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Zijun Xiong

Bio: Zijun Xiong is an academic researcher from Kunming Institute of Zoology. The author has contributed to research in topics: Genome & Comparative genomics. The author has an hindex of 17, co-authored 23 publications receiving 3689 citations. Previous affiliations of Zijun Xiong include Beijing Genomics Institute & Laboratory of Molecular Biology.

Papers
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Journal ArticleDOI
Erich D. Jarvis1, Siavash Mirarab2, Andre J. Aberer3, Bo Li4, Bo Li5, Bo Li6, Peter Houde7, Cai Li5, Cai Li4, Simon Y. W. Ho8, Brant C. Faircloth9, Benoit Nabholz, Jason T. Howard1, Alexander Suh10, Claudia C. Weber10, Rute R. da Fonseca11, Jianwen Li, Fang Zhang Zhang, Hui Li, Long Zhou, Nitish Narula7, Nitish Narula12, Liang Liu13, Ganesh Ganapathy1, Bastien Boussau, Shamsuzzoha Bayzid2, Volodymyr Zavidovych1, Sankar Subramanian14, Toni Gabaldón15, Salvador Capella-Gutierrez, Jaime Huerta-Cepas, Bhanu Rekepalli16, Bhanu Rekepalli17, Kasper Munch18, Mikkel H. Schierup18, Bent E. K. Lindow11, Wesley C. Warren19, David A. Ray, Richard E. Green20, Michael William Bruford21, Xiangjiang Zhan22, Xiangjiang Zhan21, Andrew Dixon, Shengbin Li6, Ning Li23, Yinhua Huang23, Elizabeth P. Derryberry24, Elizabeth P. Derryberry25, Mads F. Bertelsen26, Frederick H. Sheldon24, Robb T. Brumfield24, Claudio V. Mello27, Claudio V. Mello28, Peter V. Lovell27, Morgan Wirthlin27, Maria Paula Cruz Schneider28, Francisco Prosdocimi28, José Alfredo Samaniego11, Amhed Missael Vargas Velazquez11, Alonzo Alfaro-Núñez11, Paula F. Campos11, Bent O. Petersen29, Thomas Sicheritz-Pontén29, An Pas, Thomas L. Bailey, R. Paul Scofield30, Michael Bunce31, David M. Lambert14, Qi Zhou, Polina L. Perelman32, Amy C. Driskell33, Beth Shapiro20, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Quiemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnéa Smeds10, Frank E. Rheindt34, Michael J. Braun35, Jon Fjeldså11, Ludovic Orlando11, F. Keith Barker4, Knud A. Jønsson4, Warren E. Johnson33, Klaus-Peter Koepfli33, Stephen J. O'Brien36, David Haussler, Oliver A. Ryder, Carsten Rahbek4, Eske Willerslev11, Gary R. Graves4, Gary R. Graves33, Travis C. Glenn13, John E. McCormack37, Dave Burt38, Hans Ellegren10, Per Alström, Scott V. Edwards39, Alexandros Stamatakis3, David P. Mindell40, Joel Cracraft4, Edward L. Braun41, Tandy Warnow2, Tandy Warnow42, Wang Jun, M. Thomas P. Gilbert31, M. Thomas P. Gilbert4, Guojie Zhang5, Guojie Zhang11 
12 Dec 2014-Science
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

1,624 citations

Journal ArticleDOI
Guojie Zhang1, Guojie Zhang2, Cai Li2, Qiye Li2, Bo Li2, Denis M. Larkin3, Chul Hee Lee4, Jay F. Storz5, Agostinho Antunes6, Matthew J. Greenwold7, Robert W. Meredith8, Anders Ödeen9, Jie Cui10, Qi Zhou11, Luohao Xu2, Hailin Pan2, Zongji Wang12, Lijun Jin2, Pei Zhang2, Haofu Hu2, Wei Yang2, Jiang Hu2, Jin Xiao2, Zhikai Yang2, Yang Liu2, Qiaolin Xie2, Hao Yu2, Jinmin Lian2, Ping Wen2, Fang Zhang2, Hui Li2, Yongli Zeng2, Zijun Xiong2, Shiping Liu12, Long Zhou2, Zhiyong Huang2, Na An2, Jie Wang13, Qiumei Zheng2, Yingqi Xiong2, Guangbiao Wang2, Bo Wang2, Jingjing Wang2, Yu Fan14, Rute R. da Fonseca1, Alonzo Alfaro-Núñez1, Mikkel Schubert1, Ludovic Orlando1, Tobias Mourier1, Jason T. Howard15, Ganeshkumar Ganapathy15, Andreas R. Pfenning15, Osceola Whitney15, Miriam V. Rivas15, Erina Hara15, Julia Smith15, Marta Farré3, Jitendra Narayan16, Gancho T. Slavov16, Michael N Romanov17, Rui Borges6, João Paulo Machado6, Imran Khan6, Mark S. Springer18, John Gatesy18, Federico G. Hoffmann19, Juan C. Opazo20, Olle Håstad21, Roger H. Sawyer7, Heebal Kim4, Kyu-Won Kim4, Hyeon Jeong Kim4, Seoae Cho4, Ning Li22, Yinhua Huang22, Michael William Bruford23, Xiangjiang Zhan13, Andrew Dixon, Mads F. Bertelsen24, Elizabeth P. Derryberry25, Wesley C. Warren26, Richard K. Wilson26, Shengbin Li27, David A. Ray19, Richard E. Green28, Stephen J. O'Brien29, Darren K. Griffin17, Warren E. Johnson30, David Haussler28, Oliver A. Ryder, Eske Willerslev1, Gary R. Graves31, Per Alström21, Jon Fjeldså32, David P. Mindell33, Scott V. Edwards34, Edward L. Braun35, Carsten Rahbek32, David W. Burt36, Peter Houde37, Yong Zhang2, Huanming Yang38, Jian Wang2, Erich D. Jarvis15, M. Thomas P. Gilbert1, M. Thomas P. Gilbert39, Jun Wang 
12 Dec 2014-Science
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Abstract: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

872 citations

Journal ArticleDOI
TL;DR: The 385-Mb genome of S. haematobium is sequenced using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites to provide an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.
Abstract: Schistosomiasis is a neglected tropical disease caused by blood flukes (genus Schistosoma; schistosomes) and affecting 200 million people worldwide. No vaccines are available, and treatment relies on one drug, praziquantel. Schistosoma haematobium has come into the spotlight as a major cause of urogenital disease, as an agent linked to bladder cancer and as a predisposing factor for HIV/AIDS. The parasite is transmitted to humans from freshwater snails. Worms dwell in blood vessels and release eggs that become embedded in the bladder wall to elicit chronic immune-mediated disease and induce squamous cell carcinoma. Here we sequenced the 385-Mb genome of S. haematobium using Illumina-based technology at 74-fold coverage and compared it to sequences from related parasites. We included genome annotation based on function, gene ontology, networking and pathway mapping. This genome now provides an unprecedented resource for many fundamental research areas and shows great promise for the design of new disease interventions.

398 citations

Journal ArticleDOI
08 May 2014-Cell
TL;DR: It is found that genes on the polar bear lineage have been under stronger positive selection than in brown bears; nine of the top 16 genes under strong positive selection are associated with cardiomyopathy and vascular disease, implying important reorganization of the cardiovascular system.

333 citations

Journal ArticleDOI
24 Nov 2011-Nature
TL;DR: This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.
Abstract: Parasitic diseases have a devastating, long-term impact on human health, welfare and food production worldwide. More than two billion people are infected with geohelminths, including the roundworms Ascaris (common roundworm), Necator and Ancylostoma (hookworms), and Trichuris (whipworm), mainly in developing or impoverished nations of Asia, Africa and Latin America. In humans, the diseases caused by these parasites result in about 135,000 deaths annually, with a global burden comparable with that of malaria or tuberculosis in disability-adjusted life years. Ascaris alone infects around 1.2 billion people and, in children, causes nutritional deficiency, impaired physical and cognitive development and, in severe cases, death. Ascaris also causes major production losses in pigs owing to reduced growth, failure to thrive and mortality. The Ascaris-swine model makes it possible to study the parasite, its relationship with the host, and ascariasis at the molecular level. To enable such molecular studies, we report the 273 megabase draft genome of Ascaris suum and compare it with other nematode genomes. This genome has low repeat content (4.4%) and encodes about 18,500 protein-coding genes. Notably, the A. suum secretome (about 750 molecules) is rich in peptidases linked to the penetration and degradation of host tissues, and an assemblage of molecules likely to modulate or evade host immune responses. This genome provides a comprehensive resource to the scientific community and underpins the development of new and urgently needed interventions (drugs, vaccines and diagnostic tests) against ascariasis and other nematodiases.

268 citations


Cited by
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

18,940 citations

Journal ArticleDOI
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.

4,104 citations

Journal ArticleDOI
TL;DR: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses that includes the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, and new output formats to facilitate interoperability with downstream software.
Abstract: PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

3,445 citations

Journal Article
TL;DR: In this paper, a test based on two conserved CHD (chromo-helicase-DNA-binding) genes that are located on the avian sex chromosomes of all birds, with the possible exception of the ratites (ostriches, etc.).

2,554 citations

Journal ArticleDOI
Erich D. Jarvis1, Siavash Mirarab2, Andre J. Aberer3, Bo Li4, Bo Li5, Bo Li6, Peter Houde7, Cai Li5, Cai Li4, Simon Y. W. Ho8, Brant C. Faircloth9, Benoit Nabholz, Jason T. Howard1, Alexander Suh10, Claudia C. Weber10, Rute R. da Fonseca11, Jianwen Li, Fang Zhang Zhang, Hui Li, Long Zhou, Nitish Narula12, Nitish Narula7, Liang Liu13, Ganesh Ganapathy1, Bastien Boussau, Shamsuzzoha Bayzid2, Volodymyr Zavidovych1, Sankar Subramanian14, Toni Gabaldón15, Salvador Capella-Gutierrez, Jaime Huerta-Cepas, Bhanu Rekepalli16, Bhanu Rekepalli17, Kasper Munch18, Mikkel H. Schierup18, Bent E. K. Lindow11, Wesley C. Warren19, David A. Ray, Richard E. Green20, Michael William Bruford21, Xiangjiang Zhan22, Xiangjiang Zhan21, Andrew Dixon, Shengbin Li6, Ning Li23, Yinhua Huang23, Elizabeth P. Derryberry24, Elizabeth P. Derryberry25, Mads F. Bertelsen26, Frederick H. Sheldon24, Robb T. Brumfield24, Claudio V. Mello27, Claudio V. Mello28, Peter V. Lovell28, Morgan Wirthlin28, Maria Paula Cruz Schneider27, Francisco Prosdocimi27, José Alfredo Samaniego11, Amhed Missael Vargas Velazquez11, Alonzo Alfaro-Núñez11, Paula F. Campos11, Bent O. Petersen29, Thomas Sicheritz-Pontén29, An Pas, Thomas L. Bailey, R. Paul Scofield30, Michael Bunce31, David M. Lambert14, Qi Zhou, Polina L. Perelman32, Amy C. Driskell33, Beth Shapiro20, Zijun Xiong, Yongli Zeng, Shiping Liu, Zhenyu Li, Binghang Liu, Kui Wu, Jin Xiao, Xiong Yinqi, Quiemei Zheng, Yong Zhang, Huanming Yang, Jian Wang, Linnéa Smeds10, Frank E. Rheindt34, Michael J. Braun35, Jon Fjeldså11, Ludovic Orlando11, F. Keith Barker5, Knud A. Jønsson5, Warren E. Johnson33, Klaus-Peter Koepfli33, Stephen J. O'Brien36, David Haussler, Oliver A. Ryder, Carsten Rahbek5, Eske Willerslev11, Gary R. Graves5, Gary R. Graves33, Travis C. Glenn13, John E. McCormack37, Dave Burt38, Hans Ellegren10, Per Alström, Scott V. Edwards39, Alexandros Stamatakis3, David P. Mindell40, Joel Cracraft5, Edward L. Braun41, Tandy Warnow42, Tandy Warnow2, Wang Jun, M. Thomas P. Gilbert5, M. Thomas P. Gilbert31, Guojie Zhang4, Guojie Zhang11 
12 Dec 2014-Science
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

1,624 citations