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Characteristics of the draft genome of ＂Candidatus Arsenophonus nilaparvatae＂, a facultative endosymbiont of Nilaparvata lugens

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Insect Science 2016年第3期23卷 478-486页

作者： Hai-Wei Fan Jia-Bao Lu Yu-Xuan Ye Xiao-Ping Yu Chuan-Xi Zhang Institute of Insect Science Zhejiang University College of Life Science China Jiliang University Hangzhou China

There exists a kind of symbiotic bacterium named ＂Candidatus Arsenophonus nilaparvatae＂ in the brown planthopper （BPH）, Nilaparvata lugens. After being filtered and assembled from the BPH genome sequencing project, the genome sequence of this bacterial symbiont was obtained. After initial analysis based on the genome, we have found its potential role to synthesize B vitamins for the host. In order to better understand the lifestyle and the genomic changes of this symbiotic bacterium after the symbiotic relationship was established, we further report the characteristics of this draft genome. Compared with several other related bacteria, ＂Candidatus Arsenophonus nilaparvatae＂ has proven to be a facultative endosymbiont at the genomic level. Concurrently, the presence of fimbriae and flagella formation related genes indicates this maternally transmitted endosymbiont is most likely to retain the capacity to invade new hosts. Through further analysis of annotated gene sets, we also find evidence of genome reduction in its secretion system and metabolic pathways. These findings reflect its evolutionary trend to be an obligate one and enable a deeper study of microbe-insect interactions.

关键词： endosymbiont evolution facultative genome Nilaparvata lugens

genome-Wide Sequencing of 41 Rice （Oryza sativa L.） Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

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Molecular Plant 2016年第7期9卷 1078-1081页

作者： Li, Guotian Chern, Mawsheng Jain, Rashmi Martin, Joel A. Schackwitz, Wendy S. Jiang, Liangrong Vega-Sanchez, Miguel E. Lipzen, Anna M. Barry, Kerrie W. Schmutz, Jeremy Ronald, Pamela C. Univ Calif Davis Dept Plant Pathol Davis CA 95616 USA Univ Calif Davis Genome Ctr Davis CA 95616 USA Lawrence Berkeley Natl Lab Feedstocks Div Joint BioEnergy Inst Berkeley CA 94720 USA US DOE Joint Genome Inst Walnut Creek CA 94598 USA Xiamen Univ Sch Life Sci Xiamen 361102 Peoples R China HudsonAlpha Inst Biotechnol Huntsville AL 35806 USA Monsanto Co Chesterfield Village Campus Chesterfield MO 63017 USA

Fast-neutron （FN） irradiation has been used to create mutagen- ized collections of many plant species （Bolon et al., 2014）, FN- induced mutagenesis has clear advantages： it is an efficient means of saturating the genome, and it does not involve time- consuming plant transformation or tissue culture. In rice, most mutant collections, although highly valuable, were generated us- ing either T-DNA insertion or transposon tagging approaches that often induce mutations unlinked to the insertion and complicating analysis （Wang et al., 2013）. Another disadvantage of some of these collections is that they were created in rice varieties that are photoperiod-sensitive and often have long generation times.

关键词： mutagenesis genome valuable

MicroRNA-135a Modulates Hepatitis C Virus genome Replication through Downregulation of Host Antiviral Factors

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Virologica Sinica 2019年第2期34卷 197-210页

作者： Catherine Sodroski Brianna Lowey Laura Hertz T.Jake Liang Qisheng Li Liver Diseases Branch National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health

Cellular microRNAs(miRNAs) have been shown to modulate HCV infection via directly acting on the viral genome or indirectly through targeting the virus-associated host factors. Recently we generated a comprehensive map of HCV–miRNA interactions through genome-wide miRNA functional screens and transcriptomics analyses. Many previously unappreciated cellular miRNAs were identified to be involved in HCV infection, including miR-135a, a human cancerrelated miRNA. In the present study, we investigated the role of miR-135a in regulating HCV life cycle and showed that it preferentially enhances viral genome replication. Bioinformatics-based integrative analyses and subsequent functional assays revealed three antiviral host factors, including receptor interacting serine/threonine kinase 2(RIPK2), myeloid differentiation primary response 88(MYD88), and C-X-C motif chemokine ligand 12(CXCL12), as bona fide targets of miR-135a. These genes have been shown to inhibit HCV infection at the RNA replication stage. Our data demonstrated that repression of key host restriction factors mediated the proviral effect of miR-135a on HCV propagation. In addition,miR-135a hepatic abundance is upregulated by HCV infection in both cultured hepatocytes and human liver, likely mediating a more favorable environment for viral replication and possibly contributing to HCV-induced liver *** results provide novel insights into HCV–host interactions and unveil molecular pathways linking miRNA biology to HCV pathogenesis.

关键词： Hepatitis C virus (HCV) genome replication Virus-host interactions miR-135a Antiviral factors

Elimination of a Retrotransposon for Quenching genome Instability in Modern Rice

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Molecular Plant 2019年第10期12卷 1395-1407页

作者： Yu Peng Yingying Zhang Yijie Gui Dong An Junzhong Liu Xun Xu Qun Li Junmin Wang Wen Wang Chunhai Shi Longjiang Fan Baorong Lu Yiwen Deng Sheng Teng Zuhua He National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China The Protected Horticulture Institute Shanghai Academy of Agricultural SciencesShanghai 201403China School of Life Sciences Fudan UniversityShanghai 200433China College of Agriculture and Biotechnology Zhejiang UniversityHangzhou 310058China Kunming Institute of Zoology Chinese Academy of SciencesKunming 650223China Zhejiang Academy of Agricultural Sciences Hangzhou 310021China

Transposable elements(TEs)constitute the most abundant portions of plant genomes and can dramatically shape host genomes during plant *** also play important roles in crop ***,whether TEs themselves are also selected during crop domestication has remained ***,we identify an active long terminal repeat(LTR)retrotransposon,HUO,as a potential target of selection during rice domestication and *** is a low-copy-number LTR retrotransposon,and is active under natural growth conditions and transmitted through male gametogenesis,preferentially inserting into genomic regions capable of *** exists in all wild rice accessions and about half of the archaeological rice grains(1200–7000 years ago)and landraces surveyed,but is absent in almost all modern varieties,indicating its gradual elimination during rice domestication and *** analyses showed that HUO is subjected to strict gene silencing through the RNA-directed DNA methylation *** results also suggest that multiple HUO copies may trigger genomic instability through altering genome-wide DNA methylation and small RNA biogenesis and changing global gene expression,resulting in decreased disease resistance and yield,coinciding with its elimination during rice ***,our study suggests that negative selection of an active retrotransposon might be important for genome stability during crop domestication and breeding.

关键词： LTR retrotransposon genome instability evolution domestication resistance

Wheat genome editing expedited by efficient transformation techniques:Progress and perspectives

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The Crop Journal 2018年第1期6卷 22-31页

作者： Ke Wang Bisma Riaz Xingguo Ye Institute of Crop Science Chinese Academy of Agricultural Sciences

genome editing is one of the most promising biotechnologies to improve crop *** wheat is a staple food for mankind. In the past few decades both basic and applied research on common wheat has lagged behind other crop species due to its complex,polyploid genome and difficulties in genetic transformation. Recent breakthroughs in wheat transformation permit a revolution in wheat biotechnology. In this review, we summarize recent progress in wheat genetic transformation and its potential for wheat improvement. We then review recent progress in plant genome editing, which is now readily available in wheat. We also discuss measures to further increase transformation efficiency and potential applications of genome editing in wheat. We propose that, together with a high quality reference genome, the time for efficient genetic engineering and functionality studies in common wheat has arrived.

关键词： Triticum aestivum genome editing CRISPR/Cas9 Genetic transformation

Tung Tree(Vernicia fordii) genome Provides A Resource for Understanding genome Evolution and Improved Oil Production

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Genomics, Proteomics & Bioinformatics 2019年第6期17卷 558-575页

作者： Lin Zhang Meilan Liu Hongxu Long Wei Dong Asher Pasha Eddi Esteban Wenying Li Xiaoming Yang Ze Li Aixia Song Duo Ran Guang Zhao Yanling Zeng Hao Chen Ming Zou Jingjing Li Fan Liang Meili Xie Jiang Hu Depeng Wang Heping Cao Nicholas J.Provart Liangsheng Zhang Xiaofeng Tan Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees Ministry of EducationCentral South University of Forestry and TechnologyChangsha 410004China Key Lab of Non-wood Forest Products of State Forestry Administration College of ForestryCentral South University of Forestry and TechnologyChangsha 410004China Department of Cell and Systems Biology/Centre for the Analysis of genome Evolution and Function University of TorontoTorontoOntario M5S 3B2Canada State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China College of Forestry Nanjing Forestry UniversityNanjing 210037China Nextomics Biosciences Co. Wuhan 430073China Oil Crop Research Institute Chinese Academy of Agricultural SciencesWuhan 430062China US Department of Agriculture Agricultural Research ServiceSouthern Regional Research CenterNew OrleansLA 70124USA

Tung tree(Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. Here, we report a high-quality chromosome-scale genome sequence of tung tree. The genome sequence was assembled by combining Illumina short reads, Pacific Biosciences single-molecule real-time long reads, and Hi-C sequencing data. The size of tung tree genome is 1.12 Gb, with 28,422 predicted genes and over 73% repeat sequences. The V. fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca. 34.55 million years of evolutionary history of the tung tree lineage. Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms. The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance. Further, 651 oil-related genes were identified, 88 of which are predicted to be directly involved in tung oil biosynthesis. Relatively few phosphoenolpyruvate carboxykinase genes, and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed. The tung tree genome constitutes a valuable resource for understanding genome evolution, as well as for molecular breeding and genetic improvements for oil production.

关键词： Tung tree genome Tung oil genome evolution Electronic fluorescent pictographic browser Oil biosynthesis

A reference-grade genome assembly for Gossypium bickii and insights into its genome evolution and formation of pigment glands and gossypol

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Plant Communications 2023年第1期4卷 13-27页

作者： Kuang Sheng Yue Sun Meng Liu Yuefen Cao Yifei Han Cheng Li Uzair Muhammad Muhammad Khan Daud Wanru Wang Huazu Li Samrana Samrana Yixuan Hui Shuijin Zhu Jinhong Chen Tianlun Zhao Institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina Novogene Bioinformatics Institute BeijingChina Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Department of Biotechnology and Genetic Engineering Kohat University of Science and TechnologyKohatPakistan Hainan Institute Zhejiang UniversitySanyaChina

The pigment gland is a morphological characteristic of Gossypium and its related *** bickii(G_(1))is characterized by delayed pigment gland morphogenesis in the *** this study,a referencegrade genome of G_(1) was generated,and comparative genomics analysis showed that G_(1) was closest to Gossypium australe(G_(2)),followed by A-and D-genome *** large fragment translocations in chromosomes 5 and 13 were detected between the G genome and other Gossypiumgenomes and were unique to the G_(1) and G_(2) *** with the G_(2) genome,two large fragment inversions in chromosomes 12 and 13 were detected in G_(1).According to the phylogeny,divergence time,and similarity analysis of nuclear andchloroplast genomes,G_(1)was formedby hybridization between Gossypium sturtianum(C_(1))and a common ancestor of G_(2) and Gossypiumnelsonii(G_(3)).The coordinated expression patterns of pigment gland formation(GoPGF)and gossypol biosynthesis genes in G_(1) were verified to be consistent with its phenotype,and nine genes thatwere related to theprocessof pigmentgland formationwere *** gene,GbiCYP76B6,regulated by GoPGF,was found to affect gossypol *** findings offer insights into the origin and evolution of G_(1) and its mechanism of pigment gland formation and gossypol biosynthesis.

关键词： Gossypium bickii genome evolution gossypol pigment glands

Phylogenetic clusters of rhizobia revealed by genome structures

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Science China(Life Sciences) 2004年第3期47卷 268-278页

作者： ZHENG Junfang1, LIU Guirong1,2, ZHU Wanfu1, ZHOU Yuguang3 & LIU Shulin1,2 1. Department of Microbiology, School of Basic Medical Sciences, Peking University, Beijing 100083, China 2. Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, ABT2N 4N1, Canada 3. Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China Department of Microbiology School of Basic Medical Sciences Peking University Beijing China Department of Microbiology and Infectious Diseases University of Calgary Calgary Canada Institute of Microbiology Chinese Academy of Sciences Beijing China

Rhizobia, bacteria that fix atmospheric nitrogen, are important agricultural resources. In order to establish the evolutionary relationships among rhizobia isolated from different geo-graphic regions and different plant hosts for systematic studies, we evaluated the use of physical structure of the rhizobial genomes as a phylogenetic marker to categorize these bacteria. In this work, we analyzed the features of genome structures of 64 rhizobial strains. These rhizobial strains were divided into 21 phylogenetic clusters according to the features of genome structures evaluated by the endonuclease I-CeuI. These clusters were supported by 16S rRNA compari-sons and genomic sequences of four rhizobial strains, but they are largely different from those based on the current taxonomic scheme (except 16S rRNA).

关键词： rhizobia, phylogeny, genome structure.

The rough-toothed dolphin genome provides new insights into the genetic mechanism of its rough teeth

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Integrative Zoology 2023年第4期18卷 601-615页

作者： Xin HUANG Huizhong FAN Wenliang ZHOU Guang YANG Fuwen WEI CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina Center for Evolution and Conservation Biology Southern Marine Science and Engineering Guangdong Laboratory(Guangzhou)GuangzhouChina

The rough-toothed dolphin(Steno bredanensis)is characterized by having teeth covered inﬁnely wrinkled vertical ridges,which is a general manifestation of amelogenesis *** rough surfaces are hypothesized to be an evolutionary morphological trait of feeding adaptation to increase the dolphin’s grip on ***,we assembled a rough-toothed dolphin genome and performed the comparative genomic analysis to reveal the genetic basis of the special *** showed that genes related to enamel development or dental diseases have undergone diver-siﬁed adaptive changes that may shape the special enamel morphology of this dolphin species,including positive selection(CLDN19,PRKCE,SSUH2,and WDR72),rapid evolution(LAMB3),or unique amino acid substitutions(AMTN,ENAM,MMP20,and KLK4).Meanwhile,the historical demography of rough-toothed dolphin indicated several distinct populationﬂuctuations associated with climate *** genome-wide heterozygosity of this dolphin is in the middle of all published data for *** the population is considerable,there may be population or subspecies differentiation,and with the global warming and the increasing disturbance of human activities,we should pay more attention to protection in the ***,our study brings new insights into the genetic mechanisms that may have driven the evolution of the special enamel morphology in rough-toothed dolphins and provides theﬁrst results of genetic heterozygosity and population historical dynamics of this species,which have important guiding implications for the conservation of this dolphin species.

关键词： adaptive evolution amelogenesis imperfecta cetaceans genome rough-toothed dolphin