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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  
Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa 期刊论文
FUNGAL DIVERSITY, 2021, 卷号: 111, 期号: 1, 页码: 1-335
Authors:  Boonmee,Saranyaphat;  Wanasinghe,Dhanushka N.;  Calabon,Mark S.;  Huanraluek,Naruemon;  Chandrasiri,Sajini K. U.;  Jones,Gareth E. B.;  Rossi,Walter;  Leonardi,Marco;  Singh,Sanjay K.;  Rana,Shiwali;  Singh,Paras N.;  Maurya,Deepak K.;  Lagashetti,Ajay C.;  Choudhary,Deepika;  Dai,Yu-Cheng;  Zhao,Chang-Lin;  Mu,Yan-Hong;  Yuan,Hai-Sheng;  He,Shuang-Hui;  Phookamsak,Rungtiwa;  Jiang,Hong-Bo;  Martin,Maria P.;  Duenas,Margarita;  Teresa Telleria,M.;  Kalucka,Izabela L.;  Jagodzinski,Andrzej M.;  Liimatainen,Kare;  Pereira,Diana S.;  Phillips,Alan J. L.;  Suwannarach,Nakarin;  Kumla,Jaturong;  Khuna,Surapong;  Lumyong,Saisamorn;  Potter,Tarynn B.;  Shivas,Roger G.;  Sparks,Adam H.;  Vaghefi,Niloofar;  Abdel-Wahab,Mohamed A.;  Abdel-Aziz,Faten A.;  Li,Guo-Jie;  Lin,Wen-Fei;  Singh,Upendra;  Bhatt,Rajendra P.;  Lee,Hyang Burm;  Nguyen,Thuong T. T.;  Kirk,Paul M.;  Dutta,Arun Kumar;  Acharya,Krishnendu;  Sarma,V. Venkateswara;  Niranjan,M.;  Rajeshkumar,Kunhiraman C.;  Ashtekar,Nikhil;  Lad,Sneha;  Wijayawardene,Nalin N.;  Bhat,Darbe J.;  Xu,Rong-Ju;  Wijesinghe,Subodini N.;  Shen,Hong-Wei;  Luo,Zong-Long;  Zhang,Jing-Yi;  Sysouphanthong,Phongeun;  Thongklang,Naritsada;  Bao,Dan-Feng;  Aluthmuhandiram,Janith V. S.;  Abdollahzadeh,Jafar;  Javadi,Alireza;  Dovana,Francesco;  Usman,Muhammad;  Khalid,Abdul Nasir;  Dissanayake,Asha J.;  Telagathoti,Anusha;  Probst,Maraike;  Peintner,Ursula;  Garrido-Benavent,Isaac;  Bona,Lilla;  Merenyi,Zsolt;  Boros,Lajos;  Zoltan,Bratek;  Stielow,J. Benjamin;  Jiang,Ning;  Tian,Cheng-Ming;  Shams,Esmaeil;  Dehghanizadeh,Farzaneh;  Pordel,Adel;  Javan-Nikkhah,Mohammad;  Denchev,Teodor T.;  Denchev,Cvetomir M.;  Kemler,Martin;  Begerow,Dominik;  Deng,Chun-Ying;  Harrower,Emma;  Bozorov,Tohir;  Kholmuradova,Tutigul;  Gafforov,Yusufjon;  Abdurazakov,Aziz;  Xu,Jian-Chu;  Mortimer,Peter E.;  Ren,Guang-Cong;  Jeewon,Rajesh;  Maharachchikumbura,Sajeewa S. N.;  Phukhamsakda,Chayanard;  Mapook,Ausana;  Hyde,Kevin D.
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72 new taxa  One new combination  One reference specimen  51 new records  Agaricomycetes  Ascomycota  Bartheletiomycetes  Basidiomycota  Dothideomycetes  Eurotiomycetes  Exobasidiomycetes  Laboulbeniomycetes  Leotiomycetes  Mortierellomycetes  Mortierellomycota  Mucoromycetes  Mucoromycota  Phylogeny  Sordariomycetes  Taxonomy  FRESH-WATER FUNGI  NUCLEAR RIBOSOMAL DNA  RED-SEA MANGROVES  BIRDS NEST FUNGI  SP-NOV  SP.-NOV.  MOLECULAR PHYLOGENY  NATURAL CLASSIFICATION  EUTYPA-LATA  PHANEROCHAETE POLYPORALES  
The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis 期刊论文
MOLECULAR PLANT, 2020, 卷号: 13, 期号: 2, 页码: 336-350
Authors:  Liu, Jin;  Shi, Cong;  Shi, Cheng-Cheng;  Li, Wei;  Zhang, Qun-Jie;  Zhang, Yun;  Li, Kui;  Lu, Hui-Fang;  Shi, Chao;  Zhu, Si-Tao;  Xiao, Zai-Yun;  Nan, Hong;  Yue, Yao;  Zhu, Xun-Ge;  Wu, Yu;  Hong, Xiao-Ning;  Fan, Guang-Yi;  Tong, Yan;  Zhang, Dan;  Mao, Chang-Li;  Liu, Yun-Long;  Hao, Shi-Jie;  Liu, Wei-Qing;  Lv, Mei-Qi;  Zhang, Hai-Bin;  Liu, Yuan;  Hu-tang, Ge-Ran;  Wang, Jin-Peng;  Wang, Jia-Hao;  Sun, Ying-Huai;  Ni, Shu-Bang;  Chen, Wen-Bin;  Zhang, Xing-Cai;  Jiao, Yuan-Nian;  Eichler, Evan E.;  Li, Guo-Hua;  Liu, Xin;  Gao, Li-Zhi
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rubber tree  rubber biosynthesis  chromosome evolution  whole-genome duplication  domestication  
Comparative analysis of complete plastid genome reveals powerful barcode regions for identifying wood of Dalbergia odorifera and D. tonkinensis (Leguminosae) 期刊论文
JOURNAL OF SYSTEMATICS AND EVOLUTION, 2020
Authors:  Qin, Ming;  Zhu, Cheng-Jie;  Yang, Jun-Bo;  Vatanparast, Mohammad;  Schley, Rowan;  Lai, Qiang;  Zhang, Dan-Yan;  Tu, Tie-Yao;  Klitgard, Bente B.;  Li, Shi-Jin;  Zhang, Dian-Xiang
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Fungal diversity notes 1277-1386: taxonomic and phylogenetic contributions to fungal taxa 期刊论文
FUNGAL DIVERSITY, 2020
Authors:  Yuan, Hai-Sheng;  Lu, Xu;  Dai, Yu-Cheng;  Hyde, Kevin D.;  Kan, Yu-He;  Kusan, Ivana;  He, Shuang-Hui;  Liu, Ning-Guo;  Sarma, V. Venkateswara;  Zhao, Chang-Lin;  Cui, Bao-Kai;  Yousaf, Nousheen;  Sun, Guangyu;  Liu, Shu-Yan;  Wu, Fang;  Lin, Chuan-Gen;  Dayarathne, Monika C.;  Gibertoni, Tatiana Baptista;  Conceicao, Lucas B.;  Garibay-Orijel, Roberto;  Villegas-Rios, Margarita;  Salas-Lizana, Rodolfo;  Wei, Tie-Zheng;  Qiu, Jun-Zhi;  Yu, Ze-Fen;  Phookamsak, Rungtiwa;  Zeng, Ming;  Paloi, Soumitra;  Bao, Dan-Feng;  Abeywickrama, Pranami D.;  Wei, De-Ping;  Yang, Jing;  Manawasinghe, Ishara S.;  Harishchandra, Dulanjalee;  Brahmanage, Rashika S.;  de Silva, Nimali I.;  Tennakoon, Danushka S.;  Karunarathna, Anuruddha;  Gafforov, Yusufjon;  Pem, Dhandevi;  Zhang, Sheng-Nan;  de Azevedo Santiago, Andre L. C. M.;  Bezerra, Jadson Diogo Pereira;  Dima, Balint;  Acharya, Krishnendu;  Alvarez-Manjarrez, Julieta;  Bahkali, Ali H.;  Bhatt, Vinod K.;  Brandrud, Tor Erik;  Bulgakov, Timur S.;  Camporesi, E.;  Cao, Ting;  Chen, Yu-Xi;  Chen, Yuan-Yuan;  Devadatha, Bandarupalli;  Elgorban, Abdallah M.;  Fan, Long-Fei;  Du, Xing;  Gao, Liu;  Goncalves, Camila Melo;  Gusmao, Luis F. P.;  Huanraluek, Naruemon;  Jadan, Margita;  Jayawardena, Ruvishika S.;  Khalid, Abdul Nasir;  Langer, Ewald;  Lima, Diogo X.;  de Lima-Junior, Nelson Correia;  de Lira, Carla Rejane Sousa;  Liu, Jian-Kui (Jack);  Liu, Shun;  Lumyong, Saisamorn;  Luo, Zong-Long;  Matocec, Neven;  Niranjan, M.;  Oliveira-Filho, Jose Ribamar Costa;  Papp, Viktor;  Perez-Pazos, Eduardo;  Phillips, Alan J. L.;  Qiu, Peng-Lei;  Ren, Yihua;  Ruiz, Rafael F. Castaneda;  Semwal, Kamal C.;  Soop, Karl;  de Souza, Carlos A. F.;  Souza-Motta, Cristina Maria;  Sun, Li-Hua;  Xie, Meng-Le;  Yao, Yi-Jian;  Zhao, Qi;  Zhou, Li-Wei
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The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution 期刊论文
MOLECULAR PLANT, 2020
Authors:  Zhang, Qun-Jie;  Li, Wei;  Li, Kui;  Nan, Hong;  Shi, Cong;  Zhang, Yun;  Dai, Zhang-Yan;  Lin, Yang-Lei;  Yang, Xiao-Lan;  Tong, Yan;  Zhang, Dan;  Lu, Cui;  Feng, Li-Ying;  Wang, Chen-Feng;  Liu, Xiao-Xin;  Huang, Jian-An;  Jiang, Wen-Kai;  Wang, Xing-Hua;  Zhang, Xing-Cai;  Eichler, Evan E.;  Liu, Zhong-Hua;  Gao, Li-Zhi
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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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Draft genomes of two outcrossing wild rice,Oryza rufipogonandO. longistaminata, reveal genomic features associated with mating-system evolution 期刊论文
PLANT DIRECT, 2020
Authors:  Li, Wei;  Zhang, Qun-Jie;  Zhu, Ting;  Tong, Yan;  Li, Kui;  Shi, Cong;  Zhang, Yun;  Liu, Yun-Long;  Jiang, Jian-Jun;  Liu, Yuan;  Xia, En-Hua;  Huang, Hui;  Zhang, Li-Ping;  Zhang, Dan;  Shi, Chao;  Jiang, Wen-Kai;  Zhao, You-Jie;  Mao, Shu-Yan;  Jiao, Jun-ying;  Xu, Ping-Zhen;  Yang, Li-Li;  Gao, Li-Zhi
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Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata, from Illumina and PacBio sequencing reads 期刊论文
PLANT GENOME, 2020
Authors:  Li, Wei;  Li, Kui;  Zhang, Qun-jie;  Zhu, Ting;  Zhang, Yun;  Shi, Cong;  Liu, Yun-long;  Xia, En-hua;  Jiang, Jian-jun;  Shi, Chao;  Zhang, Li-ping;  Huang, Hui;  Tong, Yan;  Liu, Yuan;  Zhang, Dan;  Zhao, Yuan;  Jiang, Wen-kai;  Zhao, You-jie;  Mao, Shu-yan;  Jiao, Jun-ying;  Xu, Ping-zhen;  Yang, Li-li;  Yin, Guo-ying;  Gao, Li-zhi
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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, 2019, 页码: 11
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