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Progress, challenge and prospect of plant plastome annotation 期刊论文
FRONTIERS IN PLANT SCIENCE, 2023, 卷号: 14, 页码: 1166140
Authors:  Qu,Xiao-Jian;  Zou,Dan;  Zhang,Rui-Yu;  Stull,Gregory W.;  Yi,Ting-Shuang
View  |  Adobe PDF(12821Kb)  |  Favorite  |  View/Download:25/9  |  Submit date:2024/05/09
annotation standards  chloroplast genome  plastome  protein structure  pseudogenes  RNA-editing genes  MITOCHONDRIAL GENES  RNA  GENOME  SEQUENCE  CHLOROPLASTS  TRANSLATION  
Global urban environmental change drives adaptation in white clover 期刊论文
SCIENCE, 2022, 卷号: 375, 期号: 6586, 页码: 1275+
Authors:  Santangelo, James S.;  Ness, Rob W.;  Cohan, Beata;  Fitzpatrick, Connor R.;  Innes, Simon G.;  Koch, Sophie;  Miles, Lindsay S.;  Munim, Samreen;  Peres-Neto, Pedro R.;  Prashad, Cindy;  Tong, Alex T.;  Aguirre, Windsor E.;  Akinwole, Philips O.;  Alberti, Marina;  Alvarez, Jackie;  Anderson, Jill T.;  Anderson, Joseph J.;  Ando, Yoshino;  Andrew, Nigel R.;  Angeoletto, Fabio;  Anstett, Daniel N.;  Anstett, Julia;  Aoki-Goncalves, Felipe;  Arietta, A. Z. Andis;  Arroyo, Mary T. K.;  Austen, Emily J.;  Baena-Diaz, Fernanda;  Barker, Cory A.;  Baylis, Howard A.;  Beliz, Julia M.;  Benitez-Mora, Alfonso;  Bickford, David;  Biedebach, Gabriela;  Blackburn, Gwylim S.;  Boehm, Mannfred M. A.;  Bonser, Stephen P.;  Bonte, Dries;  Bragger, Jesse R.;  Branquinho, Cristina;  Brans, Kristien, I;  Bresciano, Jorge C.;  Brom, Peta D.;  Bucharova, Anna;  Burt, Briana;  Cahill, James F.;  Campbell, Katelyn D.;  Carlen, Elizabeth J.;  Carmona, Diego;  Castellanos, Maria Clara;  Centenaro, Giada;  Chalen, Izan;  Chaves, Jaime A.;  Chavez-Pesqueira, Mariana;  Chen, Xiao-Yong;  Chilton, Angela M.;  Chomiak, Kristina M.;  Cisneros-Heredia, Diego F.;  Cisse, Ibrahim K.;  Classen, Aimee T.;  Comerford, Mattheau S.;  Fradinger, Camila Cordoba;  Corney, Hannah;  Crawford, Andrew J.;  Crawford, Kerri M.;  Dahirel, Maxime;  David, Santiago;  De Haan, Robert;  Deacon, Nicholas J.;  Dean, Clare;  Del-Val, Ek;  Deligiannis, Eleftherios K.;  Denney, Derek;  Dettlaff, Margarete A.;  DiLeo, Michelle F.;  Ding, Yuan-Yuan;  Dominguez-Lopez, Moises E.;  Dominoni, Davide M.;  Draud, Savannah L.;  Dyson, Karen;  Ellers, Jacintha;  Espinosa, Carlos, I;  Essi, Liliana;  Falahati-Anbaran, Mohsen;  Falcao, Jessica C. F.;  Fargo, Hayden T.;  Fellowes, Mark D. E.;  Fitzpatrick, Raina M.;  Flaherty, Leah E.;  Flood, Padraic J.;  Flores, Maria F.;  Fornoni, Juan;  Foster, Amy G.;  Frost, Christopher J.;  Fuentes, Tracy L.;  Fulkerson, Justin R.;  Gagnon, Edeline;  Garbsch, Frauke;  Garroway, Colin J.;  Gerstein, Aleeza C.;  Giasson, Mischa M.;  Girdler, E. Binney;  Gkelis, Spyros;  Godsoe, William;  Golemiec, Anneke M.;  Golemiec, Mireille;  Gonzalez-Lagos, Cesar;  Gorton, Amanda J.;  Gotanda, Kiyoko M.;  Granath, Gustaf;  Greiner, Stephan;  Griffiths, Joanna S.;  Grilo, Filipa;  Gundel, Pedro E.;  Hamilton, Benjamin;  Hardin, Joyce M.;  He, Tianhua;  Heard, Stephen B.;  Henriques, Andre F.;  Hernandez-Poveda, Melissa;  Hetherington-Rauth, Molly C.;  Hill, Sarah J.;  Hochuli, Dieter F.;  Hodgins, Kathryn A.;  Hood, Glen R.;  Hopkins, Gareth R.;  Hovanes, Katherine A.;  Howard, Ava R.;  Hubbard, Sierra C.;  Ibarra-Cerdena, Carlos N.;  Iniguez-Armijos, Carlos;  Jara-Arancio, Paola;  Jarrett, Benjamin J. M.;  Jeannot, Manon;  Jimenez-Lobato, Vania;  Johnson, Mae;  Johnson, Oscar;  Johnson, Philip P.;  Johnson, Reagan;  Josephson, Matthew P.;  Jung, Meen Chel;  Just, Michael G.;  Kahilainen, Aapo;  Kailing, Otto S.;  Karinho-Betancourt, Eunice;  Karousou, Regina;  Kirn, Lauren A.;  Kirschbaum, Anna;  Laine, Anna-Liisa;  LaMontagne, Jalene M.;  Lampei, Christian;  Lara, Carlos;  Larson, Erica L.;  Lazaro-Lobo, Adrian;  Le, Jennifer H.;  Leandro, Deleon S.;  Lee, Christopher;  Lei, Yunting;  Leon, Carolina A.;  Tamara, Manuel E. Lequerica;  Levesque, Danica C.;  Liao, Wan-Jin;  Ljubotina, Megan;  Locke, Hannah;  Lockett, Martin T.;  Longo, Tiffany C.;  Lundholm, Jeremy T.;  MacGillavry, Thomas;  Mackin, Christopher R.;  Mahmoud, Alex R.;  Manju, Isaac A.;  Marien, Janine;  Martinez, D. Nayeli;  Martinez-Bartolome, Marina;  Meineke, Emily K.;  Mendoza-Arroyo, Wendy;  Merritt, Thomas J. S.;  Merritt, Lila Elizabeth L.;  Migiani, Giuditta;  Minor, Emily S.;  Mitchell, Nora;  Bazargani, Mitra Mohammadi;  Moles, Angela T.;  Monk, Julia D.;  Moore, Christopher M.;  Morales-Morales, Paula A.;  Moyers, Brook T.;  Munoz-Rojas, Miriam;  Munshi-South, Jason;  Murphy, Shannon M.;  Murua, Maureen M.;  Neila, Melisa;  Nikolaidis, Ourania;  Njunji, Iva;  Nosko, Peter;  Nunez-Farfan, Juan;  Ohgushi, Takayuki;  Olsen, Kenneth M.;  Opedal, Oystein H.;  Ornelas, Cristina;  Parachnowitsch, Amy L.;  Paratore, Aaron S.;  Parody-Merino, Angela M.;  Paule, Juraj;  Paulo, Octavio S.;  Pena, Joao Carlos;  Pfeiffer, Vera W.;  Pinho, Pedro;  Piot, Anthony;  Porth, Ilga M.;  Poulos, Nicholas;  Puentes, Adriana;  Qu, Jiao;  Quintero-Vallejo, Estela;  Raciti, Steve M.;  Raeymaekers, Joost A. M.;  Raveala, Krista M.;  Rennison, Diana J.;  Ribeiro, Milton C.;  Richardson, Jonathan L.;  Rivas-Torres, Gonzalo;  Rivera, Benjamin J.;  Roddy, Adam B.;  Rodriguez-Munoz, Erika;  Roman, Jose Raul;  Rossi, Laura S.;  Rowntree, Jennifer K.;  Ryan, Travis J.;  Salinas, Santiago;  Sanders, Nathan J.;  Santiago-Rosario, Luis Y.;  Savage, Amy M.;  Scheepens, J. F.;  Schilthuizen, Menno;  Schneider, Adam C.;  Scholier, Tiffany;  Scott, Jared L.;  Shaheed, Summer A.;  Shefferson, Richard P.;  Shepard, Caralee A.;  Shykoff, Jacqui A.;  Silveira, Georgianna;  Smith, Alexis D.;  Solis-Gabriel, Lizet;  Soro, Antonella;  Spellman, Katie, V;  Whitney, Kaitlin Stack;  Starke-Ottich, Indra;  Stephan, Jorg G.;  Stephens, Jessica D.;  Szulc, Justyna;  Szulkin, Marta;  Tack, Ayco J. M.;  Tamburrino, Italo;  Tate, Tayler D.;  Tergemina, Emmanuel;  Theodorou, Panagiotis;  Thompson, Ken A.;  Threlfall, Caragh G.;  Tinghitella, Robin M.;  Toledo-Chelala, Lilibeth;  Tong, Xin;  Uroy, Lea;  Utsumi, Shunsuke;  Vandegehuchte, Martijn L.;  VanWallendael, Acer;  Vidal, Paula M.;  Wadgymar, Susana M.;  Wang, Ai-Ying;  Wang, Nian;  Warbrick, Montana L.;  Whitney, Kenneth D.;  Wiesmeier, Miriam;  Wiles, J. Tristian;  Wu, Jianqiang;  Xirocostas, Zoe A.;  Yan, Zhaogui;  Yao, Jiahe;  Yoder, Jeremy B.;  Yoshida, Owen;  Zhang, Jingxiong;  Zhao, Zhigang;  Ziter, Carly D.;  Zuellig, Matthew P.;  Zufall, Rebecca A.;  Zurita, Juan E.;  Zytynska, Sharon E.;  Johnson, Marc T. J.
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SURFACE TEMPERATURE RETRIEVAL  CYANOGENESIS CLINES  HYDROGEN-CYANIDE  GENE FLOW  F-ST  EVOLUTION  POLYMORPHISM  EMISSIVITY  DISCOVERY  FRAMEWORK  
Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae 期刊论文
ANNALS OF BOTANY, 2022
Authors:  Zhao, Lei;  Yang, Ying-Ying;  Qu, Xiao-Jian;  Ma, Hong;  Hu, Yi;  Li, Hong-Tao;  Yi, Ting-Shuang;  Li, De-Zhu
View  |  Adobe PDF(1678Kb)  |  Favorite  |  View/Download:35/5  |  Submit date:2024/04/30
Araceae  diversification  phylogenomics  WGDs  adaptation  TRAIT-DEPENDENT SPECIATION  GENE DUPLICATION  ANGIOSPERM DIVERSIFICATION  PHYLOGENOMIC ANALYSES  NUCLEAR GENES  POLYPLOIDY  EVOLUTIONARY  FAMILY  RATES  TOOL  
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
View  |  Adobe PDF(3414Kb)  |  Favorite  |  View/Download:166/75  |  Submit date:2022/04/02
SEED PLANTS  R PACKAGE  POLYPLOIDY  CONIFERS  TREE  GENERATION  INFERENCE  ANCIENT  DISCORDANCE  ANGIOSPERMS  
Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture 期刊论文
MOLECULAR PHYLOGENETICS AND EVOLUTION, 2021, 卷号: 163, 页码: 107232
Authors:  Yang,Ying-Ying;  Qu,Xiao-Jian;  Zhang,Rong;  Stull,Gregory W.;  Yi,Ting-Shuang
View  |  Adobe PDF(2469Kb)  |  Favorite  |  View/Download:131/20  |  Submit date:2022/04/02
Betulaceae  Juglandaceae  Myricaceae  Quercus  Phylogenetics  Chloroplast capture  RESTRICTION SITE VARIATION  INTERSPECIFIC GENE FLOW  DNA-SEQUENCES  EVOLUTIONARY HISTORY  MOLECULAR PHYLOGENY  CLADISTIC-ANALYSIS  SEED PLANTS  NUCLEAR  BETULACEAE  DIVERSIFICATION  
Can plastid genome sequencing be used for species identification in Lauraceae? 期刊论文
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY, 2021, 卷号: 197, 期号: 1, 页码: 1-14
Authors:  Liu,Zhi-Fang;  Ma,Hui;  Ci,Xiu-Qin;  Li,Lang;  Song,Yu;  Liu,Bing;  Li,Hsi-Wen;  Wang,Shu-Li;  Qu,Xiao-Jian;  Hu,Jian-Lin;  Zhang,Xiao-Yan;  Conran,John G.;  Twyford,Alex D.;  Yang,Jun-Bo;  Hollingsworth,Peter M.;  Li,Jie
Favorite  |  View/Download:137/0  |  Submit date:2022/04/02
cytonuclear discordance  DNA barcoding  nrDNA  phylogenetics  plastomes  CHLOROPLAST GENOME  ALSEODAPHNOPSIS LAURACEAE  GENE ORGANIZATION  DNA BARCODES  NUCLEAR  EVOLUTION  ALIGNMENT  CLASSIFICATION  DISCORDANCE  CINNAMOMUM  
Plastome Phylogenomic and Biogeographical Study on Thuja (Cupressaceae) 期刊论文
BIOMED RESEARCH INTERNATIONAL, 2020
Authors:  Adelalu, Kole F.;  Zhang, Xu;  Qu, Xiaojian;  Landis, Jacob B.;  Shen, Jun;  Sun, Yanxia;  Meng, Aiping;  Sun, Hang;  Wang, Hengchang
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The complete chloroplast genome sequence of a rambler rose, Rosa wichuraiana (Rosaceae) 期刊论文
MITOCHONDRIAL DNA PART B-RESOURCES, 2020
Authors:  Cui, Wei-Hua;  Zhong, Mi-Cai;  Du, Xin-Yu;  Qu, Xiao-Jian;  Jiang, Xiao-Dong;  Sun, Yi-Bo;  Wang, Dan;  Chen, Sui-Yun;  Hu, Jin-Yong
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Plastome Reduction in the Only Parasitic Gymnosperm Parasitaxus Is Due to Losses of Photosynthesis but Not Housekeeping Genes and Apparently Involves the Secondary Gain of a Large Inverted Repeat 期刊论文
GENOME BIOLOGY AND EVOLUTION, 2019, 卷号: 11, 期号: 10, 页码: 2789-2796
Authors:  Qu, Xiao-Jian;  Fan, Shou-Jin;  Wicke, Susann;  Yi, Ting-Shuang
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plastome  parasitism  mycoheterotrophy  gene loss  Parasitaxus  
The Protective Roles of PPAR alpha Activation in Triptolide-Induced Liver Injury 期刊论文
TOXICOLOGICAL SCIENCES, 2019, 卷号: 171, 期号: 1, 页码: 1-12
Authors:  Hu, Dan-Dan;  Zhao, Qi;  Cheng, Yan;  Xiao, Xue-Rong;  Huang, Jian-Feng;  Qu, Yan;  Li, Xian;  Tang, Ying-Mei;  Bao, Wei-Min;  Yang, Jin-Hui;  Jiang, Tao;  Hu, Jia-Peng;  Gonzalez, Frank J.;  Li, Fei
View  |  Adobe PDF(1740Kb)  |  Favorite  |  View/Download:232/31  |  Submit date:2020/03/26
liver injury  metabolomics  PPAR alpha  acylcarnitines