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Genetic innovations: Transposable element recruitment and de novo formation lead to the birth of orphan genes in the rice genome 期刊论文
JOURNAL OF SYSTEMATICS AND EVOLUTION, 2021, 卷号: 59, 期号: 2, 页码: 341-351
Authors:  Jin,Gui-Hua;  Zhou,Yan-Li;  Yang,Hong;  Hu,Yan-Ting;  Shi,Yong;  Li,Ling;  Siddique,Abu N.;  Liu,Chang-Ning;  Zhu,An-Dan;  Zhang,Cheng-Jun;  Li,De-Zhu
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comparative genomics  origin  orphan gene  transposable element  LINEAGE-SPECIFIC GENES  EVOLUTION  ORIGIN  IDENTIFICATION  EMERGENCE  PROTEIN  DUPLICATION  ALIGNMENT  SETS  
Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae 期刊论文
MOLECULAR PLANT, 2021, 卷号: 14, 期号: 5, 页码: 748-773
Authors:  Zhao,Yiyong;  Zhang,Rong;  Jiang,Kai-Wen;  Qi,Ji;  Hu,Yi;  Guo,Jing;  Zhu,Renbin;  Zhang,Taikui;  Egan,Ashley N.;  Yi,Ting-Shuang;  Huang,Chien-Hsun;  Ma,Hong
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Fabaceae  Leguminosae  nuclear phylogeny  divergence times  whole-genome duplication  rhizobial nodulation  COMPARATIVE GENOMICS  PHYLOGENETIC PERSPECTIVES  EARLY DIVERSIFICATION  PENALIZED LIKELIHOOD  ANCESTRAL POLYPLOIDY  MOLECULAR EVOLUTION  LOTUS-JAPONICUS  ANALYSES REVEAL  GENE  LEGUMINOSAE  
Plastid phylogenomic insights into relationships of all flowering plant families 期刊论文
BMC BIOLOGY, 2021, 卷号: 19, 期号: 1, 页码: 232
Authors:  Li,Hong-Tao;  Luo,Yang;  Gan,Lu;  Ma,Peng-Fei;  Gao,Lian-Ming;  Yang,Jun-Bo;  Cai,Jie;  Gitzendanner,Matthew A.;  Fritsch,Peter W.;  Zhang,Ting;  Jin,Jian-Jun;  Zeng,Chun-Xia;  Wang,Hong;  Yu,Wen-Bin;  Zhang,Rong;  van der Bank,Michelle;  Olmstead,Richard G.;  Hollingsworth,Peter M.;  Chase,Mark W.;  Soltis,Douglas E.;  Soltis,Pamela S.;  Yi,Ting-Shuang;  Li,De-Zhu
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Mesangiospermae  Tree of life  Interfamilial relationships  Plastome  PPA II  MULTIPLE SEQUENCE ALIGNMENT  EARLY DIVERSIFICATION  CHLOROPLAST GENOME  SEED PLANTS  SCALE DATA  ANGIOSPERMS  GENES  PHYLOGENETICS  RBCL  RESOLVES  
Spatiotemporal maintenance of flora in the Himalaya biodiversity hotspot: Current knowledge and future perspectives 期刊论文
ECOLOGY AND EVOLUTION, 2021, 卷号: 11, 期号: 16, 页码: 10794-10812
Authors:  Wambulwa,Moses C.;  Milne,Richard;  Wu,Zeng-Yuan;  Spicer,Robert A.;  Provan,Jim;  Luo,Ya-Huang;  Zhu,Guang-Fu;  Wang,Wan-Ting;  Wang,Hong;  Gao,Lian-Ming;  Li,De-Zhu;  Liu,Jie
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biodiversity hotspot  climate change  elevational gradient  Himalayan flora  mountain ecosystem  spatiotemporal diversification  SPECIES RICHNESS PATTERNS  QINGHAI-TIBET PLATEAU  SOUTH ASIAN MONSOON  ELEVATIONAL GRADIENT  HENGDUAN MOUNTAINS  CLIMATE-CHANGE  BETA-DIVERSITY  QUATERNARY GLACIATION  GENETIC CONSEQUENCES  ARTIFICIAL DISPERSAL  
Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms 期刊论文
NATURE PLANTS, 2021, 卷号: 7, 期号: 8, 页码: 1015+
Authors:  Stull,Gregory W.;  Qu,Xiao-Jian;  Parins-Fukuchi,Caroline;  Yang,Ying-Ying;  Yang,Jun-Bo;  Yang,Zhi-Yun;  Hu,Yi;  Ma,Hong;  Soltis,Pamela S.;  Soltis,Douglas E.;  Li,De-Zhu;  Smith,Stephen A.;  Yi,Ting-Shuang
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SEED PLANTS  R PACKAGE  POLYPLOIDY  CONIFERS  TREE  GENERATION  INFERENCE  ANCIENT  DISCORDANCE  ANGIOSPERMS  
Adiantum japonicum, a new species of the Adiantum pedatum complex (Pteridaceae) from Japan 期刊论文
PHYTOTAXA, 2021, 卷号: 525, 期号: 1, 页码: 1-14
Authors:  Zhao,Ting;  Zuo,Zheng-Yu;  Ebihara,Atsushi;  Nakato,Narumi;  Soejima,Akiko;  Li,De-Zhu;  Wen,Jun;  Lu,Jin-Mei
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chloroplast markers  cytotype  disjunction  erect rhizome  NONCODING CHLOROPLAST DNA  NORTH-AMERICA  EASTERN ASIA  EVOLUTION  DISJUNCTIONS  LYCOPHYTES  UTILITY  FERN  
Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae 期刊论文
SYSTEMATIC BIOLOGY, 2020
Authors:  Zhang, Rong;  Wang, Yin-Huan;  Jin, Jian-Jun;  Stull, Gregory W.;  Bruneau, Anne;  Cardoso, Domingos;  De Queiroz, Luciano Paganucci;  Moore, Michael J.;  Zhang, Shu-Dong;  Chen, Si-Yun;  Wang, Jian;  Li, De-Zhu;  Yi, Ting-Shuang
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SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation 期刊论文
COMMUNICATIONS BIOLOGY, 2020
Authors:  Li, Wei;  Li, Kui;  Huang, Ying;  Shi, Cong;  Hu, Wu-Shu;  Zhang, Yun;  Zhang, Qun-Jie;  Xia, En-Hua;  Hutang, Ge-Ran;  Zhu, Xun-Ge;  Liu, Yun-Long;  Liu, Yuan;  Tong, Yan;  Zhu, Ting;  Huang, Hui;  Zhang, Dan;  Zhao, Yuan;  Jiang, Wen-Kai;  Yuan, Jie;  Niu, Yong-Chao;  Gao, Cheng-Wen;  Gao, Li-Zhi
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Gut microbiota protects from triptolide-induced hepatotoxicity: Key role of propionate and its downstream signalling events 期刊论文
PHARMACOLOGICAL RESEARCH, 2020
Authors:  Huang, Jian-Feng;  Zhao, Qi;  Dai, Man-Yun;  Xiao, Xue-Rong;  Zhang, Ting;  Zhu, Wei-Feng;  Li, Fei
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GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes 期刊论文
GENOME BIOLOGY, 2020
Authors:  Jin, Jian-Jun;  Yu, Wen-Bin;  Yang, Jun-Bo;  Song, Yu;  dePamphilis, Claude W.;  Yi, Ting-Shuang;  Li, De-Zhu
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