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Zafar UB, Shahzaib M, Atif RM, Khan SH, Niaz MZ, Shahzad K, Chughtai N, Awan FS, Azhar MT, Rana IA. De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease. Sci Rep 2023; 13:20503. [PMID: 37993468 PMCID: PMC10665356 DOI: 10.1038/s41598-023-45982-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023] Open
Abstract
Dalbergia sissoo Roxb. (Shisham) is a timber-producing species of economic, cultural, and medicinal importance in the Indian subcontinent. In the past few decades, Shisham's dieback disease caused by the fungus Botryodiplodia theobromae has become an evolving issue in the subcontinent endangering its survival. To gain insights into this issue, a standard transcriptome assembly was deployed to assess the response of D. sissoo at the transcriptomic level under the stress of B. theobromae infection. For RNA isolation, the control and infected leaf tissue samples were taken from 1-year-old greenhouse-grown D. sissoo plants after 20 days of stem-base spore inoculation. cDNA synthesis was performed from these freshly isolated RNA samples that were then sent for sequencing. About 18.14 Gb (Giga base) of data was generated using the BGISEQ-500 sequencing platform. In terms of Unigenes, 513,821 were identified after a combined assembly of all samples and then filtering the abundance. The total length of Unigenes, their average length, N50, and GC-content were 310,523,693 bp, 604 bp, 1,101 bp, and 39.95% respectively. The Unigenes were annotated using 7 functional databases i.e., 200,355 (NR: 38.99%), 164,973 (NT: 32.11%), 123,733 (Swissprot: 24.08%), 142,580 (KOG: 27.75%), 139,588 (KEGG: 27.17%), 99,752 (GO: 19.41%), and 137,281 (InterPro: 26.72%). Furthermore, the Transdecoder detected 115,762 CDS. In terms of SSR (Simple Sequence Repeat) markers, 62,863 of them were distributed on 51,508 Unigenes and on the predicted 4673 TF (Transcription Factor) coding Unigenes. A total of 16,018 up- and 19,530 down-regulated Differentially Expressed Genes (DEGs) were also identified. Moreover, the Plant Resistance Genes (PRGs) had a count of 9230. We are hopeful that in the future, these identified Unigenes, SSR markers, DEGs and PRGs will provide the prerequisites for managing Shisham dieback disease, its breeding, and in tree improvement programs.
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Affiliation(s)
- Ummul Buneen Zafar
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Shahzaib
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Rana Muhammad Atif
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan
| | - Muhammad Zeeshan Niaz
- Plant Pathology Research Institute, Ayub Agriculture Research Institute, Faisalabad, 38850, Punjab, Pakistan
| | - Khalid Shahzad
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Nighat Chughtai
- Punjab Forestry Research Institute, Faisalabad, 37620, Punjab, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan
| | - Iqrar Ahmad Rana
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, Faisalabad, 38000, Punjab, Pakistan.
- National Center for Genome Editing (Gene Editing of Biological Agents for Nutritional, Biochemicals and Therapeutic Purposes), University of Agriculture, Faisalabad, Punjab, Pakistan.
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Feng Z, Wei F, Feng H, Zhang Y, Zhao L, Zhou J, Xie J, Jiang D, Zhu H. Transcriptome Analysis Reveals the Defense Mechanism of Cotton against Verticillium dahliae Induced by Hypovirulent Fungus Gibellulopsis nigrescens CEF08111. Int J Mol Sci 2023; 24:ijms24021480. [PMID: 36674996 PMCID: PMC9863408 DOI: 10.3390/ijms24021480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/07/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Verticillium wilt is a kind of plant vascular disease caused by the soilborne fungus Verticillium dahliae, which severely limits cotton production. Our previous studies showed that the endophytic fungus Gibellulopsis nigrescens CEF08111 can effectively control Verticillium wilt and induce a defense response in cotton plants. However, the comprehensive molecular mechanism governing this response is not yet clear. To study the signaling mechanism induced by strain CEF08111, the transcriptome of cotton seedlings pretreated with CEF08111 was sequenced. The results revealed 249, 3559 and 33 differentially expressed genes (DEGs) at 3, 12 and 48 h post inoculation with CEF08111, respectively. At 12 h post inoculation with CEF08111, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that the DEGs were enriched mainly in the plant−pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and plant hormone signal transduction pathways. Gene ontology (GO) analysis revealed that these DEGs were enriched mainly in the following terms: response to external stimulus, systemic acquired resistance, kinase activity, phosphotransferase activity, xyloglucan: xyloglucosyl transferase activity, xyloglucan metabolic process, cell wall polysaccharide metabolic process and hemicellulose metabolic process. Moreover, many genes, such as calcium-dependent protein kinase (CDPK), flagellin-sensing 2 (FLS2), resistance to Pseudomonas syringae pv. maculicola 1(RPM1) and myelocytomatosis protein 2 (MYC2), that regulate crucial points in defense-related pathways were identified and may contribute to V. dahliae resistance in cotton. Seven DEGs of the pathway phenylpropanoid biosynthesis were identified by weighted gene co-expression network analysis (WGCNA), and these genes are related to lignin synthesis. The above genes were compared and analyzed, a total of 710 candidate genes that may be related to the resistance of cotton to Verticillium wilt were identified. These results provide a basis for understanding the molecular mechanism by which the biocontrol fungus CEF08111 increases the resistance of cotton to Verticillium wilt.
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Affiliation(s)
- Zili Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Feng Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hongjie Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Yalin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jinglong Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jiatao Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Daohong Jiang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: (D.J.); (H.Z.)
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: (D.J.); (H.Z.)
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Tan YC, Kumar AU, Wong YP, Ling APK. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 2022; 20:106. [PMID: 35838847 PMCID: PMC9287518 DOI: 10.1186/s43141-022-00394-5] [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: 11/30/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set. MAIN BODY Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed. CONCLUSION There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.
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Affiliation(s)
- Yung Cheng Tan
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Asqwin Uthaya Kumar
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.,School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia
| | - Ying Pei Wong
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Anna Pick Kiong Ling
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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Kushwaha SK, Åhman I, Bengtsson T. ResCap: plant resistance gene prediction and probe generation pipeline for resistance gene sequence capture. BIOINFORMATICS ADVANCES 2021; 1:vbab033. [PMID: 36700100 PMCID: PMC9710708 DOI: 10.1093/bioadv/vbab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/15/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
Summary The discovery of novel resistance genes (R-genes) is an important component in disease resistance breeding. Nevertheless, R-gene identification from wild species and close relatives of plants is not only a difficult but also a cumbersome process. In this study, ResCap, a support vector machine-based high-throughput R-gene prediction and probe generation pipeline has been developed to generate probes from genomic datasets. ResCap contains two integral modules. The first module identifies the R-genes and R-gene like sequences under four categories containing different domains such as TIR-NBS-LRR (TNL), CC-NBS-LRR (CNL), Receptor-like kinase (RLK) and Receptor-like proteins (RLPs). The second module generates probes from extracted nucleotide sequences of resistance genes to conduct sequence capture (SeqCap) experiments. For the validation of ResCap pipeline, ResCap generated probes were synthesized and a sequence capture experiment was performed to capture expressed resistance genes among six spring barley genotypes. The developed ResCap pipeline in combination with the performed sequence capture experiment has shown to increase precision of R-gene identification while simultaneously allowing rapid gene validation including non-sequenced plants. Availability and implementation The ResCap pipeline is available at http://rescap.ltj.slu.se/ResCap/. Contact sandeep.kushwaha@slu.se or sandeep@niab.org.in. Supplementary information Supplementary materials are available at Bioinformatics Advances online.
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Affiliation(s)
- Sandeep K Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden,Bioinformatics, National Institute of Animal Biotechnology, Hyderabad 500 032, India,To whom correspondence should be addressed.
| | - Inger Åhman
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma 234 22, Sweden
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Transcriptome Analysis of a Cotton Cultivar Provides Insights into the Differentially Expressed Genes Underlying Heightened Resistance to the Devastating Verticillium Wilt. Cells 2021; 10:cells10112961. [PMID: 34831184 PMCID: PMC8616101 DOI: 10.3390/cells10112961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022] Open
Abstract
Cotton is an important economic crop worldwide. Verticillium wilt (VW) caused by Verticillium dahliae (V. dahliae) is a serious disease in cotton, resulting in massive yield losses and decline of fiber quality. Breeding resistant cotton cultivars is an efficient but elaborate method to improve the resistance of cotton against V. dahliae infection. However, the functional mechanism of several excellent VW resistant cotton cultivars is poorly understood at present. In our current study, we carried out RNA-seq to discover the differentially expressed genes (DEGs) in the roots of susceptible cotton Gossypium hirsutum cultivar Junmian 1 (J1) and resistant cotton G.hirsutum cultivar Liaomian 38 (L38) upon Vd991 inoculation at two time points compared with the mock inoculated control plants. The potential function of DEGs uniquely expressed in J1 and L38 was also analyzed by GO enrichment and KEGG pathway associations. Most DEGs were assigned to resistance-related functions. In addition, resistance gene analogues (RGAs) were identified and analyzed for their role in the heightened resistance of the L38 cultivar against the devastating Vd991. In summary, we analyzed the regulatory network of genes in the resistant cotton cultivar L38 during V. dahliae infection, providing a novel and comprehensive insight into VW resistance in cotton.
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Genetic Loci Associated with Resistance to Zucchini Yellow Mosaic Virus in Squash. PLANTS 2021; 10:plants10091935. [PMID: 34579467 PMCID: PMC8465829 DOI: 10.3390/plants10091935] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
Zucchini Yellow Mosaic Virus (ZYMV) is an aphid-transmitted potyvirus that causes severe yield losses in squash (Cucurbita moschata) production worldwide. Development of resistant cultivars using traditional breeding approaches relies on rigorous and resource-intensive phenotypic assays. QTL-seq, a whole genome re-sequencing based bulked segregant analysis, is a powerful tool for mapping quantitative trait loci (QTL) in crop plants. In the current study, the QTL-seq approach was used to identify genetic loci associated with ZYMV resistance in an F2 population (n = 174) derived from a cross between Nigerian Local (resistant) and Butterbush (susceptible). Whole genome re-sequencing of the parents and bulks of resistant and susceptible F2 progeny revealed a mapping rate between 94.04% and 98.76%, and a final effective mapping depth ranging from 81.77 to 101.73 across samples. QTL-seq analysis identified four QTLs significantly (p < 0.05) associated with ZYMV resistance on chromosome 2 (QtlZYMV-C02), 4 (QtlZYMV-C04), 8 (QtlZYMV-C08) and 20 (QtlZYMV-C20). Seven markers within the QTL intervals were tested for association with ZYMV resistance in the entire F2 population. For QtlZYMV-C08, one single nucleotide polymorphism (SNP) marker (KASP-6) was found to be significantly (p < 0.05) associated with ZYMV resistance, while two SNPs (KASP-1 and KASP-3) and an indel (Indel-2) marker were linked to resistance within QtlZYMV-C20. KASP-3 and KASP-6 are non-synonymous SNPs leading to amino acid substitutions in candidate disease resistant gene homologs on chromosomes 20 (CmoCh20G003040.1) and 8 (CmoCh08G007140.1), respectively. Identification of QTL and SNP markers associated with ZYMV resistance will facilitate marker-assisted selection for ZYMV resistance in squash.
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Dong AY, Wang Z, Huang JJ, Song BA, Hao GF. Bioinformatic tools support decision-making in plant disease management. TRENDS IN PLANT SCIENCE 2021; 26:953-967. [PMID: 34039514 DOI: 10.1016/j.tplants.2021.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/10/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Food loss due to pathogens is a major concern in agriculture, requiring the need for advanced disease detection and prevention measures to minimize pathogen damage to plants. Novel bioinformatic tools have opened doors for the low-cost rapid identification of pathogens and prevention of disease. The number of these tools is growing fast and a comprehensive and comparative summary of these resources is currently lacking. Here, we review all current bioinformatic tools used to identify the mechanisms of pathogen pathogenicity, plant resistance protein identification, and the detection and treatment of plant disease. We compare functionality, data volume, data sources, performance, and applicability of all tools to provide a comprehensive toolbox for researchers in plant disease management.
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Affiliation(s)
- An-Yu Dong
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Zheng Wang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China.
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Structural and Functional Genomics of the Resistance of Cacao to Phytophthora palmivora. Pathogens 2021; 10:pathogens10080961. [PMID: 34451425 PMCID: PMC8398157 DOI: 10.3390/pathogens10080961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 11/17/2022] Open
Abstract
Black pod disease, caused by Phytophthora spp., is one of the main diseases that attack cocoa plantations. This study validated, by association mapping, 29 SSR molecular markers flanking to QTL (Quantitative Trait Loci) associated with Phytophthora palmivora Butler (Butler) (PP) resistance, in three local ancient varieties of the Bahia (Comum, Pará, and Maranhão), varieties that have a high potential in the production of gourmet chocolate. Four SSR loci associated with resistance to PP were detected, two on chromosome 8, explaining 7.43% and 3.72% of the Phenotypic Variation (%PV), one on chromosome 2 explaining 2.71%PV and one on chromosome 3 explaining 1.93%PV. A functional domains-based annotation was carried out, in two Theobroma cacao (CRIOLLO and MATINA) reference genomes, of 20 QTL regions associated with cocoa resistance to the pathogen. It was identified 164 (genome CRIOLLO) and 160 (genome MATINA) candidate genes, hypothetically involved in the recognition and activation of responses in the interaction with the pathogen. Genomic regions rich in genes with Coiled-coils (CC), nucleotide binding sites (NBS) and Leucine-rich repeat (LRR) domains were identified on chromosomes 1, 3, 6, 8, and 10, likewise, regions rich in Receptor-like Kinase domain (RLK) and Ginkbilobin2 (GNK2) domains were identified in chromosomes 4 and 6.
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Seong K, Seo E, Witek K, Li M, Staskawicz B. Evolution of NLR resistance genes with noncanonical N-terminal domains in wild tomato species. THE NEW PHYTOLOGIST 2020; 227:1530-1543. [PMID: 32344448 DOI: 10.1111/nph.16628] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/11/2020] [Indexed: 06/11/2023]
Abstract
Nucleotide-binding and leucine-rich repeat immune receptors (NLRs) provide resistance against diverse pathogens. To create comparative NLR resources, we conducted resistance gene enrichment sequencing (RenSeq) with single-molecule real-time sequencing of PacBio for 18 accessions in Solanaceae, including 15 accessions of five wild tomato species. We investigated the evolution of a class of NLRs, CNLs with extended N-terminal sequences previously named Solanaceae Domain. Through comparative genomic analysis, we revealed that the extended CNLs (exCNLs) anciently emerged in the most recent common ancestor between Asterids and Amaranthaceae, far predating the Solanaceae family. In tomatoes, the exCNLs display exceptional modes of evolution in a clade-specific manner. In the clade G3, exCNLs have substantially elongated their N-termini through tandem duplications of exon segments. In the clade G1, exCNLs have evolved through recent proliferation and sequence diversification. In the clade G6, an ancestral exCNL has lost its N-terminal domains in the course of evolution. Our study provides high-quality NLR gene models for close relatives of domesticated tomatoes that can serve as a useful resource for breeding and molecular engineering for disease resistance. Our findings regarding the exCNLs offer unique backgrounds and insights for future functional studies of the NLRs.
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Affiliation(s)
- Kyungyong Seong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Eunyoung Seo
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Kamil Witek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Meng Li
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
| | - Brian Staskawicz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94704, USA
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Santana Silva RJ, Micheli F. RRGPredictor, a set-theory-based tool for predicting pathogen-associated molecular pattern receptors (PRRs) and resistance (R) proteins from plants. Genomics 2020; 112:2666-2676. [DOI: 10.1016/j.ygeno.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 12/22/2022]
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Maghuly F, Deák T, Vierlinger K, Pabinger S, Tafer H, Laimer M. Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas. BMC Genomics 2020; 21:290. [PMID: 32272887 PMCID: PMC7146973 DOI: 10.1186/s12864-020-6666-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 03/11/2020] [Indexed: 11/10/2022] Open
Abstract
Background Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronomic performance, a two-step approach was performed in six different maturation stages of seeds: 1) generation of the entire transcriptome of J. curcas seeds using 454-Roche sequencing of a cDNA library, 2) comparison of transcriptional expression levels using a custom Agilent 8x60K oligonucleotide microarray. Results A total of 793,875 high-quality reads were assembled into 19,382 unique full-length contigs, of which 13,507 could be annotated with Gene Ontology (GO) terms. Microarray data analysis identified 9111 probes (out of 57,842 probes), which were differentially expressed between the six maturation stages. The expression results were validated for 75 selected transcripts based on expression levels, predicted function, pathway, and length. Result from cluster analyses showed that transcripts associated with fatty acid, flavonoid, and phenylpropanoid biosynthesis were over-represented in the early stages, while those of lipid storage were over-represented in the late stages. Expression analyses of different maturation stages of J. curcas seed showed that most changes in transcript abundance occurred between the two last stages, suggesting that the timing of metabolic pathways during seed maturation in J. curcas occurs in late stages. The co-expression results showed that the hubs (CB5-D, CDR1, TT8, DFR, HVA22) with the highest number of edges, associated with fatty acid and flavonoid biosynthesis, are showing a decrease in their expression during seed maturation. Furthermore, seed development and hormone pathways are significantly well connected. Conclusion The obtained results revealed differentially expressed sequences (DESs) regulating important pathways related to seed maturation, which could contribute to the understanding of the complex regulatory network during seed maturation with the focus on lipid, flavonoid and phenylpropanoid biosynthesis. This study provides detailed information on transcriptional changes during J. curcas seed maturation and provides a starting point for a genomic survey of seed quality traits. The results highlighted specific genes and processes relevant to the molecular mechanisms involved in Jatropha seed maturation. These data can also be utilized regarding other Euphorbiaceae species.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Functional Genomics, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
| | - Tamás Deák
- Department of Viticulture, Szent István University, Villányi út 29-43, 1118 Budapest, Hungary
| | - Klemens Vierlinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Stephan Pabinger
- Center for Health and Bioresources, Molecular Diagnostics, Austrian Institute of Technology (AIT), Giefinggasse 4, 1210, Vienna, Austria
| | - Hakim Tafer
- Austrian Center of Biological Resources (ACBR), Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, Department of Biotechnology, BOKU-VIBT, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria
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Zhang Y, Yang N, Zhao L, Zhu H, Tang C. Transcriptome analysis reveals the defense mechanism of cotton against Verticillium dahliae in the presence of the biocontrol fungus Chaetomium globosum CEF-082. BMC PLANT BIOLOGY 2020; 20:89. [PMID: 32106811 PMCID: PMC7047391 DOI: 10.1186/s12870-019-2221-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/30/2019] [Indexed: 05/31/2023]
Abstract
BACKGROUND Verticillium wilt of cotton is a serious soil-borne disease that causes a substantial reduction in cotton yields. A previous study showed that the endophytic fungus Chaetomium globosum CEF-082 could control Verticillium wilt of cotton, and induce a defense response in cotton plants. However, the comprehensive molecular mechanism governing this response is not yet clear. RESULTS To study the signalling mechanism induced by CEF-082, the transcriptome of cotton seedlings pretreated with CEF-082 was sequenced. The results revealed 5638 DEGs at 24 h post inoculation with CEF-082, and 2921 and 2153 DEGs at 12 and 48 h post inoculation with Verticillium dahliae, respectively. At 24 h post inoculation with CEF-082, KEGG enrichment analysis indicated that the DEGs were enriched mainly in the plant-pathogen interaction, MAPK signalling pathway-plant, flavonoid biosynthesis, and phenylpropanoid biosynthesis pathways. There were 1209 DEGs specifically induced only in cotton plants inoculated with V. dahliae in the presence of the biocontrol fungus CEF-082, and not when cotton plants were only inoculated with V. dahliae. GO analysis revealed that these DEGs were enriched mainly in the following terms: ROS metabolic process, H2O2 metabolic process, defense response, superoxide dismutase activity, and antioxidant activity. Moreover, many genes, such as ERF, CNGC, FLS2, MYB, GST and CML, that regulate crucial points in defense-related pathways were identified and may contribute to V. dahliae resistance in cotton. These results provide a basis for understanding the molecular mechanism by which the biocontrol fungus CEF-082 increases the resistance of cotton to Verticillium wilt. CONCLUSIONS The results of this study showed that CEF-082 could regulate multiple metabolic pathways in cotton. After treatment with V. dahliae, the defense response of cotton plants preinoculated with CEF-082 was strengthened.
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Affiliation(s)
- Yun Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
| | - Na Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
| | - Lihong Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan People’s Republic of China
| | - Heqin Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan People’s Republic of China
| | - Canming Tang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agronomy, Nanjing Agricultural University, Nanjing, 210095 Jiangsu People’s Republic of China
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Alioto T, Alexiou KG, Bardil A, Barteri F, Castanera R, Cruz F, Dhingra A, Duval H, Fernández i Martí Á, Frias L, Galán B, García JL, Howad W, Gómez‐Garrido J, Gut M, Julca I, Morata J, Puigdomènech P, Ribeca P, Rubio Cabetas MJ, Vlasova A, Wirthensohn M, Garcia‐Mas J, Gabaldón T, Casacuberta JM, Arús P. Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:455-472. [PMID: 31529539 PMCID: PMC7004133 DOI: 10.1111/tpj.14538] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/29/2019] [Accepted: 09/02/2019] [Indexed: 05/19/2023]
Abstract
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27 969 protein-coding genes and 6747 non-coding transcripts. By phylogenomic comparison with the genomes of 16 additional close and distant species we estimated that almond and peach (Prunus persica) diverged around 5.88 million years ago. These two genomes are highly syntenic and show a high degree of sequence conservation (20 nucleotide substitutions per kb). However, they also exhibit a high number of presence/absence variants, many attributable to the movement of transposable elements (TEs). Transposable elements have generated an important number of presence/absence variants between almond and peach, and we show that the recent history of TE movement seems markedly different between them. Transposable elements may also be at the origin of important phenotypic differences between both species, and in particular for the sweet kernel phenotype, a key agronomic and domestication character for almond. Here we show that in sweet almond cultivars, highly methylated TE insertions surround a gene involved in the biosynthesis of amygdalin, whose reduced expression has been correlated with the sweet almond phenotype. Altogether, our results suggest a key role of TEs in the recent history and diversification of almond and its close relative peach.
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Affiliation(s)
- Tyler Alioto
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Konstantinos G. Alexiou
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Amélie Bardil
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fabio Barteri
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Raúl Castanera
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Fernando Cruz
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Amit Dhingra
- Department of HorticultureWashington State University99164-6414PullmanWAUSA
| | - Henri Duval
- INRA, UR1052Unité de Génétique et Amélioration des Fruits et Légumes (GAFL)Domaine St. Maurice CS 6009484143Montfavet CedexFrance
| | - Ángel Fernández i Martí
- Department of Environmental Science Policy and ManagementUniversity of CaliforniaBerkeley94720CAUSA
- Innovative Genomics Institute (IGI)94720BerkeleyCAUSA
| | - Leonor Frias
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Beatriz Galán
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - José L. García
- Department of Environmental BiologyCenter for Biological Research (CIB‐CSIC)Spanish National Research Council (CSIC)Ramiro de Maeztu 928040MadridSpain
| | - Werner Howad
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Jèssica Gómez‐Garrido
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Marta Gut
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
| | - Irene Julca
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Jordi Morata
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Puigdomènech
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Paolo Ribeca
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)Baldiri i Reixac 408028BarcelonaSpain
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- The Pirbright InstituteWokingSurreyGU24 0NFUK
| | - María J. Rubio Cabetas
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)Unidad de HortofruticulturaGobierno de Aragón, Avda. Montañana 93050059ZaragozaSpain
- Instituto Agroalimentario de Aragón – IA2 (CITA‐Universidad de Zaragoza)Calle Miguel Servet 17750013ZaragozaSpain
| | - Anna Vlasova
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
| | - Michelle Wirthensohn
- University of AdelaideWaite Research InstituteSchool of Agriculture, Food and WinePMB 1Glen OsmondSA5064Australia
| | - Jordi Garcia‐Mas
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Toni Gabaldón
- Universitat Pompeu Fabra (UPF)08005BarcelonaSpain
- Bioinformatics and Genomics ProgrammeCentre for Genomic Regulation (CRG)Dr Aiguader, 8808003BarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Pg Lluís Companys 2308010BarcelonaSpain
| | - Josep M. Casacuberta
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
| | - Pere Arús
- IRTA, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Campus UABEdifici CRAGCerdanyola del Vallès (Bellaterra)08193BarcelonaSpain
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Naveed ZA, Wei X, Chen J, Mubeen H, Ali GS. The PTI to ETI Continuum in Phytophthora-Plant Interactions. FRONTIERS IN PLANT SCIENCE 2020; 11:593905. [PMID: 33391306 PMCID: PMC7773600 DOI: 10.3389/fpls.2020.593905] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/24/2020] [Indexed: 05/15/2023]
Abstract
Phytophthora species are notorious pathogens of several economically important crop plants. Several general elicitors, commonly referred to as Pathogen-Associated Molecular Patterns (PAMPs), from Phytophthora spp. have been identified that are recognized by the plant receptors to trigger induced defense responses in a process termed PAMP-triggered Immunity (PTI). Adapted Phytophthora pathogens have evolved multiple strategies to evade PTI. They can either modify or suppress their elicitors to avoid recognition by host and modulate host defense responses by deploying hundreds of effectors, which suppress host defense and physiological processes by modulating components involved in calcium and MAPK signaling, alternative splicing, RNA interference, vesicle trafficking, cell-to-cell trafficking, proteolysis and phytohormone signaling pathways. In incompatible interactions, resistant host plants perceive effector-induced modulations through resistance proteins and activate downstream components of defense responses in a quicker and more robust manner called effector-triggered-immunity (ETI). When pathogens overcome PTI-usually through effectors in the absence of R proteins-effectors-triggered susceptibility (ETS) ensues. Qualitatively, many of the downstream defense responses overlap between PTI and ETI. In general, these multiple phases of Phytophthora-plant interactions follow the PTI-ETS-ETI paradigm, initially proposed in the zigzag model of plant immunity. However, based on several examples, in Phytophthora-plant interactions, boundaries between these phases are not distinct but are rather blended pointing to a PTI-ETI continuum.
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Affiliation(s)
- Zunaira Afzal Naveed
- Department of Plant Pathology, Institute of Food and Agriculture Sciences, University of Florida, Gainesville, FL, United States
- Mid-Florida Research and Education Center, Institute of Food and Agriculture Sciences, University of Florida, Apopka, FL, United States
| | - Xiangying Wei
- Mid-Florida Research and Education Center, Institute of Food and Agriculture Sciences, University of Florida, Apopka, FL, United States
- Institute of Oceanography, Minjiang University, Fuzhou, China
- Xiangying Wei
| | - Jianjun Chen
- Mid-Florida Research and Education Center, Institute of Food and Agriculture Sciences, University of Florida, Apopka, FL, United States
| | - Hira Mubeen
- Departement of Biotechnology, University of Central Punjab, Lahore, Pakistan
| | - Gul Shad Ali
- Department of Plant Pathology, Institute of Food and Agriculture Sciences, University of Florida, Gainesville, FL, United States
- Mid-Florida Research and Education Center, Institute of Food and Agriculture Sciences, University of Florida, Apopka, FL, United States
- EukaryoTech LLC, Apopka, FL, United States
- *Correspondence: Gul Shad Ali
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15
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Acquadro A, Torello Marinoni D, Sartor C, Dini F, Macchio M, Botta R. Transcriptome characterization and expression profiling in chestnut cultivars resistant or susceptible to the gall wasp Dryocosmus kuriphilus. Mol Genet Genomics 2019; 295:107-120. [PMID: 31506717 DOI: 10.1007/s00438-019-01607-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 08/27/2019] [Indexed: 02/07/2023]
Abstract
The oriental gall wasp Dryocosmus kuriphilus represents a limiting pest for the European Chestnut (Castanea sativa, Fagaceae) as it creates severe yield losses. The European Chestnut is a deciduous tree, having major social, economic and environmental importance in Southern Europe, covering an area of 2.53 million hectares, including 75,000 ha devoted to fruit production. Cultivars show different susceptibility and very few are resistant to gall wasp. To deeply investigate the plant response and understand which factors can lead the plant to develop or not the gall, the study of transcriptome is basic (fundamental). To date, little transcriptomic information are available for C. sativa species. Hence, we present a de novo assembly of the chestnut transcriptome of the resistant Euro-Japanese hybrid 'Bouche de Bétizac' (BB) and the susceptible cultivar 'Madonna' (M), collecting RNA from buds at different stages of budburst. The two transcriptomes were assembled into 34,081 (BB) and 30,605 (M) unigenes, respectively. The former was used as a reference sequence for further characterization analyses, highlighting the presence of 1444 putative resistance gene analogs (RGAs) and about 1135 unigenes, as putative MiRNA targets. A global quantitative transcriptome profiling comparing the resistant and the susceptible cultivars, in the presence or not of the gall wasp, revealed some GO enrichments as "response to stimulus" (GO:0050896), and "developmental processes" (e.g., post-embryonic development, GO:0009791). Many up-regulated genes appeared to be transcription factors (e.g., RAV1, AP2/ERF, WRKY33) or protein regulators (e.g., RAPTOR1B) and storage proteins (e.g., LEA D29) involved in "post-embryonic development". Our analysis was able to provide a large amount of information, including 7k simple sequence repeat (SSR) and 335k single-nucleotide polymorphism (SNP)/INDEL markers, and generated the first reference unigene catalog for the European Chestnut. The transcriptome data for C. sativa will contribute to understand the genetic basis of the resistance to gall wasp and will provide useful information for next molecular genetic studies of this species and its relatives.
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Affiliation(s)
- Alberto Acquadro
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Daniela Torello Marinoni
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy.
| | - Chiara Sartor
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Francesca Dini
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Matteo Macchio
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy
| | - Roberto Botta
- DISAFA, Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo Paolo Braccini 2, 10095, Grugliasco, Italy
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16
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Osuna-Cruz CM, Paytuvi-Gallart A, Di Donato A, Sundesha V, Andolfo G, Aiese Cigliano R, Sanseverino W, Ercolano MR. PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. Nucleic Acids Res 2019; 46:D1197-D1201. [PMID: 29156057 PMCID: PMC5753367 DOI: 10.1093/nar/gkx1119] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 11/28/2022] Open
Abstract
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and algae genomes. The DRAGO 2 tool, which automatically annotates and predicts (PRGs) from DNA and amino acid with high accuracy and sensitivity, has been added. BLAST search has been implemented to offer users the opportunity to annotate and compare their own sequences. The improved section on plant diseases displays useful information linked to genes and genomes to connect complementary data and better address specific needs. Through, a revised and enlarged collection of data, the development of new tools and a renewed portal, PRGdb 3.0 engages the plant science community in developing a consensus plan to improve knowledge and strategies to fight diseases that afflict main crops and other plants.
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Affiliation(s)
| | | | - Antimo Di Donato
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | - Vicky Sundesha
- Sequentia Biotech SL, Calle Comte D'Urgell 240, 08036 Barcelona, Spain
| | - Giuseppe Andolfo
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
| | | | | | - Maria R Ercolano
- Dipartimento di Agraria, Università di Napoli 'Federico II', Via Università 100, 80055 Portici, Italy
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17
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Li TG, Wang BL, Yin CM, Zhang DD, Wang D, Song J, Zhou L, Kong ZQ, Klosterman SJ, Li JJ, Adamu S, Liu TL, Subbarao KV, Chen JY, Dai XF. The Gossypium hirsutum TIR-NBS-LRR gene GhDSC1 mediates resistance against Verticillium wilt. MOLECULAR PLANT PATHOLOGY 2019; 20:857-876. [PMID: 30957942 DOI: 10.5897/ajmr11.781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Improving genetic resistance is a preferred method to manage Verticillium wilt of cotton and other hosts. Identifying host resistance is difficult because of the dearth of resistance genes against this pathogen. Previously, a novel candidate gene involved in Verticillium wilt resistance was identified by a genome-wide association study using a panel of Gossypium hirsutum accessions. In this study, we cloned the candidate resistance gene from cotton that encodes a protein sharing homology with the TIR-NBS-LRR receptor-like defence protein DSC1 in Arabidopsis thaliana (hereafter named GhDSC1). GhDSC1 expressed at higher levels in response to Verticillium wilt and jasmonic acid (JA) treatment in resistant cotton cultivars as compared to susceptible cultivars and its product was localized to nucleus. The transfer of GhDSC1 to Arabidopsis conferred Verticillium resistance in an A. thaliana dsc1 mutant. This resistance response was associated with reactive oxygen species (ROS) accumulation and increased expression of JA-signalling-related genes. Furthermore, the expression of GhDSC1 in response to Verticillium wilt and JA signalling in A. thaliana displayed expression patterns similar to GhCAMTA3 in cotton under identical conditions, suggesting a coordinated DSC1 and CAMTA3 response in A. thaliana to Verticillium wilt. Analyses of GhDSC1 sequence polymorphism revealed a single nucleotide polymorphism (SNP) difference between resistant and susceptible cotton accessions, within the P-loop motif encoded by GhDSC1. This SNP difference causes ineffective activation of defence response in susceptible cultivars. These results demonstrated that GhDSC1 confers Verticillium resistance in the model plant system of A. thaliana, and therefore represents a suitable candidate for the genetic engineering of Verticillium wilt resistance in cotton.
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Affiliation(s)
- Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bao-Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chun-Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jian Song
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, California, USA
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Sabiu Adamu
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ting-Li Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o United States Agricultural Research Station, Salinas, California, USA
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, 100193, China
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18
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Li T, Wang B, Yin C, Zhang D, Wang D, Song J, Zhou L, Kong Z, Klosterman SJ, Li J, Adamu S, Liu T, Subbarao KV, Chen J, Dai X. The Gossypium hirsutum TIR-NBS-LRR gene GhDSC1 mediates resistance against Verticillium wilt. MOLECULAR PLANT PATHOLOGY 2019; 20:857-876. [PMID: 30957942 PMCID: PMC6637886 DOI: 10.1111/mpp.12797] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Improving genetic resistance is a preferred method to manage Verticillium wilt of cotton and other hosts. Identifying host resistance is difficult because of the dearth of resistance genes against this pathogen. Previously, a novel candidate gene involved in Verticillium wilt resistance was identified by a genome-wide association study using a panel of Gossypium hirsutum accessions. In this study, we cloned the candidate resistance gene from cotton that encodes a protein sharing homology with the TIR-NBS-LRR receptor-like defence protein DSC1 in Arabidopsis thaliana (hereafter named GhDSC1). GhDSC1 expressed at higher levels in response to Verticillium wilt and jasmonic acid (JA) treatment in resistant cotton cultivars as compared to susceptible cultivars and its product was localized to nucleus. The transfer of GhDSC1 to Arabidopsis conferred Verticillium resistance in an A. thaliana dsc1 mutant. This resistance response was associated with reactive oxygen species (ROS) accumulation and increased expression of JA-signalling-related genes. Furthermore, the expression of GhDSC1 in response to Verticillium wilt and JA signalling in A. thaliana displayed expression patterns similar to GhCAMTA3 in cotton under identical conditions, suggesting a coordinated DSC1 and CAMTA3 response in A. thaliana to Verticillium wilt. Analyses of GhDSC1 sequence polymorphism revealed a single nucleotide polymorphism (SNP) difference between resistant and susceptible cotton accessions, within the P-loop motif encoded by GhDSC1. This SNP difference causes ineffective activation of defence response in susceptible cultivars. These results demonstrated that GhDSC1 confers Verticillium resistance in the model plant system of A. thaliana, and therefore represents a suitable candidate for the genetic engineering of Verticillium wilt resistance in cotton.
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Affiliation(s)
- Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Bao‐Li Wang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Chun‐Mei Yin
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Dan Wang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Jian Song
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Zhi‐Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Steven J. Klosterman
- United States Department of AgricultureAgricultural Research ServiceSalinasCaliforniaUSA
| | - Jun‐Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Sabiu Adamu
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
| | - Ting‐Li Liu
- Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjingJiangsu210014China
| | - Krishna V. Subbarao
- Department of Plant PathologyUniversity of California, Davis, c/o United States Agricultural Research StationSalinasCaliforniaUSA
| | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing100193China
- Key Laboratory of Agro‐products Quality and Safety Control in Storage and Transport Process, Ministry of AgricultureBeijing100193China
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Li N, ma X, Short DPG, Li T, Zhou L, Gui Y, Kong Z, Zhang D, Zhang W, Li J, Subbarao KV, Chen J, Dai X. The island cotton NBS-LRR gene GbaNA1 confers resistance to the non-race 1 Verticillium dahliae isolate Vd991. MOLECULAR PLANT PATHOLOGY 2018; 19:1466-1479. [PMID: 29052967 PMCID: PMC6638185 DOI: 10.1111/mpp.12630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/06/2017] [Accepted: 10/14/2017] [Indexed: 05/21/2023]
Abstract
Wilt caused by Verticillium dahliae significantly reduces cotton yields, as host resistance in commercially cultivated Gossypium species is lacking. Understanding the molecular basis of disease resistance in non-commercial Gossypium species could galvanize the development of Verticillium wilt resistance in cultivated species. Nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins play a central role in plant defence against pathogens. In this study, we focused on the relationship between a locus enriched with eight NBS-LRR genes and Verticillium wilt resistance in G. barbadense. Independent virus-induced gene silencing of each of the eight NBS-LRR genes in G. barbadense cultivar Hai 7124 revealed that silencing of GbaNA1 alone compromised the resistance of G. barbadense to V. dahliae isolate Vd991. In cultivar Hai 7124, GbaNA1 could be induced by V. dahliae isolate Vd991 and by ethylene, jasmonic acid and salicylic acid. Nuclear protein localization of GbaNA1 was demonstrated by transient expression. Sequencing of the GbaNA1 orthologue in nine G. hirsutum accessions revealed that all carried a non-functional allele, caused by a premature peptide truncation. In addition, all 10 G. barbadense and nine G. hirsutum accessions tested carried a full-length (∼1140 amino acids) homologue of the V. dahliae race 1 resistance gene Gbve1, although some sequence polymorphisms were observed. Verticillium dahliae Vd991 is a non-race 1 isolate that lacks the Ave1 gene. Thus, the resistance imparted by GbaNA1 appears to be mediated by a mechanism distinct from recognition of the fungal effector Ave1.
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Affiliation(s)
- Nan‐Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xue‐Feng ma
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dylan P. G. Short
- Department of Plant PathologyUniversity of CaliforniaDavisCA 95616USA
| | - Ting‐Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Yue‐Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Zhi‐Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Dan‐Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Wen‐Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Jun‐Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | | | - Jie‐Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
| | - Xiao‐Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijing 100193China
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20
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Rosli R, Amiruddin N, Ab Halim MA, Chan PL, Chan KL, Azizi N, Morris PE, Leslie Low ET, Ong-Abdullah M, Sambanthamurthi R, Singh R, Murphy DJ. Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm. PLoS One 2018; 13:e0194792. [PMID: 29672525 PMCID: PMC5908059 DOI: 10.1371/journal.pone.0194792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/10/2018] [Indexed: 01/10/2023] Open
Abstract
Comparative genomics and transcriptomic analyses were performed on two agronomically important groups of genes from oil palm versus other major crop species and the model organism, Arabidopsis thaliana. The first analysis was of two gene families with key roles in regulation of oil quality and in particular the accumulation of oleic acid, namely stearoyl ACP desaturases (SAD) and acyl-acyl carrier protein (ACP) thioesterases (FAT). In both cases, these were found to be large gene families with complex expression profiles across a wide range of tissue types and developmental stages. The detailed classification of the oil palm SAD and FAT genes has enabled the updating of the latest version of the oil palm gene model. The second analysis focused on disease resistance (R) genes in order to elucidate possible candidates for breeding of pathogen tolerance/resistance. Ortholog analysis showed that 141 out of the 210 putative oil palm R genes had homologs in banana and rice. These genes formed 37 clusters with 634 orthologous genes. Classification of the 141 oil palm R genes showed that the genes belong to the Kinase (7), CNL (95), MLO-like (8), RLK (3) and Others (28) categories. The CNL R genes formed eight clusters. Expression data for selected R genes also identified potential candidates for breeding of disease resistance traits. Furthermore, these findings can provide information about the species evolution as well as the identification of agronomically important genes in oil palm and other major crops.
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Affiliation(s)
- Rozana Rosli
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Pek-Lan Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Priscilla E. Morris
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Denis J. Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom
- * E-mail:
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21
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Yang X, Islam MS, Sood S, Maya S, Hanson EA, Comstock J, Wang J. Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane ( Saccharum spp.). FRONTIERS IN PLANT SCIENCE 2018; 9:350. [PMID: 29616061 PMCID: PMC5868124 DOI: 10.3389/fpls.2018.00350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 03/02/2018] [Indexed: 05/18/2023]
Abstract
Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance (R) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.
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Affiliation(s)
- Xiping Yang
- Department of Agronomy, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Md. S. Islam
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal Point, FL, United States
| | - Sushma Sood
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal Point, FL, United States
| | - Stephanie Maya
- Department of Agronomy, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Erik A. Hanson
- Department of Agronomy, Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Jack Comstock
- Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal Point, FL, United States
| | - Jianping Wang
- Department of Agronomy, Genetics Institute, University of Florida, Gainesville, FL, United States
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fujian, China
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22
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Li NY, Zhou L, Zhang DD, Klosterman SJ, Li TG, Gui YJ, Kong ZQ, Ma XF, Short DPG, Zhang WQ, Li JJ, Subbarao KV, Chen JY, Dai XF. Heterologous Expression of the Cotton NBS-LRR Gene GbaNA1 Enhances Verticillium Wilt Resistance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:119. [PMID: 29467784 PMCID: PMC5808209 DOI: 10.3389/fpls.2018.00119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/22/2018] [Indexed: 05/06/2023]
Abstract
Verticillium wilt caused by Verticillium dahliae results in severe losses in cotton, and is economically the most destructive disease of this crop. Improving genetic resistance is the cleanest and least expensive option to manage Verticillium wilt. Previously, we identified the island cotton NBS-LRR-encoding gene GbaNA1 that confers resistance to the highly virulent V. dahliae isolate Vd991. In this study, we expressed cotton GbaNA1 in the heterologous system of Arabidopsis thaliana and investigated the defense response mediated by GbaNA1 following inoculations with V. dahliae. Heterologous expression of GbaNA1 conferred Verticillium wilt resistance in A. thaliana. Moreover, overexpression of GbaNA1 enabled recovery of the resistance phenotype of A. thaliana mutants that had lost the function of GbaNA1 ortholog gene. Investigations of the defense response in A. thaliana showed that the reactive oxygen species (ROS) production and the expression of genes associated with the ethylene signaling pathway were enhanced significantly following overexpression of GbaNA1. Intriguingly, overexpression of the GbaNA1 ortholog from Gossypium hirsutum (GhNA1) in A. thaliana did not induce the defense response of ROS production due to the premature termination of GhNA1, which lacks the encoded NB-ARC and LRR motifs. GbaNA1 therefore confers Verticillium wilt resistance in A. thaliana by the activation of ROS production and ethylene signaling. These results demonstrate the functional conservation of the NBS-LRR-encoding GbaNA1 in a heterologous system, and the mechanism of this resistance, both of which may prove valuable in incorporating GbaNA1-mediated resistance into other plant species.
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Affiliation(s)
- Nan-Yang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Lei Zhou
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dan-Dan Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Steven J. Klosterman
- Crop Improvement and Protection Research Unit, United States Department of Agriculture, Agricultural Research Service, Salinas, CA, United States
| | - Ting-Gang Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Yue-Jing Gui
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Zhi-Qiang Kong
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Xue-Feng Ma
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Dylan P. G. Short
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Wen-Qi Zhang
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Jun-Jiao Li
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
| | - Krishna V. Subbarao
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, c/o Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture, Beijing, China
- *Correspondence: Xiao-Feng Dai, Jie-Yin Chen, Krishna V. Subbarao,
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Tao F, Wang J, Guo Z, Hu J, Xu X, Yang J, Chen X, Hu X. Transcriptomic Analysis Reveal the Molecular Mechanisms of Wheat Higher-Temperature Seedling-Plant Resistance to Puccinia striiformis f. sp. tritici. FRONTIERS IN PLANT SCIENCE 2018; 9:240. [PMID: 29541084 PMCID: PMC5835723 DOI: 10.3389/fpls.2018.00240] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive disease of wheat worldwide. The disease is preferably controlled by growing resistant cultivars. Wheat cultivar Xiaoyan 6 (XY 6) has been resistant to stripe rust since its release. In the previous studies, XY 6 was found to have higher-temperature seedling-plant (HTSP) resistance. However, the molecular mechanisms of HTSP resistance were not clear. To identify differentially expressed genes (DEGs) involved in HTSP resistance, we sequenced 30 cDNA libraries constructed from XY 6 seedlings exposed to several temperature treatments. Compared to the constant normal (15°C) and higher (20°C) temperature treatments, 1395 DEGs were identified in seedlings exposed to 20°C for 24 h (to activate HTSP resistance) and then kept at 15°C. These DEGs were located on all 21 chromosomes, with 29.2% on A, 41.1% on B and 29.7% on D genomes, by mapping to the Chinese Spring wheat genome. The 1395 DEGs were enriched in ribosome, plant-pathogen interaction and glycerolipid metabolism pathways, and some of them were identified as hub proteins (phosphatase 2C10), resistance protein homologs, WRKY transcription factors and protein kinases. The majority of these genes were up-regulated in HTSP resistance. Based on the differential expression, we found that phosphatase 2C10 and LRR receptor-like serine/threonine protein kinases are particularly interesting as they may be important for HTSP resistance through interacting with different resistance proteins, leading to a hypersensitive response.
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Affiliation(s)
- Fei Tao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Junjuan Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zhongfeng Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jingjing Hu
- Wuhan UnigueGene Bioinformatics Science and Technology Co., Ltd, Wuhan, China
| | - Xiangming Xu
- NIAB East Malling Research (EMR), East Malling, United Kingdom
| | - Jiarong Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- *Correspondence: Jiarong Yang
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, United States
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Xiaoping Hu
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24
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Nepal MP, Andersen EJ, Neupane S, Benson BV. Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. Genes (Basel) 2017; 8:E249. [PMID: 28973974 PMCID: PMC5664099 DOI: 10.3390/genes8100249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 09/14/2017] [Accepted: 09/20/2017] [Indexed: 12/19/2022] Open
Abstract
Disease resistance genes (R genes), as part of the plant defense system, have coevolved with corresponding pathogen molecules. The main objectives of this project were to identify non-Toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (nTNL) genes and elucidate their evolutionary divergence across six plant genomes. Using reference sequences from Arabidopsis, we investigated nTNL orthologs in the genomes of common bean, Medicago, soybean, poplar, and rice. We used Hidden Markov Models for sequence identification, performed model-based phylogenetic analyses, visualized chromosomal positioning, inferred gene clustering, and assessed gene expression profiles. We analyzed 908 nTNL R genes in the genomes of the six plant species, and classified them into 12 subgroups based on the presence of coiled-coil (CC), nucleotide binding site (NBS), leucine rich repeat (LRR), resistance to Powdery mildew 8 (RPW8), and BED type zinc finger domains. Traditionally classified CC-NBS-LRR (CNL) genes were nested into four clades (CNL A-D) often with abundant, well-supported homogeneous subclades of Type-II R genes. CNL-D members were absent in rice, indicating a unique R gene retention pattern in the rice genome. Genomes from Arabidopsis, common bean, poplar and soybean had one chromosome without any CNL R genes. Medicago and Arabidopsis had the highest and lowest number of gene clusters, respectively. Gene expression analyses suggested unique patterns of expression for each of the CNL clades. Differential gene expression patterns of the nTNL genes were often found to correlate with number of introns and GC content, suggesting structural and functional divergence.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Ethan J Andersen
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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25
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Yang S, Li H, He H, Zhou Y, Zhang Z. Critical assessment and performance improvement of plant–pathogen protein–protein interaction prediction methods. Brief Bioinform 2017; 20:274-287. [DOI: 10.1093/bib/bbx123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Indexed: 01/15/2023] Open
Affiliation(s)
- Shiping Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University
| | - Hong Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University
| | - Yuan Zhou
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University
| | - Ziding Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University
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26
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Chan KL, Tatarinova TV, Rosli R, Amiruddin N, Azizi N, Halim MAA, Sanusi NSNM, Jayanthi N, Ponomarenko P, Triska M, Solovyev V, Firdaus-Raih M, Sambanthamurthi R, Murphy D, Low ETL. Evidence-based gene models for structural and functional annotations of the oil palm genome. Biol Direct 2017; 12:21. [PMID: 28886750 PMCID: PMC5591544 DOI: 10.1186/s13062-017-0191-4] [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: 04/27/2017] [Accepted: 08/07/2017] [Indexed: 11/13/2022] Open
Abstract
Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and characterization of genes associated with traits of interest, such as those for fatty acid biosynthesis and disease resistance, were also limited. Lipid-, especially fatty acid (FA)-related genes are of particular interest for the oil palm as they specify oil yields and quality. This paper presents the characterization of the oil palm genome using different gene prediction methods and comparative genomics analysis, identification of FA biosynthesis and disease resistance genes, and the development of an annotation database and bioinformatics tools. Results Using two independent gene-prediction pipelines, Fgenesh++ and Seqping, 26,059 oil palm genes with transcriptome and RefSeq support were identified from the oil palm genome. These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3-rich genes (GC3 ≥ 0.75286) being intronless. In comparison, only one-seventh of the oil palm genes identified are intronless. Using comparative genomics analysis, characterization of conserved domains and active sites, and expression analysis, 42 key genes involved in FA biosynthesis in oil palm were identified. For three of them, namely EgFABF, EgFABH and EgFAD3, segmental duplication events were detected. Our analysis also identified 210 candidate resistance genes in six classes, grouped by their protein domain structures. Conclusions We present an accurate and comprehensive annotation of the oil palm genome, focusing on analysis of important categories of genes (GC3-rich and intronless), as well as those associated with important functions, such as FA biosynthesis and disease resistance. The study demonstrated the advantages of having an integrated approach to gene prediction and developed a computational framework for combining multiple genome annotations. These results, available in the oil palm annotation database (http://palmxplore.mpob.gov.my), will provide important resources for studies on the genomes of oil palm and related crops. Reviewers This article was reviewed by Alexander Kel, Igor Rogozin, and Vladimir A. Kuznetsov. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0191-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, California, 91750, USA.,Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.,Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Nadzirah Amiruddin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Mohd Amin Ab Halim
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nik Shazana Nik Mohd Sanusi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Petr Ponomarenko
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Martin Triska
- Children's Hospital Los Angeles, University of Southern California, Los Angeles, CA, 90089, USA
| | - Victor Solovyev
- Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY, 10549, USA
| | - Mohd Firdaus-Raih
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ravigadevi Sambanthamurthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
| | - Denis Murphy
- Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, CF371DL, UK
| | - Eng-Ti Leslie Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, No. 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia.
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27
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Chandra S, Kazmi AZ, Ahmed Z, Roychowdhury G, Kumari V, Kumar M, Mukhopadhyay K. Genome-wide identification and characterization of NB-ARC resistant genes in wheat (Triticum aestivum L.) and their expression during leaf rust infection. PLANT CELL REPORTS 2017; 36:1097-1112. [PMID: 28401336 DOI: 10.1007/s00299-017-2141-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/04/2017] [Indexed: 05/06/2023]
Abstract
NB-ARC domain-containing resistance genes from the wheat genome were identified, characterized and localized on chromosome arms that displayed differential yet positive response during incompatible and compatible leaf rust interactions. Wheat (Triticum aestivum L.) is an important cereal crop; however, its production is affected severely by numerous diseases including rusts. An efficient, cost-effective and ecologically viable approach to control pathogens is through host resistance. In wheat, high numbers of resistance loci are present but only few have been identified and cloned. A comprehensive analysis of the NB-ARC-containing genes in complete wheat genome was accomplished in this study. Complete NB-ARC encoding genes were mined from the Ensembl Plants database to predict 604 NB-ARC containing sequences using the HMM approach. Genome-wide analysis of orthologous clusters in the NB-ARC-containing sequences of wheat and other members of the Poaceae family revealed maximum homology with Oryza sativa indica and Brachypodium distachyon. The identification of overlap between orthologous clusters enabled the elucidation of the function and evolution of resistance proteins. The distributions of the NB-ARC domain-containing sequences were found to be balanced among the three wheat sub-genomes. Wheat chromosome arms 4AL and 7BL had the most NB-ARC domain-containing contigs. The spatio-temporal expression profiling studies exemplified the positive role of these genes in resistant and susceptible wheat plants during incompatible and compatible interaction in response to the leaf rust pathogen Puccinia triticina. Two NB-ARC domain-containing sequences were modelled in silico, cloned and sequenced to analyze their fine structures. The data obtained in this study will augment isolation, characterization and application NB-ARC resistance genes in marker-assisted selection based breeding programs for improving rust resistance in wheat.
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Affiliation(s)
- Saket Chandra
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Andaleeb Z Kazmi
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Zainab Ahmed
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Gargi Roychowdhury
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Veena Kumari
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Manish Kumar
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Kunal Mukhopadhyay
- Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
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Peng FY, Yang RC. Prediction and analysis of three gene families related to leaf rust (Puccinia triticina) resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:108. [PMID: 28633642 PMCID: PMC5477749 DOI: 10.1186/s12870-017-1056-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/06/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND The resistance to leaf rust (Lr) caused by Puccinia triticina in wheat (Triticum aestivum L.) has been well studied over the past decades with over 70 Lr genes being mapped on different chromosomes and numerous QTLs (quantitative trait loci) being detected or mapped using DNA markers. Such resistance is often divided into race-specific and race-nonspecific resistance. The race-nonspecific resistance can be further divided into resistance to most or all races of the same pathogen and resistance to multiple pathogens. At the molecular level, these three types of resistance may cover across the whole spectrum of pathogen specificities that are controlled by genes encoding different protein families in wheat. The objective of this study is to predict and analyze genes in three such families: NBS-LRR (nucleotide-binding sites and leucine-rich repeats or NLR), START (Steroidogenic Acute Regulatory protein [STaR] related lipid-transfer) and ABC (ATP-Binding Cassette) transporter. The focus of the analysis is on the patterns of relationships between these protein-coding genes within the gene families and QTLs detected for leaf rust resistance. RESULTS We predicted 526 ABC, 1117 NLR and 144 START genes in the hexaploid wheat genome through a domain analysis of wheat proteome. Of the 1809 SNPs from leaf rust resistance QTLs in seedling and adult stages of wheat, 126 SNPs were found within coding regions of these genes or their neighborhood (5 Kb upstream from transcription start site [TSS] or downstream from transcription termination site [TTS] of the genes). Forty-three of these SNPs for adult resistance and 18 SNPs for seedling resistance reside within coding or neighboring regions of the ABC genes whereas 14 SNPs for adult resistance and 29 SNPs for seedling resistance reside within coding or neighboring regions of the NLR gene. Moreover, we found 17 nonsynonymous SNPs for adult resistance and five SNPs for seedling resistance in the ABC genes, and five nonsynonymous SNPs for adult resistance and six SNPs for seedling resistance in the NLR genes. Most of these coding SNPs were predicted to alter encoded amino acids and such information may serve as a starting point towards more thorough molecular and functional characterization of the designated Lr genes. Using the primer sequences of 99 known non-SNP markers from leaf rust resistance QTLs, we found candidate genes closely linked to these markers, including Lr34 with distances to its two gene-specific markers being 1212 bases (to cssfr1) and 2189 bases (to cssfr2). CONCLUSION This study represents a comprehensive analysis of ABC, NLR and START genes in the hexaploid wheat genome and their physical relationships with QTLs for leaf rust resistance at seedling and adult stages. Our analysis suggests that the ABC (and START) genes are more likely to be co-located with QTLs for race-nonspecific, adult resistance whereas the NLR genes are more likely to be co-located with QTLs for race-specific resistance that would be often expressed at the seedling stage. Though our analysis was hampered by inaccurate or unknown physical positions of numerous QTLs due to the incomplete assembly of the complex hexaploid wheat genome that is currently available, the observed associations between (i) QTLs for race-specific resistance and NLR genes and (ii) QTLs for nonspecific resistance and ABC genes will help discover SNP variants for leaf rust resistance at seedling and adult stages. The genes containing nonsynonymous SNPs are promising candidates that can be investigated in future studies as potential new sources of leaf rust resistance in wheat breeding.
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Affiliation(s)
- Fred Y Peng
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
| | - Rong-Cai Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 410 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada.
- Feed Crops Section, Alberta Agriculture and Forestry, 7000 - 113 Street, Edmonton, AB, T6H 5T6, Canada.
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Xiang L, Liu J, Wu C, Deng Y, Cai C, Zhang X, Cai Y. Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species. BMC Genomics 2017; 18:292. [PMID: 28403834 PMCID: PMC5388996 DOI: 10.1186/s12864-017-3682-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 04/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimondii, and the two allotetraploid cotton species, Gossypium hirsutum (TM-1) and Gossypium barbadense allow for a more comprehensive and systematic comparative study of NBS-encoding genes to elucidate the mechanisms of cotton disease resistance. Results Based on the genome assembly data, 246, 365, 588 and 682 NBS-encoding genes were identified in G. arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. The distribution of NBS-encoding genes among the chromosomes was nonrandom and uneven, and was tended to form clusters. Gene structure analysis showed that G. arboreum and G. hirsutum possessed a greater proportion of CN, CNL, and N genes and a lower proportion of NL, TN and TNL genes compared to that of G. raimondii and G. barbadense, while the percentages of RN and RNL genes remained relatively unchanged. The percentage changes among them were largest for TNL genes, about 7 times. Exon statistics showed that the average exon numbers per NBS gene in G. raimondii and G. barbadense were all greater than that in G. arboretum and G. hirsutum. Phylogenetic analysis revealed that the TIR-NBS genes of G. barbadense were closely related with that of G. raimondii. Sequence similarity analysis showed that diploid cotton G. arboreum possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. hirsutum, while diploid G. raimondii possessed a larger proportion of NBS-encoding genes similar to that of allotetraploid cotton G. barbadense. The synteny analysis showed that more NBS genes in G. raimondii and G. arboreum were syntenic with that in G. barbadense and G. hirsutum, respectively. Conclusions The structural architectures, amino acid sequence similarities and synteny of NBS-encoding genes between G. arboreum and G. hirsutum, and between G. raimondii and G. barbadense were the highest among comparisons between the diploid and allotetraploid genomes, indicating that G. hirsutum inherited more NBS-encoding genes from G. arboreum, while G. barbadense inherited more NBS-encoding genes from G. raimondii. This asymmetric evolution of NBS-encoding genes may help to explain why G. raimondii and G. barbadense are more resistant to Verticillium wilt, whereas G. arboreum and G. hirsutum are more susceptible to Verticillium wilt. The disease resistances of the allotetraploid cotton were related to their NBS-encoding genes especially in regard from which diploid progenitor they were derived, and the TNL genes may have a significant role in disease resistance to Verticillium wilt in G. raimondii and G. barbadense. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3682-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Liuxin Xiang
- State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China.,College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Jinggao Liu
- United States Department of Agriculture, Southern Plains Agricultural Research Center, Agricultural Research Service, 2765 F & B Rd, College Station, TX, 77845, USA
| | - Chaofeng Wu
- College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Yushan Deng
- College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Chaowei Cai
- State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China
| | - Xiao Zhang
- State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China
| | - Yingfan Cai
- State Key Laboratory of Cotton Biology, College of Life Science, Henan Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, 475004, China.
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Genome-wide identification and resistance expression analysis of the NBS gene family in Triticum urartu. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0526-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Lana UGDP, Prazeres de Souza IR, Noda RW, Pastina MM, Magalhaes JV, Guimaraes CT. Quantitative Trait Loci and Resistance Gene Analogs Associated with Maize White Spot Resistance. PLANT DISEASE 2017; 101:200-208. [PMID: 30682293 DOI: 10.1094/pdis-06-16-0899-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Maize white spot (MWS), caused by the bacterium Pantoea ananatis, is one of the most important maize foliar diseases in tropical and subtropical regions, causing significant yield losses. Despite its economic importance, genetic studies of MWS are scarce. The aim of this study was to map quantitative trait loci (QTL) associated with MWS resistance and to identify resistance gene analogs (RGA) underlying these QTL. QTL mapping was performed in a tropical maize F2:3 population, which was genotyped with simple-sequence repeat and RGA-tagged markers and phenotyped for the response to MWS in two Brazilian southeastern locations. Nine QTL explained approximately 70% of the phenotypic variance for MWS resistance at each location, with two of them consistently detected in both environments. Data mining using 112 resistance genes cloned from different plant species revealed 1,697 RGA distributed in clusters within the maize genome. The RGA Pto19, Pto20, Pto99, and Xa26.151.4 were genetically mapped within MWS resistance QTL on chromosomes 4 and 8 and were preferentially expressed in the resistant parental line at locations where their respective QTL occurred. The consistency of QTL mapping, in silico prediction, and gene expression analyses revealed RGA and genomic regions suitable for marker-assisted selection to improve MWS resistance.
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Long N, Ren X, Xiang Z, Wan W, Dong Y. Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2016; 23:6. [PMID: 27096138 PMCID: PMC4835900 DOI: 10.1186/s40709-016-0048-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/05/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND Nicotiana belongs to the Solanaceae family that includes important crops such as tomato, potato, eggplant, and pepper. Nicotiana species are of worldwide economic importance and are important model plants for scientific research. Here we present the comparative analysis of the transcriptomes of six wild diploid Nicotiana species. Wild relatives provide an excellent study system for the analysis of the genetic basis for various traits, especially disease resistance. RESULTS Whole transcriptome sequencing (RNA-seq) was performed for leaves of six diploid Nicotiana species, i.e. Nicotiana glauca, Nicotiana noctiflora, Nicotiana cordifolia, Nicotiana knightiana, Nicotiana setchellii and Nicotiana tomentosiformis. For each species, 9.0-22.3 Gb high-quality clean data were generated, and 67,073-182,046 transcripts were assembled with lengths greater than 100 bp. Over 90 % of the ORFs in each species had significant similarity with proteins in the NCBI non-redundant protein sequence (NR) database. A total of 2491 homologs were identified and used to construct a phylogenetic tree from the respective transcriptomes in Nicotiana. Bioinformatic analysis identified resistance gene analogs, major transcription factor families, and alkaloid transporter genes linked to plant defense. CONCLUSIONS This is the first report on the leaf transcriptomes of six wild Nicotiana species by Illumina paired-end sequencing and de novo assembly without a reference genome. These sequence resources hopefully will provide an opportunity for identifying genes involved in plant defense and several important quality traits in wild Nicotiana and will accelerate functional genomic studies and genetic improvement efforts of Nicotiana or other important Solanaceae crops in the future.
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Affiliation(s)
- Ni Long
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
| | - Xueliang Ren
- />Guizhou Tobacco Research Institute, North Yuntan Road, Jinyang District, Guiyang, 550003 Guizhou China
| | - Zhidan Xiang
- />State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming, 650223 Yunnan China
| | - Wenting Wan
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
| | - Yang Dong
- />Faculty of Life Science and Technology, Kunming University of Science and Technology, South Jingming Road No.727, Kunming, 650500 Yunnan China
- />Biological Big Data College, Yunnan Agricultural University, Kunming, 650201 Yunnan China
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DRPPP: A machine learning based tool for prediction of disease resistance proteins in plants. Comput Biol Med 2016; 78:42-48. [DOI: 10.1016/j.compbiomed.2016.09.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 11/22/2022]
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Zhang Y, Xia R, Kuang H, Meyers BC. The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them. Mol Biol Evol 2016; 33:2692-705. [PMID: 27512116 PMCID: PMC5026261 DOI: 10.1093/molbev/msw154] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High expression of plant nucleotide binding site leucine-rich repeat (NBS-LRR) defense genes is often lethal to plant cells, a phenotype perhaps associated with fitness costs. Plants implement several mechanisms to control the transcript level of NBS-LRR defense genes. As negative transcriptional regulators, diverse miRNAs target NBS-LRRs in eudicots and gymnosperms. To understand the evolutionary benefits of this miRNA-NBS-LRR regulatory system, we investigated the NBS-LRRs of 70 land plants, coupling this analysis with extensive small RNA data. A tight association between the diversity of NBS-LRRs and miRNAs was found. The miRNAs typically target highly duplicated NBS-LRRs In comparison, families of heterogeneous NBS-LRRs were rarely targeted by miRNAs in Poaceae and Brassicaceae genomes. We observed that duplicated NBS-LRRs from different gene families periodically gave birth to new miRNAs. Most of these newly emerged miRNAs target the same conserved, encoded protein motif of NBS-LRRs, consistent with a model of convergent evolution for these miRNAs. By assessing the interactions between miRNAs and NBS-LRRs, we found nucleotide diversity in the wobble position of the codons in the target site drives the diversification of miRNAs. Taken together, we propose a co-evolutionary model of plant NBS-LRRs and miRNAs hypothesizing how plants balance the benefits and costs of NBS-LRR defense genes.
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Affiliation(s)
- Yu Zhang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China Donald Danforth Plant Science Center, St. Louis
| | - Rui Xia
- Donald Danforth Plant Science Center, St. Louis
| | - Hanhui Kuang
- Key Laboratory of Horticulture Biology, Ministry of Education, and Department of Vegetable Crops, College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis Division of Plant Sciences, University of Missouri - Columbia
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Using Genotyping by Sequencing to Map Two Novel Anthracnose Resistance Loci in Sorghum bicolor. G3-GENES GENOMES GENETICS 2016; 6:1935-46. [PMID: 27194807 PMCID: PMC4938647 DOI: 10.1534/g3.116.030510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Colletotrichum sublineola is an aggressive fungal pathogen that causes anthracnose in sorghum [Sorghum bicolor (L.) Moench]. The obvious symptoms of anthracnose are leaf blight and stem rot. Sorghum, the fifth most widely grown cereal crop in the world, can be highly susceptible to the disease, most notably in hot and humid environments. In the southeastern United States the acreage of sorghum has been increasing steadily in recent years, spurred by growing interest in producing biofuels, bio-based products, and animal feed. Resistance to anthracnose is, therefore, of paramount importance for successful sorghum production in this region. To identify anthracnose resistance loci present in the highly resistant cultivar ‘Bk7’, a biparental mapping population of F3:4 and F4:5 sorghum lines was generated by crossing ‘Bk7’ with the susceptible inbred ‘Early Hegari-Sart’. Lines were phenotyped in three environments and in two different years following natural infection. The population was genotyped by sequencing. Following a stringent custom filtering protocol, totals of 5186 and 2759 informative SNP markers were identified in the two populations. Segregation data and association analysis identified resistance loci on chromosomes 7 and 9, with the resistance alleles derived from ‘Bk7’. Both loci contain multiple classes of defense-related genes based on sequence similarity and gene ontologies. Genetic analysis following an independent selection experiment of lines derived from a cross between ‘Bk7’ and sweet sorghum ‘Mer81-4’ narrowed the resistance locus on chromosome 9 substantially, validating this QTL. As observed in other species, sorghum appears to have regions of clustered resistance genes. Further characterization of these regions will facilitate the development of novel germplasm with resistance to anthracnose and other diseases.
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Natarajan S, Kim HT, Thamilarasan SK, Veerappan K, Park JI, Nou IS. Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon. PLoS One 2016; 11:e0157524. [PMID: 27311063 PMCID: PMC4911151 DOI: 10.1371/journal.pone.0157524] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 06/01/2016] [Indexed: 11/30/2022] Open
Abstract
Powdery mildew is one of the most common fungal diseases in the world. This disease frequently affects melon (Cucumis melo L.) and other Cucurbitaceous family crops in both open field and greenhouse cultivation. One of the goals of genomics is to identify the polymorphic loci responsible for variation in phenotypic traits. In this study, powdery mildew disease assessment scores were calculated for four melon accessions, 'SCNU1154', 'Edisto47', 'MR-1', and 'PMR5'. To investigate the genetic variation of these accessions, whole genome re-sequencing using the Illumina HiSeq 2000 platform was performed. A total of 754,759,704 quality-filtered reads were generated, with an average of 82.64% coverage relative to the reference genome. Comparisons of the sequences for the melon accessions revealed around 7.4 million single nucleotide polymorphisms (SNPs), 1.9 million InDels, and 182,398 putative structural variations (SVs). Functional enrichment analysis of detected variations classified them into biological process, cellular component and molecular function categories. Further, a disease-associated QTL map was constructed for 390 SNPs and 45 InDels identified as related to defense-response genes. Among them 112 SNPs and 12 InDels were observed in powdery mildew responsive chromosomes. Accordingly, this whole genome re-sequencing study identified SNPs and InDels associated with defense genes that will serve as candidate polymorphisms in the search for sources of resistance against powdery mildew disease and could accelerate marker-assisted breeding in melon.
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Affiliation(s)
- Sathishkumar Natarajan
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 540–950, Republic of Korea
| | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 540–950, Republic of Korea
| | | | - Karpagam Veerappan
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 540–950, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 540–950, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam 540–950, Republic of Korea
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A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 2016; 48:657-66. [PMID: 27158781 DOI: 10.1038/ng.3565] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 04/11/2016] [Indexed: 11/09/2022]
Abstract
We report a high-quality chromosome-scale assembly and analysis of the carrot (Daucus carota) genome, the first sequenced genome to include a comparative evolutionary analysis among members of the euasterid II clade. We characterized two new polyploidization events, both occurring after the divergence of carrot from members of the Asterales order, clarifying the evolutionary scenario before and after radiation of the two main asterid clades. Large- and small-scale lineage-specific duplications have contributed to the expansion of gene families, including those with roles in flowering time, defense response, flavor, and pigment accumulation. We identified a candidate gene, DCAR_032551, that conditions carotenoid accumulation (Y) in carrot taproot and is coexpressed with several isoprenoid biosynthetic genes. The primary mechanism regulating carotenoid accumulation in carrot taproot is not at the biosynthetic level. We hypothesize that DCAR_032551 regulates upstream photosystem development and functional processes, including photomorphogenesis and root de-etiolation.
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Kroj T, Chanclud E, Michel‐Romiti C, Grand X, Morel J. Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread. THE NEW PHYTOLOGIST 2016; 210:618-26. [PMID: 26848538 PMCID: PMC5067614 DOI: 10.1111/nph.13869] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/16/2015] [Indexed: 05/18/2023]
Abstract
Plant immune receptors of the class of nucleotide-binding and leucine-rich repeat domain (NLR) proteins can contain additional domains besides canonical NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC)) and leucine-rich repeat (LRR) domains. Recent research suggests that these additional domains act as integrated decoys recognizing effectors from pathogens. Proteins homologous to integrated decoys are suspected to be effector targets and involved in disease or resistance. Here, we scrutinized 31 entire plant genomes to identify putative integrated decoy domains in NLR proteins using the Interpro search. The involvement of the Zinc Finger-BED type (ZBED) protein containing a putative decoy domain, called BED, in rice (Oryza sativa) resistance was investigated by evaluating susceptibility to the blast fungus Magnaporthe oryzae in rice over-expression and knock-out mutants. This analysis showed that all plants tested had integrated various atypical protein domains into their NLR proteins (on average 3.5% of all NLR proteins). We also demonstrated that modifying the expression of the ZBED gene modified disease susceptibility. This study suggests that integration of decoy domains in NLR immune receptors is widespread and frequent in plants. The integrated decoy model is therefore a powerful concept to identify new proteins involved in disease resistance. Further in-depth examination of additional domains in NLR proteins promises to unravel many new proteins of the plant immune system.
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Affiliation(s)
- Thomas Kroj
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Emilie Chanclud
- Université Montpellier2 Place Eugène Bataillon34095Montpellier Cedex 5France
| | - Corinne Michel‐Romiti
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Xavier Grand
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
| | - Jean‐Benoit Morel
- INRACIRADSupAgroUMR BGPI INRA/CIRAD/SupAgroCampus International de BaillarguetTA A 54/K34398MontpellierFrance
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Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R. Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. Genome Biol 2016; 17:32. [PMID: 26911872 PMCID: PMC4766624 DOI: 10.1186/s13059-016-0883-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/22/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million year old whole genome duplication shared by most crop legumes. RESULTS We report the genome and the transcription atlas of coding and non-coding genes of a Mesoamerican genotype of common bean (Phaseolus vulgaris L., BAT93). Using a comprehensive phylogenomics analysis, we assessed the past and recent evolution of common bean, and traced the diversification of patterns of gene expression following duplication. We find that successive rounds of gene duplications in legumes have shaped tissue and developmental expression, leading to increased levels of specialization in larger gene families. We also find that many long non-coding RNAs are preferentially expressed in germ-line-related tissues (pods and seeds), suggesting that they play a significant role in fruit development. Our results also suggest that most bean-specific gene family expansions, including resistance gene clusters, predate the split of the Mesoamerican and Andean gene pools. CONCLUSIONS The genome and transcriptome data herein generated for a Mesoamerican genotype represent a counterpart to the genomic resources already available for the Andean gene pool. Altogether, this information will allow the genetic dissection of the characters involved in the domestication and adaptation of the crop, and their further implementation in breeding strategies for this important crop.
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Affiliation(s)
- Anna Vlasova
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584 LT, Utrecht, The Netherlands
| | - Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Miguel Hernández-Oñate
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - André E Minoche
- Garvan Institute of Medical Research, 384 Victoria Street, Sydney, NSW, 2010, Australia
| | - Ionas Erb
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Francisco Câmara
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Pablo Prieto-Barja
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - André Corvelo
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Walter Sanseverino
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Gastón Westergaard
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Juliane C Dohm
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Georgios J Pappas
- Department of Cellular Biology, University of Brasilia, Biological Science Institute, Brasília, DF, 70790-160, Brazil
| | - Soledad Saburido-Alvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico
| | - Darek Kedra
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Irene Gonzalez
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Luca Cozzuto
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jessica Gómez-Garrido
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - María A Aguilar-Morón
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Nuria Andreu
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | - Jordi Garcia-Mas
- IRTA, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, 08193 Bellaterra, Barcelona, Catalonia, Spain
| | - Maik Zehnsdorf
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Catalonia, Spain
| | - Martín P Vázquez
- Instituto de Agrobiotecnología Rosario (INDEAR), Rosario, Santa Fe, 2000, Argentina
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Ernesto Lowy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Alejandro Mentaberry
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires (UBA), C1428EGA, Buenos Aires, Argentina
| | | | - José Luís García
- Environmental Biology Department, Centro de Investigaciones Biológicas, (CSIC), 28040, Madrid, Spain
| | - Tyler Alioto
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Federico Sánchez
- Depto. de Biología Molecular de Plantas, Instituto Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Morelos, Mexico
| | - Heinz Himmelbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Cinvestav-Irapuato, CP 36821, Irapuato, Guanajuato, Mexico.
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain.
- IMIM (Hospital del Mar Medical Research Institute), 08003, Barcelona, Spain.
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Yang X, Wang J. Genome-Wide Analysis of NBS-LRR Genes in Sorghum Genome Revealed Several Events Contributing to NBS-LRR Gene Evolution in Grass Species. Evol Bioinform Online 2016; 12:9-21. [PMID: 26792976 PMCID: PMC4714652 DOI: 10.4137/ebo.s36433] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/02/2015] [Accepted: 12/04/2015] [Indexed: 11/28/2022] Open
Abstract
The nucleotide-binding site (NBS)–leucine-rich repeat (LRR) gene family is crucially important for offering resistance to pathogens. To explore evolutionary conservation and variability of NBS-LRR genes across grass species, we identified 88, 107, 24, and 44 full-length NBS-LRR genes in sorghum, rice, maize, and Brachypodium, respectively. A comprehensive analysis was performed on classification, genome organization, evolution, expression, and regulation of these NBS-LRR genes using sorghum as a representative of grass species. In general, the full-length NBS-LRR genes are highly clustered and duplicated in sorghum genome mainly due to local duplications. NBS-LRR genes have basal expression levels and are highly potentially targeted by miRNA. The number of NBS-LRR genes in the four grass species is positively correlated with the gene clustering rate. The results provided a valuable genomic resource and insights for functional and evolutionary studies of NBS-LRR genes in grass species.
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Affiliation(s)
- Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA.; Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, USA.; FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Kushwaha SK, Chauhan P, Hedlund K, Ahrén D. NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. Bioinformatics 2015; 32:1223-5. [PMID: 26656003 DOI: 10.1093/bioinformatics/btv714] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/02/2015] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED The nucleotide binding site leucine-rich repeats (NBSLRRs) belong to one of the largest known families of disease resistance genes that encode resistance proteins (R-protein) against the pathogens of plants. Various defence mechanisms have explained the regulation of plant immunity, but still, we have limited understanding about plant defence against different pathogens. Identification of R-proteins and proteins having R-protein-like features across the genome, transcriptome and proteome would be highly useful to develop the global understanding of plant defence mechanisms, but it is laborious and time-consuming task. Therefore, we have developed a support vector machine-based high-throughput pipeline called NBSPred to differentiate NBSLRR and NBSLRR-like protein from Non-NBSLRR proteins from genome, transcriptome and protein sequences. The pipeline was tested and validated with input sequences from three dicot and two monocot plants including Arabidopsis thaliana, Boechera stricta, Brachypodium distachyon Solanum lycopersicum and Zea mays. AVAILABILITY AND IMPLEMENTATION The NBSPred pipeline is available at http://soilecology.biol.lu.se/nbs/ SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT sandeep.kushwaha@biol.lu.se.
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Affiliation(s)
- Sandeep K Kushwaha
- Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden, PlantLink, Department of Plant Protection, Swedish University of Agricultural Sciences, Alnarp, Sweden and Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden
| | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden
| | - Katarina Hedlund
- Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden
| | - Dag Ahrén
- Department of Biology, Lund University, Ecology Building, Lund 22363, Sweden, Bioinformatics Infrastructure for Life Sciences (BILS), Lund University, Lund, Sweden
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Zhen G, Zhang L, Du Y, Yu R, Liu X, Cao F, Chang Q, Deng X, Xia M, He H. De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments. SCIENCE CHINA-LIFE SCIENCES 2015; 58:1099-110. [PMID: 26563176 DOI: 10.1007/s11427-015-4961-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 06/16/2013] [Indexed: 12/22/2022]
Abstract
Panax ginseng C. A. Meyer is an important traditional herb in eastern Asia. It contains ginsenosides, which are primary bioactive compounds with medicinal properties. Although ginseng has been cultivated since at least the Ming dynasty to increase production, cultivated ginseng has lower quantities of ginsenosides and lower disease resistance than ginseng grown under natural conditions. We extracted root RNA from six varieties of fifth-year P. ginseng cultivars representing four different growth conditions, and performed Illumina paired-end sequencing. In total, 163,165,706 raw reads were obtained and used to generate a de novo transcriptome that consisted of 151,763 contigs (76,336 unigenes), of which 100,648 contigs (66.3%) were successfully annotated. Differential expression analysis revealed that most differentially expressed genes (DEGs) were upregulated (246 out of 258, 95.3%) in ginseng grown under natural conditions compared with that grown under artificial conditions. These DEGs were enriched in gene ontology (GO) terms including response to stimuli and localization. In particular, some key ginsenoside biosynthesis-related genes, including HMG-CoA synthase (HMGS), mevalonate kinase (MVK), and squalene epoxidase (SE), were upregulated in wild-grown ginseng. Moreover, a high proportion of disease resistance-related genes were upregulated in wild-grown ginseng. This study is the first transcriptome analysis to compare wild-grown and cultivated ginseng, and identifies genes that may produce higher ginsenoside content and better disease resistance in the wild; these genes may have the potential to improve cultivated ginseng grown in artificial environments.
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Affiliation(s)
- Gang Zhen
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Lei Zhang
- Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, 100085, China
| | - YaNan Du
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - RenBo Yu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - XinMin Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - FangRui Cao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - Qi Chang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
| | - XingWang Deng
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
| | - Mian Xia
- Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, 100085, China.
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China.
- School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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Hazzouri KM, Flowers JM, Visser HJ, Khierallah HSM, Rosas U, Pham GM, Meyer RS, Johansen CK, Fresquez ZA, Masmoudi K, Haider N, El Kadri N, Idaghdour Y, Malek JA, Thirkhill D, Markhand GS, Krueger RR, Zaid A, Purugganan MD. Whole genome re-sequencing of date palms yields insights into diversification of a fruit tree crop. Nat Commun 2015; 6:8824. [PMID: 26549859 PMCID: PMC4667612 DOI: 10.1038/ncomms9824] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 10/07/2015] [Indexed: 12/13/2022] Open
Abstract
Date palms (Phoenix dactylifera) are the most significant perennial crop in arid regions of the Middle East and North Africa. Here, we present a comprehensive catalogue of approximately seven million single nucleotide polymorphisms in date palms based on whole genome re-sequencing of a collection of 62 cultivars. Population structure analysis indicates a major genetic divide between North Africa and the Middle East/South Asian date palms, with evidence of admixture in cultivars from Egypt and Sudan. Genome-wide scans for selection suggest at least 56 genomic regions associated with selective sweeps that may underlie geographic adaptation. We report candidate mutations for trait variation, including nonsense polymorphisms and presence/absence variation in gene content in pathways for key agronomic traits. We also identify a copia-like retrotransposon insertion polymorphism in the R2R3 myb-like orthologue of the oil palm virescens gene associated with fruit colour variation. This analysis documents patterns of post-domestication diversification and provides a genomic resource for this economically important perennial tree crop.
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Affiliation(s)
- Khaled M Hazzouri
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Hendrik J Visser
- Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates
| | - Hussam S M Khierallah
- Date Palm Research Unit, College of Agriculture, PO Box 47054, University of Baghdad, Baghdad, Iraq
| | - Ulises Rosas
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Gina M Pham
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Rachel S Meyer
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Caryn K Johansen
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Zoë A Fresquez
- Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
| | - Khaled Masmoudi
- International Center for Biosaline Agriculture, Academic City, Al Ruwayyah 2, PO Box 14660, Dubai, United Arab Emirates
| | - Nadia Haider
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria, PO Box 6091, Damascus, Syria
| | - Nabila El Kadri
- Technical Center of Dates, Ministry of Agriculture, Kebili, Tunisia
| | - Youssef Idaghdour
- Division of Science and Mathematics, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Joel A Malek
- Genomics Core Laboratory, Weill Cornell Medical College in Qatar, Doha 24144, Qatar
| | - Deborah Thirkhill
- Arizona State University Date Palm Collection, Arizona State University Tempe, Arizona, Arizona 85281, USA
| | - Ghulam S Markhand
- Date Palm Research Institute (DPRI), Shah Abdul Latif University, Khairpur, Sindh, Pakistan
| | - Robert R Krueger
- United States Department of Agriculture, Riverside, California 92507, USA
| | - Abdelouahhab Zaid
- Date Palm Research and Development Unit, United Arab Emirates University, Al-Ain, PO Box 15551, Abu Dhabi, United Arab Emirates
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, PO Box 129188, Abu Dhabi, United Arab Emirates.,Department of Biology, Center for Genomics and Systems Biology, 12 Waverly Place, New York University, New York, New York 10003, USA
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Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E. A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. FRONTIERS IN PLANT SCIENCE 2015; 6:718. [PMID: 26442032 PMCID: PMC4585127 DOI: 10.3389/fpls.2015.00718] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/27/2015] [Indexed: 05/18/2023]
Abstract
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
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Affiliation(s)
| | | | | | | | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural SciencesAlnarp, Sweden
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Zhang J, Yu J, Pei W, Li X, Said J, Song M, Sanogo S. Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton. BMC Genomics 2015; 16:577. [PMID: 26239843 PMCID: PMC4524102 DOI: 10.1186/s12864-015-1682-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/01/2015] [Indexed: 12/12/2022] Open
Abstract
Background Verticillium wilt (VW) and Fusarium wilt (FW), caused by the soil-borne fungi Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, respectively, are two most destructive diseases in cotton production worldwide. Root-knot nematodes (Meloidogyne incognita, RKN) and reniform nematodes (Rotylenchulus reniformis, RN) cause the highest yield loss in the U.S. Planting disease resistant cultivars is the most cost effective control method. Numerous studies have reported mapping of quantitative trait loci (QTLs) for disease resistance in cotton; however, very few reliable QTLs were identified for use in genomic research and breeding. Results This study first performed a 4-year replicated test of a backcross inbred line (BIL) population for VW resistance, and 10 resistance QTLs were mapped based on a 2895 cM linkage map with 392 SSR markers. The 10 VW QTLs were then placed to a consensus linkage map with other 182 VW QTLs, 75 RKN QTLs, 27 FW QTLs, and 7 RN QTLs reported from 32 publications. A meta-analysis of QTLs identified 28 QTL clusters including 13, 8 and 3 QTL hotspots for resistance to VW, RKN and FW, respectively. The number of QTLs and QTL clusters on chromosomes especially in the A-subgenome was significantly correlated with the number of nucleotide-binding site (NBS) genes, and the distribution of QTLs between homeologous A- and D- subgenome chromosomes was also significantly correlated. Conclusions Ten VW resistance QTL identified in a 4-year replicated study have added useful information to the understanding of the genetic basis of VW resistance in cotton. Twenty-eight disease resistance QTL clusters and 24 hotspots identified from a total of 306 QTLs and linked SSR markers provide important information for marker-assisted selection and high resolution mapping of resistance QTLs and genes. The non-overlapping of most resistance QTL hotspots for different diseases indicates that their resistances are controlled by different genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1682-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of China, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of China, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
| | - Xingli Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of China, Chinese Academy of Agricultural Science, Anyang, Henan, 455000, China.
| | - Joseph Said
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, NM, 88003, USA.
| | - Soum Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA.
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Isolation of NBS-LRR RGAs from invasive Wedelia trilobata and the calculation of evolutionary rates to understand bioinvasion from a molecular evolution perspective. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chen JY, Huang JQ, Li NY, Ma XF, Wang JL, Liu C, Liu YF, Liang Y, Bao YM, Dai XF. Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt. BMC PLANT BIOLOGY 2015; 15:148. [PMID: 26084488 PMCID: PMC4471920 DOI: 10.1186/s12870-015-0508-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 04/27/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND Gossypium raimondii is a Verticillium wilt-resistant cotton species whose genome encodes numerous disease resistance genes that play important roles in the defence against pathogens. However, the characteristics of resistance gene analogues (RGAs) and Verticillium dahliae response loci (VdRLs) have not been investigated on a global scale. In this study, the characteristics of RGA genes were systematically analysed using bioinformatics-driven methods. Moreover, the potential VdRLs involved in the defence response to Verticillium wilt were identified by RNA-seq and correlations with known resistance QTLs. RESULTS The G. raimondii genome encodes 1004 RGA genes, and most of these genes cluster in homology groups based on high levels of similarity. Interestingly, nearly half of the RGA genes occurred in 26 RGA-gene-rich clusters (Rgrcs). The homology analysis showed that sequence exchanges and tandem duplications frequently occurred within Rgrcs, and segmental duplications took place among the different Rgrcs. An RNA-seq analysis showed that the RGA genes play roles in cotton defence responses, forming 26 VdRLs inside in the Rgrcs after being inoculated with V. dahliae. A correlation analysis found that 12 VdRLs were adjacent to the known Verticillium wilt resistance QTLs, and that 5 were rich in NB-ARC domain-containing disease resistance genes. CONCLUSIONS The cotton genome contains numerous RGA genes, and nearly half of them are located in clusters, which evolved by sequence exchanges, tandem duplications and segmental duplications. In the Rgrcs, 26 loci were induced by the V. dahliae inoculation, and 12 are in the vicinity of known Verticillium wilt resistance QTLs.
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Affiliation(s)
- Jie-Yin Chen
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | | | - Nan-Yang Li
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xue-Feng Ma
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Jin-Long Wang
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chuan Liu
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.
| | | | - Yong Liang
- BGI-Shenzhen, Shenzhen, Guangdong, 518083, China.
| | - Yu-Ming Bao
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Xiao-Feng Dai
- Laboratory of Cotton Disease, Institute of Agro-Products Processing Science & Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Nepal MP, Benson BV. CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence. Evol Bioinform Online 2015; 11:49-63. [PMID: 25922568 PMCID: PMC4395141 DOI: 10.4137/ebo.s21782] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/01/2015] [Accepted: 02/01/2015] [Indexed: 01/29/2023] Open
Abstract
Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. The objectives of this study were to identify coiled-coil NBS-LRR (= CNL) R-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the R-genes. Profile hidden Markov models were used for sequence identification and model-based maximum likelihood was used for phylogenetic analysis, and variation in chromosomal positioning, gene clustering, and functional divergence were assessed. We identified 188 soybean CNL genes nested into four clades consistent to their orthologs in Arabidopsis. Gene clustering analysis revealed the presence of 41 gene clusters located on 13 different chromosomes. Analyses of the K s-values and chromosomal positioning suggest duplication events occurring at varying timescales, and an extrapericentromeric positioning may have facilitated their rapid evolution. Each of the four CNL clades exhibited distinct patterns of gene expression. Phylogenetic analysis further supported the extrapericentromeric positioning effect on the divergence and retention of the CNL genes. The results are important for understanding the diversity and divergence of CNL genes in soybean, which would have implication in soybean crop improvement in future.
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Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Benjamin V Benson
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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Abstract
Tomato (Solanum lycopersicum), along with many other economically valuable species, belongs to the Solanaceae family. Understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. Such changes can implicate the affected gene as participating in plant defense. Testing the involvement of these candidate genes in defense has relied largely on posttranscriptional gene silencing, particularly virus-induced gene silencing. We discuss how functional genomics has played a key role in our current understanding of the defense response in tomato and related species and what are the challenges and opportunities for the future.
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Peele HM, Guan N, Fogelqvist J, Dixelius C. Loss and retention of resistance genes in five species of the Brassicaceae family. BMC PLANT BIOLOGY 2014; 14:298. [PMID: 25365911 PMCID: PMC4232680 DOI: 10.1186/s12870-014-0298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/20/2014] [Indexed: 05/02/2023]
Abstract
BACKGROUND Plants have evolved disease resistance (R) genes encoding for nucleotide-binding site (NB) and leucine-rich repeat (LRR) proteins with N-terminals represented by either Toll/Interleukin-1 receptor (TIR) or coiled-coil (CC) domains. Here, a genome-wide study of presence and diversification of CC-NB-LRR and TIR-NB-LRR encoding genes, and shorter domain combinations in 19 Arabidopsis thaliana accessions and Arabidopsis lyrata, Capsella rubella, Brassica rapa and Eutrema salsugineum are presented. RESULTS Out of 528 R genes analyzed, 12 CC-NB-LRR and 17 TIR-NB-LRR genes were conserved among the 19 A. thaliana genotypes, while only two CC-NB-LRRs, including ZAR1, and three TIR-NB-LRRs were conserved when comparing the five species. The RESISTANCE TO LEPTOSPHAERIA MACULANS 1 (RLM1) locus confers resistance to the Brassica pathogen L. maculans the causal agent of blackleg disease and has undergone conservation and diversification events particularly in B. rapa. On the contrary, the RLM3 locus important in the immune response towards Botrytis cinerea and Alternaria spp. has recently evolved in the Arabidopsis genus. CONCLUSION Our genome-wide analysis of the R gene repertoire revealed a large sequence variation in the 23 cruciferous genomes. The data provides further insights into evolutionary processes impacting this important gene family.
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Affiliation(s)
- Hanneke M Peele
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Na Guan
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, Linnean Center for Plant Biology, P.O. Box 7080, S-75007 Uppsala, Sweden
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