ET pathogenesis.The identified genes allude to the GABAergic hypothesis which supports the notation that ET is a neurodegenerative disease,particularly involving the cerebellum. 展开更多
关键词 DNA methylome reduced representation bisulfite sequencing essential tremor CEREBELLUM EPIGENETICS CpGs
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Des=gn of efficient simplified genomic DNA and bisulfite sequencing in large plant populations
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作者 Jinhua Wu Zewei Luo Ning Jiang 《Frontiers of Electrical and Electronic Engineering in China》 CSCD 2016年第3期226-239,共14页
The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and geno... The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing (RRGS), which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion (up to 60%) of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD- seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations. 展开更多
关键词 plant/crop genomes next generation sequencing GENOTYPING restriction-enzyme sites associated DNA(RAD) DNA methylation reduced representation bisulfite sequencing
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