1
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Sun C, Xie YH, Li Z, Liu YJ, Sun XM, Li JJ, Quan WP, Zeng QY, Van de Peer Y, Zhang SG. The Larix kaempferi genome reveals new insights into wood properties. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1364-1373. [PMID: 35442564 DOI: 10.1111/jipb.13265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.
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Affiliation(s)
- Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Yan-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Jing-Jing Li
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Wei-Peng Quan
- Nextomics Biosciences Co., Ltd, Wuhan, 430073, China
| | - Qing-Yin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
- Department of Biochemistry, Genetics and Microbiology, Pretoria, South Africa
| | - Shou-Gong Zhang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Chen Z, Zhang Z, Zhang H, Li K, Cai D, Zhao L, Liu J, Chen H. A pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize. Nat Commun 2022; 13:1993. [PMID: 35422051 PMCID: PMC9010485 DOI: 10.1038/s41467-022-29729-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022] Open
Abstract
Maize unilateral cross-incompatibility (UCI) that causes non-Mendelian segregation ratios has been documented for more than a century. Ga1, Ga2, and Tcb1 are three major UCI systems, described but not fully understood. Here, we report comprehensive genetic studies on the Ga2 locus and map-based cloning of the tightly linked male determinant ZmGa2P and female determinant ZmGa2F that govern pollen-silk compatibility among different maize genotypes. Both determinants encode putative pectin methylesterases (PME). A significantly higher degree of methyl esterification is detected in the apical region of pollen tubes growing in incompatible silks. No direct interaction between ZmGa2P and ZmGa2F is detected in the yeast two-hybrid system implying a distinct mechanism from that of self-incompatibility (SI). We also demonstrate the feasibility of Ga2 as a reproductive barrier in commercial breeding programs and stacking Ga2 with Ga1 could strengthen the UCI market potentials. Unilaterial cross-incompatibility (UCI) systems are regulated by a male-female gene pair that are genetically linked, but no pair of the male and female determinants has been isolated so far. Here, the authors report the cloning of a pair of pectin methylesterases encoding genes at the Ga2 locus confer UCI in maize.
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3
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Pan L, Lu Z, Yan L, Zeng W, Shen Z, Yu M, Bu L, Cui G, Niu L, Wang Z. NLR1 is a strong candidate for the Rm3 dominant green peach aphid (Myzus persicae) resistance trait in peach. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1357-1369. [PMID: 35022695 DOI: 10.1093/jxb/erab506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 11/19/2021] [Indexed: 06/14/2023]
Abstract
The green peach aphid (GPA), Myzus persicae, is a polyphagous, sap-sucking aphid and a vector of many plant viruses. In peach, Prunus persica, three individual dominant GPA resistance loci have been genetically defined (Rm1-3), but knowledge of the underlying genes is limited. In this study, we focused on the Rm3 locus. Bulk segregant analysis (BSA) mapping in segregating progeny populations delimited Rm3 to an interval spanning 160 kb containing 21 genes on chromosome 1. RNA-seq data provided no evidence of candidate genes, but chromosomal structural variations were predicted around a nucleotide-binding site-leucine-rich repeat (NLR) gene (ppa000596m) within the Rm3 fine-mapping interval. Following bacterial artificial chromosome (BAC) library construction for a GPA-resistant peach cultivar and the sequencing of three target BAC clones, a chromosomal structural variation encompassing two novel TIR-NLR-class disease resistance (R) protein-coding genes was identified, and the expressed NLR gene (NLR1) was identified as a candidate for M. persicae resistance. Consistent with its proposed role in controlling GPA resistance, NLR1 was only expressed in the leaves of resistant peach phenotypes. A molecular marker that was designed based on the NLR1 sequence co-segregated with the GPA-resistant phenotype in four segregating populations, 162 peach cultivars, and 14 wild relatives, demonstrating the dominant inheritance of the Rm3 locus. Our findings can be exploited to facilitate future breeding for GPA-resistance in peach.
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Affiliation(s)
- Lei Pan
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhenhua Lu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lele Yan
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenfang Zeng
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhijun Shen
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Mingliang Yu
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Lulu Bu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Guochao Cui
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Liang Niu
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Zhiqiang Wang
- Key Laboratory of Fruit Breeding Technology of the Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Xu W, Liang M, Yang X, Wang H, Luo M. Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline. BMC Genom Data 2021; 22:46. [PMID: 34724898 PMCID: PMC8561967 DOI: 10.1186/s12863-021-01003-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Background With high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resource is of great importance. Results Herein, we constructed a BAC library for broomcorn millet, generated BAC end sequences based on the clone-array pooled shotgun sequencing strategy and Illumina sequencing technology, and integrated BAC clones into genome by a novel pipeline for BAC end profiling. The BAC library consisted of 76,023 clones with an average insert length of 123.48 Kb, covering about 9.9-fold of the 850 Mb genome. Of 9216 clones tested using our pipeline, 8262 clones were mapped on the broomcorn millet cultivar longmi4 genome. These mapped clones covered 308 of the 829 gaps left by the genome. To our knowledge, this is the only BAC resource for broomcorn millet. Conclusions We constructed a high-quality BAC libraray for broomcorn millet and designed a novel pipeline for BAC end profiling. BAC clones can be browsed and obtained from our website (http://eightstarsbio.com/gresource/JBrowse-1.16.5/index.html). The high-quality BAC clones mapped on genome in this study will provide a powerful genomic resource for genome gap filling, complex segment sequencing, FISH, functional research and genetic engineering of broomcorn millet. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01003-z.
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Affiliation(s)
- Wei Xu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mengjie Liang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xue Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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5
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She W, Ye W, Cheng A, Liu X, Tang J, Lan Y, Chen F, Qian PY. Discovery, Bioactivity Evaluation, Biosynthetic Gene Cluster Identification, and Heterologous Expression of Novel Albofungin Derivatives. Front Microbiol 2021; 12:635268. [PMID: 33633715 PMCID: PMC7902042 DOI: 10.3389/fmicb.2021.635268] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/08/2021] [Indexed: 01/07/2023] Open
Abstract
The crude extract of Streptomyces chrestomyceticus exhibited strong and broad activities against most “ESKAPE pathogens.” We conducted a comprehensive chemical investigation for secondary metabolites from the S. chrestomyceticus strain and identified two novel albofungin (alb) derivatives, i.e., albofungins A (1) and B (2), along with two known compounds, i.e., albofungin (3) and chloroalbofungin (4). The chemical structures of the novel compounds were elucidated using HRMS, 1D and 2D NMR, and electronic circular dichroism spectroscopy. The draft genome of S. chrestomyceticus was sequenced, and a 72 kb albofungin (alb) gene cluster with 72 open reading frames encoding type II polyketide synthases (PKSs), regulators, and transporters, and tailoring enzymes were identified using bioinformatics analysis. The alb gene cluster was confirmed using the heterologous expression in Streptomyces coelicolor, which successfully produced the compounds 3 and 4. Furthermore, compounds 1–4 displayed remarkable activities against Gram-positive bacteria and antitumor activities toward various cancer cells. Notably, compounds 1 and 3 showed potent activities against Gram-negative pathogenic bacteria. The terminal deoxynucleotidyl transferase (dUTP) nick-end labeling and flow cytometry analysis verified that compound 1 inhibited cancer cell proliferation by inducing cellular apoptosis. These results indicated that albofungins might be potential candidates for the development of antibiotics and antitumor drugs.
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Affiliation(s)
- Weiyi She
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Wenkang Ye
- SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, China.,Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Aifang Cheng
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Xin Liu
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Jianwei Tang
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Yi Lan
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
| | - Feng Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Pei-Yuan Qian
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong, Laboratory (Guangzhou), Hong Kong University of Science and Technology, Hong Kong, China.,Division of Ocean Science, Hong Kong University of Science and Technology, Hong Kong, China
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6
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Zhang M, Li Z, Li J, Huang T, Peng G, Tang W, Yi G, Zhang L, Song Y, Liu T, Hu X, Ren L, Liu H, Butler JE, Han H, Zhao Y. Revisiting the Pig IGHC Gene Locus in Different Breeds Uncovers Nine Distinct IGHG Genes. THE JOURNAL OF IMMUNOLOGY 2020; 205:2137-2145. [PMID: 32929042 DOI: 10.4049/jimmunol.1901483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/13/2020] [Indexed: 11/19/2022]
Abstract
IgG subclass diversification is common in placental mammals. It has been well documented in humans and mice that different IgG subclasses, with diversified functions, synergistically regulate humoral immunity. However, our knowledge on the genomic and functional diversification of IgG subclasses in the pig, a mammalian species with high agricultural and biomedical importance, is incomplete. Using bacterial artificial chromosome sequencing and newly assembled genomes generated by the PacBio sequencing approach, we characterized and mapped the IgH C region gene locus in three indigenous Chinese breeds (Erhualian, Xiang, and Luchuan) and compared them to that of Duroc. Our data revealed that IGHG genes in Chinese pigs differ from the Duroc, whereas the IGHM, IGHD, IGHA, and IGHE genes were all single copy and highly conserved in the pig breeds examined. Most striking were differences in numbers of IGHG genes: there are seven genes in Erhualian pigs, six in the Duroc, but only five in Xiang pigs. Phylogenetic analysis suggested that all reported porcine IGHG genes could be classified into nine subclasses: IGHG1, IGHG2a, IGHG2b, IGHG2c, IGHG3, IGHG4, IGHG5a, IGHG5b, and IGHG5c. Using sequence information, we developed a mouse mAb specific for IgG3. This study offers a starting point to investigate the structure-function relationship of IgG subclasses in pigs.
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Affiliation(s)
- Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Zhenrong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jingying Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tian Huang
- School of Life Sciences, Henan University, Kaifeng 475004, People's Republic of China
| | - Gaochuang Peng
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Wenda Tang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Guoqiang Yi
- Research Centre for Animal Genome, Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; and
| | - Yu Song
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Tianran Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Liming Ren
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China; and
| | - John E Butler
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA 52242
| | - Haitang Han
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
| | - Yaofeng Zhao
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing 100193, People's Republic of China;
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7
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Wang H, Sun S, Ge W, Zhao L, Hou B, Wang K, Lyu Z, Chen L, Xu S, Guo J, Li M, Su P, Li X, Wang G, Bo C, Fang X, Zhuang W, Cheng X, Wu J, Dong L, Chen W, Li W, Xiao G, Zhao J, Hao Y, Xu Y, Gao Y, Liu W, Liu Y, Yin H, Li J, Li X, Zhao Y, Wang X, Ni F, Ma X, Li A, Xu SS, Bai G, Nevo E, Gao C, Ohm H, Kong L. Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science 2020; 368:science.aba5435. [PMID: 32273397 DOI: 10.1126/science.aba5435] [Citation(s) in RCA: 304] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/26/2020] [Indexed: 12/22/2022]
Abstract
Fusarium head blight (FHB), a fungal disease caused by Fusarium species that produce food toxins, currently devastates wheat production worldwide, yet few resistance resources have been discovered in wheat germplasm. Here, we cloned the FHB resistance gene Fhb7 by assembling the genome of Thinopyrum elongatum, a species used in wheat distant hybridization breeding. Fhb7 encodes a glutathione S-transferase (GST) and confers broad resistance to Fusarium species by detoxifying trichothecenes through de-epoxidation. Fhb7 GST homologs are absent in plants, and our evidence supports that Th. elongatum has gained Fhb7 through horizontal gene transfer (HGT) from an endophytic Epichloë species. Fhb7 introgressions in wheat confers resistance to both FHB and crown rot in diverse wheat backgrounds without yield penalty, providing a solution for Fusarium resistance breeding.
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Affiliation(s)
- Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Silong Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenyang Ge
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Lanfei Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Bingqian Hou
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing 100083, PR China
| | - Zhongfan Lyu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing 100083, PR China
| | - Shoushen Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jun Guo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, PR China
| | - Min Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Peisen Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xuefeng Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guiping Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Cunyao Bo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xiaojian Fang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenwen Zhuang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xinxin Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jianwen Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Luhao Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wen Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guilian Xiao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jinxiao Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Ying Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yu Gao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenjing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yanhe Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Huayan Yin
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jiazhu Li
- College of Chemistry and Chemical Engineering, Yantai University, Yantai, Shandong 264005, PR China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xin Ma
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Herbert Ohm
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
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8
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Dai Z, Li T, Li J, Han Z, Pan Y, Tang S, Diao X, Luo M. High-throughput long paired-end sequencing of a Fosmid library by PacBio. PLANT METHODS 2019; 15:142. [PMID: 31788019 PMCID: PMC6878638 DOI: 10.1186/s13007-019-0525-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries. RESULTS A Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2-3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5-10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations. CONCLUSIONS We developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.
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Affiliation(s)
- Zhaozhao Dai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jiadong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhifei Han
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yonglong Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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9
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Ma KY, Yu SH, Du YX, Feng SQ, Qiu LJ, Ke DY, Luo MZ, Qiu GF. Construction of a Genomic Bacterial Artificial Chromosome (BAC) Library for the Prawn Macrobrachium rosenbergii and Initial Analysis of ZW Chromosome-Derived BAC Inserts. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:206-216. [PMID: 30632018 DOI: 10.1007/s10126-018-09873-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/27/2018] [Indexed: 06/09/2023]
Abstract
Knowledge on sex determination has proven valuable for commercial production of the prawn Macrobrachium rosenbergii due to sex dimorphism of the male and female individuals. Previous studies indicated that prawn sex is determined by a ZW-ZZ chromosomal system, but no genomic information is available for the sex chromosome. Herein, we constructed a genomic bacterial artificial chromosome (BAC) library and identified the ZW-derived BAC clones for initial analysis of the sex chromosomal DNA sequence. The arrayed BAC library contains 200,448 clones with average insert size of 115.4 kb, corresponding to ∼ 4× coverage of the estimated 5.38 Gb genome. Based on a short female-specific marker, a Z- and a W-fragment were retrieved with the genomic walking method. Screening the BAC library using a ZW-specific marker as probe resulted in 12 positive clones. From these, a Z-derived (P331M17) and a W-derived (P122G2) BAC clones were randomly selected and sequenced by PacBio method. We report the construction of a large insert, deep-coverage, and high-quality BAC library for M. rosenbergii that provides a useful resource for positional cloning of target genes, genomic organization, and comparative genomics analysis. Our study not only confirmed the ZW/ZZ system but also discovered sex-linked genes on ZW chromosomes for the first time, contributing to a comprehensive understanding of the genomic structure of sex chromosomes in M. rosenbergii.
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Affiliation(s)
- Ke-Yi Ma
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Shu-Hui Yu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Yu-Xin Du
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Shi-Qing Feng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Liang-Jie Qiu
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Dai-Yi Ke
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China
| | - Mei-Zhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, 430070, Wuhan, People's Republic of China
| | - Gao-Feng Qiu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, National Demonstration Center for Experimental Fisheries Science Education, Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, 201306, Shanghai, People's Republic of China.
- College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Pudong New Area, 201306, Shanghai, People's Republic of China.
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10
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Dan C, Lin Q, Gong G, Yang T, Xiong S, Xiong Y, Huang P, Gui JF, Mei J. A novel PDZ domain-containing gene is essential for male sex differentiation and maintenance in yellow catfish (Pelteobagrus fulvidraco). Sci Bull (Beijing) 2018; 63:1420-1430. [PMID: 36658982 DOI: 10.1016/j.scib.2018.08.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 07/20/2018] [Accepted: 08/15/2018] [Indexed: 01/21/2023]
Abstract
The sex-determining genes are found to be variable among different fish species. Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture fish species in China with XX/XY sex-determining type. Recently, YY super-male yellow catfish has been successfully produced by combining hormonal-induced sex reversal method with sex chromosome-linked markers. Here, we identified a novel PDZ domain-containing gene in yellow catfish designated as pfpdz1, in whose intron the sex-linked marker was located. The coding sequence of pfpdz1 in Y chromosome was identical to that in X chromosome except a missense SNP (A/T) that changes an amino acid (E8V) in the N-terminal region. Pfpdz1 displayed male-specific expression during sex differentiation. Overexpression of pfpdz1 using additive transgenesis induces XX ovary to differentiate into testis-like tissue, while the targeted inactivation of pfpdz1 in Y chromosome using CRISPR/Cas9-mediated mutagenesis triggers ovarian differentiation. Furthermore, we demonstrated that pfpdz1 initiates testicular differentiation through upregulating expression of amh, dmrt1 and sox9a1, as well as downregulating expression of cyp19a1, foxl2 and wnt4. Our data provide functional evidence that pfpdz1 is significant for male differentiation and maintenance in yellow catfish.
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Affiliation(s)
- Cheng Dan
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiaohong Lin
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaorui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Tianyi Yang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuting Xiong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Xiong
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Peipei Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, China.
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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11
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A PECTIN METHYLESTERASE gene at the maize Ga1 locus confers male function in unilateral cross-incompatibility. Nat Commun 2018; 9:3678. [PMID: 30202064 PMCID: PMC6131150 DOI: 10.1038/s41467-018-06139-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/04/2018] [Indexed: 11/08/2022] Open
Abstract
Unilateral cross-incompatibility (UCI) is a unidirectional inter/intra-population reproductive barrier when both parents are self-compatible. Maize Gametophyte factor1 (Ga1) is an intraspecific UCI system and has been utilized in breeding. However, the mechanism underlying maize UCI specificity has remained mysterious for decades. Here, we report the cloning of ZmGa1P, a pollen-expressed PECTIN METHYLESTERASE (PME) gene at the Ga1 locus that can confer the male function in the maize UCI system. Homozygous transgenic plants expressing ZmGa1P in a ga1 background can fertilize Ga1-S plants and can be fertilized by pollen of ga1 plants. ZmGa1P protein is predominantly localized to the apex of growing pollen tubes and may interact with another pollen-specific PME protein, ZmPME10-1, to maintain the state of pectin methylesterification required for pollen tube growth in Ga1-S silks. Our study discloses a PME-mediated UCI mechanism and provides a tool to manipulate hybrid breeding. Unilateral cross-incompatibility between certain varieties of maize prevents cross-fertilization and can facilitate hybrid breeding. Here the authors show that a PECTIN METHYLESTERASE gene is able to overcome this reproductive barrier and confer fertility when expressed in pollen of the male parent.
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12
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Tark-Dame M, Weber B, de Sain M, Anggoro DT, Bader R, Walmsley A, Oka R, Stam M. Generating Transgenic Plants with Single-copy Insertions Using BIBAC-GW Binary Vector. J Vis Exp 2018. [PMID: 29658919 DOI: 10.3791/57295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
When generating transgenic plants, generally the objective is to have stable expression of a transgene. This requires a single, intact integration of the transgene, as multi-copy integrations are often subjected to gene silencing. The Gateway-compatible binary vector based on bacterial artificial chromosomes (pBIBAC-GW), like other pBIBAC derivatives, allows the insertion of single-copy transgenes with high efficiency. As an improvement to the original pBIBAC, a Gateway cassette has been cloned into pBIBAC-GW, so that the sequences of interest can now be easily incorporated into the vector transfer DNA (T-DNA) by Gateway cloning. Commonly, the transformation with pBIBAC-GW results in an efficiency of 0.2-0.5%, whereby half of the transgenics carry an intact single-copy integration of the T-DNA. The pBIBAC-GW vectors are available with resistance to Glufosinate-ammonium or DsRed fluorescence in seed coats for selection in plants, and with resistance to kanamycin as a selection in bacteria. Here, a series of protocols is presented that guide the reader through the process of generating transgenic plants using pBIBAC-GW: starting from recombining the sequences of interest into the pBIBAC-GW vector of choice, to plant transformation with Agrobacterium, selection of the transgenics, and testing the plants for intactness and copy number of the inserts using DNA blotting. Attention is given to designing a DNA blotting strategy to recognize single- and multi-copy integrations at single and multiple loci.
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Affiliation(s)
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Mara de Sain
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | | | - Rechien Bader
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Aimee Walmsley
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Rurika Oka
- Swammerdam Institute for Life Sciences, University of Amsterdam
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam;
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13
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Partier A, Gay G, Tassy C, Beckert M, Feuillet C, Barret P. Molecular and FISH analyses of a 53-kbp intact DNA fragment inserted by biolistics in wheat (Triticum aestivum L.) genome. PLANT CELL REPORTS 2017; 36:1547-1559. [PMID: 28667403 DOI: 10.1007/s00299-017-2173-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
A large, 53-kbp, intact DNA fragment was inserted into the wheat ( Triticum aestivum L.) genome. FISH analyses of individual transgenic events revealed multiple insertions of intact fragments. Transferring large intact DNA fragments containing clusters of resistance genes or complete metabolic pathways into the wheat genome remains a challenge. In a previous work, we showed that the use of dephosphorylated cassettes for wheat transformation enabled the production of simple integration patterns. Here, we used the same technology to produce a cassette containing a 44-kb Arabidopsis thaliana BAC, flanked by one selection gene and one reporter gene. This 53-kb linear cassette was integrated in the bread wheat (Triticum aestivum L.) genome by biolistic transformation. Our results showed that transgenic plants harboring the entire cassette were generated. The inheritability of the cassette was demonstrated in the T1 and T2 generation. Surprisingly, FISH analysis performed on T1 progeny of independent events identified double genomic insertions of intact fragments in non-homoeologous positions. Inheritability of these double insertions was demonstrated by FISH analysis of the T1 generation. Relative conclusions that can be drawn from molecular or FISH analysis are discussed along with future prospects of the engineering of large fragments for wheat transformation or genome editing.
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Affiliation(s)
- A Partier
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France
| | - G Gay
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France
| | - C Tassy
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France
| | - M Beckert
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France
| | - C Feuillet
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France
| | - P Barret
- Unité Mixte de Recherche 1095-Institut National de la Recherche Agronomique-Génétique, Diversité et Écophysiologie des Céréales, Domaine de Crouël, 63039, Clermont-Ferrand Cedex 2, France.
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14
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Galvão CE, Fragoso SP, de Oliveira CE, Forner O, Pereira RRB, Soares CO, Rosinha GMS. Identification of new Corynebacterium pseudotuberculosis antigens by immunoscreening of gene expression library. BMC Microbiol 2017; 17:202. [PMID: 28934943 PMCID: PMC5609009 DOI: 10.1186/s12866-017-1110-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/13/2017] [Indexed: 11/10/2022] Open
Abstract
Background Caseous lymphadenitis (CLA) is a disease that affects sheep, goats and occasionally humans. The etiologic agent is the Corynebacterium pseudotuberculosis bacillus. The objective of this study was to build a gene expression library from C. pseudotuberculosis and use immunoscreening to identify genes that encode potential antigenic proteins for the development of DNA and subunit vaccines against CLA. Results A wild strain of C. pseudotuberculosis was used for extraction and partial digestion of genomic DNA. Sequences between 1000 and 5000 base pairs (bp) were excised from the gel, purified, and the digested DNA fragments were joined to bacteriophage vector ZAP Express, packaged into phage and transfected into Escherichia coli. For immunoscreening a positive sheep sera pool and a negative sera pool for CLA were used. Four clones were identified that strongly reacted to sera. The clones were confirmed by polymerase chain reaction (PCR) followed by sequencing for genomic comparison of C. pseudotuberculosis in GenBank. The genes identified were dak2, fagA, fagB, NlpC/P60 protein family and LPxTG putative protein family. Conclusion Proteins of this type can be antigenic which could aid in the development of subunit or DNA vaccines against CLA as well as in the development of serological tests for diagnosis. Immunoscreening of the gene expression library was shown to be a sensitive and efficient technique to identify probable immunodominant genes.
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Affiliation(s)
| | | | | | - Odinéia Forner
- Federal University of Paraná (UFPR), Curitiba, PR, Brazil
| | | | - Cleber Oliveira Soares
- Embrapa Beef Cattle, Animal Health - Animal Genetic Engineering Laboratory, Campo Grande, MS, Brazil
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15
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Tan GY, Deng K, Liu X, Tao H, Chang Y, Chen J, Chen K, Sheng Z, Deng Z, Liu T. Heterologous Biosynthesis of Spinosad: An Omics-Guided Large Polyketide Synthase Gene Cluster Reconstitution in Streptomyces. ACS Synth Biol 2017; 6:995-1005. [PMID: 28264562 DOI: 10.1021/acssynbio.6b00330] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the advent of the genomics era, heterologous gene expression has been used extensively as a means of accessing natural products (NPs) from environmental DNA samples. However, the heterologous production of NPs often has very low efficiency or is unable to produce targeted NPs. Moreover, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in native producers, especially in the cases of genome mining, it is also difficult to rationally and systematically engineer synthetic pathways to improved NPs biosynthetic efficiency. In this study, various strategies ranging from heterologous production of a NP to subsequent application of omics-guided synthetic modules optimization for efficient biosynthesis of NPs with complex structure have been developed. Heterologous production of spinosyn in Streptomyces spp. has been demonstrated as an example of the application of these approaches. Combined with the targeted omics approach, several rate-limiting steps of spinosyn heterologous production in Streptomyces spp. have been revealed. Subsequent engineering work overcame three of selected rate-limiting steps, and the production of spinosad was increased step by step and finally reached 1460 μg/L, which is about 1000-fold higher than the original strain S. albus J1074 (C4I6-M). These results indicated that the omics platform developed in this work was a powerful tool for guiding the rational refactoring of heterologous biosynthetic pathway in Streptomyces host. Additionally, this work lays the foundation for further studies aimed at the more efficient production of spinosyn in a heterologous host. And the strategy developed in this study is expected to become readily adaptable to highly efficient heterologous production of other NPs with complex structure.
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Affiliation(s)
- Gao-Yi Tan
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- State
Key Laboratory of Bioreactor Engineering, School of Bioengineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Kunhua Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Xinhua Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Hui Tao
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Yingying Chang
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Jia Chen
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Kai Chen
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zhi Sheng
- Shenyang Research Institute of Chemical Industry Ltd., Co., SINOCHEM Group, Shengyang 110021, China
| | - Zixin Deng
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Tiangang Liu
- Key
Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan
University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China
- Hubei
Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
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16
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Ni F, Qi J, Hao Q, Lyu B, Luo MC, Wang Y, Chen F, Wang S, Zhang C, Epstein L, Zhao X, Wang H, Zhang X, Chen C, Sun L, Fu D. Wheat Ms2 encodes for an orphan protein that confers male sterility in grass species. Nat Commun 2017; 8:15121. [PMID: 28452349 PMCID: PMC5414350 DOI: 10.1038/ncomms15121] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/01/2017] [Indexed: 11/30/2022] Open
Abstract
Male sterility is a valuable trait for plant breeding and hybrid seed production. The dominant male-sterile gene Ms2 in common wheat has facilitated the release of hundreds of breeding lines and cultivars in China. Here, we describe the map-based cloning of the Ms2 gene and show that Ms2 confers male sterility in wheat, barley and Brachypodium. MS2 appears as an orphan gene within the Triticinae and expression of Ms2 in anthers is associated with insertion of a retroelement into the promoter. The cloning of Ms2 has substantial potential to assemble practical pipelines for recurrent selection and hybrid seed production in wheat.
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Affiliation(s)
- Fei Ni
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Juan Qi
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Qunqun Hao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Bo Lyu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Yan Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Fengjuan Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Shuyun Wang
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Chaozhong Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, California 95616, USA
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Honggang Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Cuixia Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Lanzhen Sun
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Daolin Fu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, China
- Department of Plant, Soil and Entomological Sciences, University of Idaho, Moscow, Idaho 83844, USA
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Deng Q, Zhou L, Luo M, Deng Z, Zhao C. Heterologous expression of Avermectins biosynthetic gene cluster by construction of a Bacterial Artificial Chromosome library of the producers. Synth Syst Biotechnol 2017; 2:59-64. [PMID: 29062962 PMCID: PMC5625734 DOI: 10.1016/j.synbio.2017.03.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 03/15/2017] [Accepted: 03/19/2017] [Indexed: 12/13/2022] Open
Abstract
Avermectins, a group of polyketide natural products, are widely used as anthelmintics in agriculture. Metabolic engineering and combinatorial biosynthesis were extensively employed to improve Avermectins production and create novel Avermectin derivatives, including Ivermectin and Doramectin. It is labor intensive and time cost to genetically manipulate Avermectins producer Streptomyces avermitilis in vivo. Cloning and heterologous expression of Avermectins biosynthetic gene cluster will make it possible to tailor the cluster in vitro. We constructed a Bacterial Artificial Chromosome (BAC) library of S. avermitilis ATCC 31267 with inserted DNA fragments ranged from 100 to 130 Kb. Five recombinant BAC clones which carried the Avermectins biosynthetic gene cluster ave (81 Kb in size) were screened out from the library. Then, ave was hetero-expressed in S. lividans. Three Avermectin components, A2a, B1a and A1a were detected from the cell extracts of recombinant strains. It will facilitate the development of Avermectin derivatives by polyketide synthase domain swapping and provide functional element for Avermectins synthetic biology study.
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Affiliation(s)
- Qian Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Li Zhou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430073, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Changming Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
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BIBAC-GW-based vectors for generating reporter lines for site-specific genome editing in planta. Plasmid 2016; 89:27-36. [PMID: 28034789 DOI: 10.1016/j.plasmid.2016.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/13/2016] [Accepted: 12/22/2016] [Indexed: 11/18/2022]
Abstract
When generating transgenic plants, one of the objectives is to achieve stable expression of the transgene. Transgene silencing can be avoided by single copy integration of the transgene. Binary systems that predominantly result in single copy integrations, such as BIBAC vectors, are also single-copy in E. coli, the organism in which the T-DNA to be delivered to the plant is assembled. Although a low-copy number is important for stable maintenance of large DNA fragments in E. coli, it hampers cloning into the vector due to a low DNA yield. Here we describe BIBAC vectors to which Gateway site-specific recombination sites are added. These sites provide a fast and easy introduction of sequences of interest into any vector. Our Gateway-compatible BIBAC vectors are available with two selectable markers for plants - resistance to Basta (BIBAC-BAR-GW) and DsRed fluorescence in the seed coat (BIBAC-RFP-GW). Using the BIBAC-BAR-GW vector we have generated different fluorescence-based reporter constructs that, when delivered to plant cells, can be used to study and optimize precise, template-dependent site-specific genome editing by CRISPR-Cas9, TALENs or ZFP-nuclease complexes, and oligonucleotide-directed mutagenesis. We have generated 59 reporter lines in A. thaliana with our reporter constructs, and for the lines carrying single T-DNA integrations (32 out of 59) we have determined the integrity of the integrations, their genomic locations and the expression level of the reporters. Similarly to its original counterpart, BIBAC-BAR-GW generates single T-DNA integrations in Arabidopsis with 50% efficiency, and 90% of those are intact. The reporter constructs in the independent transgenic lines exhibit only an up to 3-fold difference in expression level. These features combined with an easy manipulation of the vector due to the added Gateway sites make the BIBAC-GW vectors an attractive tool for generating transgenic plants.
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Lv L, Liang XF, Tian C, Li L, He S, Guo W. Construction and characterization of a bacterial artificial chromosome library for mandarin fish Siniperca chuatsi (Basilewsky). Genes Genet Syst 2016; 91:189-191. [PMID: 27321190 DOI: 10.1266/ggs.15-00076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Siniperca chuatsi (Basilewsky), a demersal piscivore, is an endemic freshwater fish species in China. For the purpose of genomics research, we have constructed the first bacterial artificial chromosome (BAC) library for S. chuatsi. The BAC library comprised a total of 84,480 clones with an average insert size of 124.6 kb and less than 2.5% empty clones, corresponding to a 10.5-fold coverage of the S. chuatsi genome. The probability of isolating genes of interest was more than 99%. To validate the library, we screened 220 superpools and found that 1-19 were positive for six SSR markers, while none was positive for two mitochondrial gene markers. Therefore, the S. chuatsi BAC library will provide useful genomics resources and tools for cloning, functional genomics research and identification of economically important genes in this species.
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Affiliation(s)
- Liyuan Lv
- College of Fisheries of Huazhong Agricultural University, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province
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Deng Z, Li X, Wang Z, Jiang Y, Wan L, Dong F, Chen F, Hong D, Yang G. Map-based cloning reveals the complex organization of the BnRf locus and leads to the identification of BnRf(b), a male sterility gene, in Brassica napus. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:53-64. [PMID: 26433826 DOI: 10.1007/s00122-015-2608-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/18/2015] [Indexed: 05/28/2023]
Abstract
Sequencing of BAC clones reveals the complex organization of the BnRf locus and allowed us to clone BnRf (b) , which encodes a nucleus-localized chimeric protein BnaA7.mtHSP70-1-like. The male sterility in an extensively used genic male sterility (GMS) line (9012A) in Brassica napus was regarded to be conferred by BnMs3/Bnms3 and the multiallelic BnRf locus including three alleles. We previously mapped BnRf to a 13.8 kb DNA fragment on the B. napus chromosome A7. In the present study, we isolated bacterial artificial chromosome clones individually covering the restorer allele BnRf (a) and the male-sterile allele BnRf (b) , and revealed that the candidate regions of BnRf (a) and BnRf (b) show complex structural variations relative to the maintainer allele BnRf (c). By analyzing the recombination events and the newly developed markers, we delimited BnRf (a) to a 35.9 kb DNA fragment that contained seven predicted open-reading frames (ORFs). However, genetic transformation of the ORF G14 from both the male-sterile and restorer lines into wild-type Arabidopsis plants led to a stable male-sterile phenotype matching a 9012A-derived GMS line (RG206A); moreover, the male sterility caused by G14 could be fully recovered by the restorer gene BnMs3. These facts indicate that BnRf (b) corresponds to G14 while BnRf (a) likely associates with another flanking ORF. G14 encodes a nucleus-localized chimeric protein designated as BnaA7.mtHSP70-1-like. Ectopic expression of G14 in Arabidopsis negatively regulates some vital genes responsible for tapetum degeneration, and delayed programmed cell death of tapetum and led to the developmental arrest of tetrads. Our work not only presents new insights on the hereditary model of sterility control but also lays a solid foundation for dissecting the molecular basis underlying male sterility and restoration in 9012A.
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Affiliation(s)
- Zonghan Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zengzeng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingfen Jiang
- Institute of Crop Science, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Lili Wan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Faming Dong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengxiang Chen
- Institute of Crop Science, Anhui Academy of Agricultural Science, Hefei, 230031, China
| | - Dengfeng Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Guangsheng Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Wang Y, Zeng H, Zhou X, Huang F, Peng W, Liu L, Xiong W, Shi X, Luo M. Transformation of rice with large maize genomic DNA fragments containing high content repetitive sequences. PLANT CELL REPORTS 2015; 34:1049-1061. [PMID: 25700981 DOI: 10.1007/s00299-015-1764-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/28/2015] [Accepted: 02/10/2015] [Indexed: 06/04/2023]
Abstract
Large and complex maize BIBAC inserts, even with a length of about 164 kb and repeat sequences of 88.1%, were transferred into rice. The BIBAC vector has been established to clone large DNA fragments and directly transfer them into plants. Previously, we have constructed a maize B73 BIBAC library and demonstrated that the BIBAC clones were stable in Agrobacterium. In this study, we demonstrated that the maize BIBAC clones could be used for rice genetic transformation through Agrobacterium-mediated method, although the average transformation efficiency for the BIBAC clones (0.86%) is much lower than that for generally used binary vectors containing small DNA fragments (15.24%). The 164-kb B73 genomic DNA insert of the BIBAC clone B2-6 containing five maize gene models and 88.1% of repetitive sequences was transferred into rice. In 18.75% (3/16) of the T1, 13.79% (4/29) of the T2, and 5.26% (1/19) of the T3 generation transgenic rice plants positive for the GUS and HYG marker genes, all the five maize genes can be detected. To our knowledge, this is the largest and highest content of repeat sequence-containing DNA fragment that was successfully transferred into plants. Gene expression analysis (RT-PCR) showed that the expression of three out of five genes could be detected in the leaves of the transgenic rice plants. Our study showed a potential to massively use maize genome resource for rice breeding by mass transformation of rice with large maize genomic DNA fragment BIBAC clones.
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Wang Y, Peng W, Zhou X, Huang F, Shao L, Luo M. The putative Agrobacterium transcriptional activator-like virulence protein VirD5 may target T-complex to prevent the degradation of coat proteins in the plant cell nucleus. THE NEW PHYTOLOGIST 2014; 203:1266-1281. [PMID: 24865527 DOI: 10.1111/nph.12866] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
Agrobacterium exports at least five virulence proteins (VirE2, VirE3, VirF, VirD2, VirD5) into host cells and hijacks some host plant factors to facilitate its transformation process. Random DNA binding selection assays (RDSAs), electrophoretic mobility shift assays (EMSAs) and yeast one-hybrid systems were used to identify protein-bound DNA elements. Bimolecular fluorescence complementation, glutathione S-transferase pull-down and yeast two-hybrid assays were used to detect protein interactions. Protoplast transformation, coprecipitation, competitive binding and cell-free degradation assays were used to analyze the relationships among proteins. We found that Agrobacterium VirD5 exhibits transcriptional activation activity in yeast, is located in the plant cell nucleus, and forms homodimers. A specific VirD5-bound DNA element designated D5RE (VirD5 response element) was identified. VirD5 interacted directly with Arabidopsis VirE2 Interacting Protein 1 (AtVIP1). However, the ternary complex of VirD5-AtVIP1-VirE2 could be detected, whereas that of VirD5-AtVIP1-VBF (AtVIP1 Binding F-box protein) could not. We demonstrated that VirD5 competes with VBF for binding to AtVIP1 and stabilizes AtVIP1 and VirE2 in the cell-free degradation system. Our results indicated that VirD5 may act as both a transcriptional activator-like effector to regulate host gene expression and a protector preventing the coat proteins of the T-complex from being quickly degraded by the host's ubiquitin proteasome system (UPS).
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Affiliation(s)
- Yafei Wang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Peng
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xu Zhou
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Huang
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingyun Shao
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement and College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
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Li XY, Zhang XJ, Li Z, Hong W, Liu W, Zhang J, Gui JF. Evolutionary history of two divergent Dmrt1 genes reveals two rounds of polyploidy origins in gibel carp. Mol Phylogenet Evol 2014; 78:96-104. [PMID: 24859683 DOI: 10.1016/j.ympev.2014.05.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/30/2014] [Accepted: 05/03/2014] [Indexed: 11/27/2022]
Abstract
Polyploidy lineages, despite very rare in vertebrates, have been proposed to play significant role in speciation and evolutionary success, but the occurrence history and consequences are still largely unknown. In this study, we used the conserved Dmrt1 to analyze polyploidy occurrence and evolutionary process in polyploid gibel carp. We identified two divergent Dmrt1 genes and respectively localized the two genes on three homologous chromosomes. Subsequently, the corresponding full-length cDNAs and genomic sequences of Dmrt1 genes were also characterized from the closely related species including Carassius auratus auratus and Cyprinus carpio, and their two Dmrt1 genes were respectively localized on two homologous chromosomes. Significantly, the evolutionary relationship analyses among cDNA and genomic DNA sequences of these Dmrt1 genes revealed two rounds of polyploidy origins in the gibel carp: an early polyploidy might result in an common tetraploid ancestor of Carassius auratus gibelio, Carassius auratus auratus and Cyprinus carpio before 18.49 million years ago (Mya), and an late polyploidy might occur from evolutionary branch of Carassius auratus at around 0.51 Mya, which lead to the occurrence of the hexaploid gibel carp. Therefore, this study provides clear genetic evidence for understanding occurrence time and historical process of polyploidy in polyploid vertebrates.
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Affiliation(s)
- Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Hong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Liu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jun Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China.
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Pan Y, Deng Y, Lin H, Kudrna DA, Wing RA, Li L, Zhang Q, Luo M. Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:795-805. [PMID: 24330235 DOI: 10.1111/tpj.12412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/10/2023]
Abstract
Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.
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Affiliation(s)
- Yonglong Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Wang X, Liu Q, Wang H, Luo CX, Wang G, Luo M. A BAC based physical map and genome survey of the rice false smut fungus Villosiclava virens. BMC Genomics 2013; 14:883. [PMID: 24341590 PMCID: PMC3878662 DOI: 10.1186/1471-2164-14-883] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 12/04/2013] [Indexed: 01/08/2023] Open
Abstract
Background Rice false smut caused by Villosiclava virens is a devastating fungal disease that spreads in major rice-growing regions throughout the world. However, the genomic information for this fungal pathogen is limited and the pathogenic mechanism of this disease is still not clear. To facilitate genetic, molecular and genomic studies of this fungal pathogen, we constructed the first BAC-based physical map and performed the first genome survey for this species. Results High molecular weight genomic DNA was isolated from young mycelia of the Villosiclava virens strain UV-8b and a high-quality, large-insert and deep-coverage Bacterial Artificial Chromosome (BAC) library was constructed with the restriction enzyme HindIII. The BAC library consisted of 5,760 clones, which covers 22.7-fold of the UV-8b genome, with an average insert size of 140 kb and an empty clone rate of lower than 1%. BAC fingerprinting generated successful fingerprints for 2,290 BAC clones. Using the fingerprints, a whole genome-wide BAC physical map was constructed that contained 194 contigs (2,035 clones) spanning 51.2 Mb in physical length. Bidirectional-end sequencing of 4,512 BAC clones generated 6,560 high quality BAC end sequences (BESs), with a total length of 3,030,658 bp, representing 8.54% of the genome sequence. Analysis of the BESs revealed general genome information, including 51.52% GC content, 22.51% repetitive sequences, 376.12/Mb simple sequence repeat (SSR) density and approximately 36.01% coding regions. Sequence comparisons to other available fungal genome sequences through BESs showed high similarities to Metarhizium anisopliae, Trichoderma reesei, Nectria haematococca and Cordyceps militaris, which were generally in agreement with the 18S rRNA gene analysis results. Conclusion This study provides the first BAC-based physical map and genome information for the important rice fungal pathogen Villosiclava virens. The BAC clones, physical map and genome information will serve as fundamental resources to accelerate the genetic, molecular and genomic studies of this pathogen, including positional cloning, comparative genomic analysis and whole genome sequencing. The BAC library and physical map have been opened to researchers as public genomic resources (http://gresource.hzau.edu.cn/resource/resource.html).
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Affiliation(s)
| | | | | | | | | | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, PR China.
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Genomic resources for gene discovery, functional genome annotation, and evolutionary studies of maize and its close relatives. Genetics 2013; 195:723-37. [PMID: 24037269 DOI: 10.1534/genetics.113.157115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Maize is one of the most important food crops and a key model for genetics and developmental biology. A genetically anchored and high-quality draft genome sequence of maize inbred B73 has been obtained to serve as a reference sequence. To facilitate evolutionary studies in maize and its close relatives, much like the Oryza Map Alignment Project (OMAP) (www.OMAP.org) bacterial artificial chromosome (BAC) resource did for the rice community, we constructed BAC libraries for maize inbred lines Zheng58, Chang7-2, and Mo17 and maize wild relatives Zea mays ssp. parviglumis and Tripsacum dactyloides. Furthermore, to extend functional genomic studies to maize and sorghum, we also constructed binary BAC (BIBAC) libraries for the maize inbred B73 and the sorghum landrace Nengsi-1. The BAC/BIBAC vectors facilitate transfer of large intact DNA inserts from BAC clones to the BIBAC vector and functional complementation of large DNA fragments. These seven Zea Map Alignment Project (ZMAP) BAC/BIBAC libraries have average insert sizes ranging from 92 to 148 kb, organellar DNA from 0.17 to 2.3%, empty vector rates between 0.35 and 5.56%, and genome equivalents of 4.7- to 8.4-fold. The usefulness of the Parviglumis and Tripsacum BAC libraries was demonstrated by mapping clones to the reference genome. Novel genes and alleles present in these ZMAP libraries can now be used for functional complementation studies and positional or homology-based cloning of genes for translational genomics.
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