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Rijzaani H, Bayer PE, Rouard M, Doležel J, Batley J, Edwards D. The pangenome of banana highlights differences between genera and genomes. THE PLANT GENOME 2022; 15:e20100. [PMID: 34227250 DOI: 10.1002/tpg2.20100] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 05/19/2023]
Abstract
Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.
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Affiliation(s)
- Habib Rijzaani
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
- Indonesian Agency for Agricultural Research and Development, Jakarta, Indonesia
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, Montpellier, 34397, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Šlechtitelů 31, Olomouc, 77900, Czech Republic
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Cortaga CQ, Latina RA, Habunal RR, Lantican DV. Identification and characterization of genome-wide resistance gene analogs (RGAs) of durian (Durio zibethinus L.). JOURNAL OF GENETIC ENGINEERING AND BIOTECHNOLOGY 2022; 20:29. [PMID: 35157163 PMCID: PMC8844316 DOI: 10.1186/s43141-022-00313-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/04/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Durian (Durio zibethinus L.) is a tropical fruit crop which is popular in Southeast Asia but recently gaining popularity in other parts of the world. In this study, we analyzed the resistance gene analogs (RGAs) of durian through mining of the currently available reference genome of its 'Musang King' cultivar (PRJNA400310). RESULTS A total of 2586 RGAs were identified in the durian genome consisting of 47 nucleotide binding site proteins (NBS), 158 NBS-leucine rich repeat proteins (NL), 400 coiled-coil NBS-LRR (CNL), 72 toll/interleukin-1 receptor NBS-LRR (TNL), 54 coiled-coil NBS (CN), 10 toll/interleukin-1 receptor NBS (TN), 19 toll/interleukin-1 receptor with unknown domain (TX), 246 receptor-like proteins (RLP), 1,377 receptor-like kinases (RLK), 185 TM-CC, and 18 other NBS-containing proteins with other domains. These RGAs were functionally annotated and characterized via gene ontology (GO) analysis. Among the RGAs with the highest copies in durian genome include the putative disease resistance RPP13-like protein 1, disease resistance protein At4g27190, disease resistance protein RPS6, Probable disease resistance protein At4g27220, and putative disease resistance protein RGA3, while 35 RGAs were found to be novel. Phylogenetic analyses revealed that the genome-wide RGAs were broadly clustered into four major clades based on their domain classification. CONCLUSION To our knowledge, this is the most comprehensive analysis of durian RGAs which provides a valuable resource for genetic, agronomic, and other biological research of this important tropical fruit crop.
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Affiliation(s)
- Cris Q Cortaga
- Institute of Plant Breeding (IPB), College of Agriculture, University of the Philippines Los Baños, 4031, College, Laguna, Philippines
| | - Romnick A Latina
- Institute of Weed Science, Entomology, and Plant Pathology (IWEP), College of Agriculture and Food Science, University of the Philippines Los Baños, 4031, College, Laguna, Philippines
| | - Rosteo R Habunal
- Institute of Plant Breeding (IPB), College of Agriculture, University of the Philippines Los Baños, 4031, College, Laguna, Philippines
| | - Darlon V Lantican
- Institute of Plant Breeding (IPB), College of Agriculture, University of the Philippines Los Baños, 4031, College, Laguna, Philippines.
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Zheng J, Meinhardt LW, Goenaga R, Matsumoto T, Zhang D, Yin Y. The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes. HORTICULTURE RESEARCH 2022; 9:uhac014. [PMID: 35147197 PMCID: PMC9002659 DOI: 10.1093/hr/uhac014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/20/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Jinfang Zheng
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Lyndel W Meinhardt
- USDA-ARS, Sustainable Perennial Crops Laboratory, Beltsville, MD 20705, USA
| | - Ricardo Goenaga
- USDA-ARS, Tropical Agriculture Research Station, Mayaguez, PR 00680
| | - Tracie Matsumoto
- USDA-ARS, Daniel K. Inouye Pacific Basin Agricultural Research Center, Hilo, 96720, HI, USA
| | - Dapeng Zhang
- USDA-ARS, Sustainable Perennial Crops Laboratory, Beltsville, MD 20705, USA
| | - Yanbin Yin
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
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Hu H, Scheben A, Verpaalen B, Tirnaz S, Bayer PE, Hodel RGJ, Batley J, Soltis DE, Soltis PS, Edwards D. Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation. THE NEW PHYTOLOGIST 2022; 233:1548-1555. [PMID: 34328223 PMCID: PMC9292397 DOI: 10.1111/nph.17658] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/26/2021] [Indexed: 05/03/2023]
Affiliation(s)
- Haifei Hu
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Armin Scheben
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
- Simons Center for Quantitative BiologyCold Spring Harbor LaboratoryCold Spring Harbor,NY11724USA
| | - Brent Verpaalen
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Soodeh Tirnaz
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Richard G. J. Hodel
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20013‐7012USA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
| | - Douglas E. Soltis
- Department of BiologyUniversity of FloridaGainesvilleFL32611USA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFL32611USA
- The Genetics InstituteUniversity of FloridaGainesvilleFL32610USA
- The Biodiversity InstituteUniversity of FloridaGainesvilleFL32611USA
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureUniversity of Western AustraliaPerthWA6009Australia
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Zhang X, Liu T, Wang J, Wang P, Qiu Y, Zhao W, Pang S, Li X, Wang H, Song J, Zhang W, Yang W, Sun Y, Li X. Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes. MOLECULAR PLANT 2021; 14:2032-2055. [PMID: 34384905 DOI: 10.1016/j.molp.2021.08.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/27/2021] [Accepted: 08/05/2021] [Indexed: 05/22/2023]
Abstract
Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.
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Affiliation(s)
- Xiaohui Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tongjin Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
| | - Jinglei Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Peng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yang Qiu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Pang
- Berry Genomics Corporation, Beijing 100015, China
| | - Xiaoman Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiping Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiangping Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenlin Zhang
- Berry Genomics Corporation, Beijing 100015, China
| | - Wenlong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuyan Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xixiang Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Bayer PE, Scheben A, Golicz AA, Yuan Y, Faure S, Lee H, Chawla HS, Anderson R, Bancroft I, Raman H, Lim YP, Robbens S, Jiang L, Liu S, Barker MS, Schranz ME, Wang X, King GJ, Pires JC, Chalhoub B, Snowdon RJ, Batley J, Edwards D. Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2488-2500. [PMID: 34310022 PMCID: PMC8633514 DOI: 10.1111/pbi.13674] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/11/2021] [Accepted: 07/20/2021] [Indexed: 05/26/2023]
Abstract
Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.
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Affiliation(s)
- Philipp E. Bayer
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Armin Scheben
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneParkvilleVICAustralia
| | - Yuxuan Yuan
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - HueyTyng Lee
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Harmeet Singh Chawla
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Robyn Anderson
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | | | - Harsh Raman
- NSW Department of Primary IndustriesWagga Wagga Agricultural Institute, PMBWagga WaggaNSWAustralia
| | - Yong Pyo Lim
- Department of HorticultureChungnam National UniversityDaejeonSouth Korea
| | | | - Lixi Jiang
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Shengyi Liu
- Chinese Academy of Agricultural SciencesOil Crops Research InstituteWuhanChina
| | - Michael S. Barker
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - M. Eric Schranz
- Biosystematics GroupWageningen University and Research CenterWageningenThe Netherlands
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural Sciences (IVF, CAAS)BeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - J. Chris Pires
- Division of Biological SciencesBond Life Sciences CenterUniversity of MissouriColumbiaMissouriUSA
| | - Boulos Chalhoub
- Institute of crop scienceDepartment of Agronomy and Plant BreedingZhejiang UniversityHangzhouChina
| | - Rod J. Snowdon
- Department of Plant BreedingIFZ Research Centre for BiosystemsLand Use and NutritionJustus Liebig University GiessenGiessenGermany
| | - Jacqueline Batley
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- School of Biological Sciences and the Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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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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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J Adv Res 2021; 42:315-329. [PMID: 36513421 PMCID: PMC9788938 DOI: 10.1016/j.jare.2021.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. OBJECTIVES Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. METHODS We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. RESULTS We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. CONCLUSION This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.
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Chung O, Kim J, Bolser D, Kim HM, Jun JH, Choi JP, Jang HD, Cho YS, Bhak J, Kwak M. A chromosome-scale genome assembly and annotation of the spring orchid (Cymbidium goeringii). Mol Ecol Resour 2021; 22:1168-1177. [PMID: 34687590 DOI: 10.1111/1755-0998.13537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 12/13/2022]
Abstract
Cymbidium goeringii, commonly known as the spring orchid, has long been favoured for horticultural purposes in Asian countries. It is a popular orchid with much demand for improvement and development for its valuable varieties. Until now, its reference genome has not been published despite its popularity and conservation efforts. Here, we report the de novo assembly of the C. goeringii genome, which is the largest among the orchids published to date, using a strategy that combines short- and long-read sequencing and chromosome conformation capture (Hi-C) information. The total length of all scaffolds is 3.99 Gb, with an N50 scaffold size of 178.2 Mb. A total of 29,556 protein-coding genes were annotated and 3.55 Gb (88.87% of genome) repetitive sequences were identified. We constructed pseudomolecular chromosomes using Hi-C, incorporating 89.4% of the scaffolds in 20 chromosomes. We identified 220 expanded and 106 contracted genes families in C. goeringii after divergence from its close relative. We also identified new gene families, resistance gene analogues and changes within the MADS-box genes, which control a diverse set of developmental processes during orchid evolution. Our high quality chromosomal-level assembly of C. goeringii can provide a platform for elucidating the genomic evolution of orchids, mining functional genes for agronomic traits and for developing molecular markers for accelerated breeding as well as accelerating conservation efforts.
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Affiliation(s)
- Oksung Chung
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, Korea
| | - Dan Bolser
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Geromics Ltd., Cambridge, UK
| | - Hak-Min Kim
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Je Hoon Jun
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jae-Pil Choi
- Personal Genomics Institute (PGI), Genome Research Foundation, Cheongju, Korea
| | - Hyun-Do Jang
- National Institute of Biological Resources, Environmental Research Complex, Incheon, Korea
| | - Yun Sung Cho
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Jong Bhak
- Clinomics, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Geromics Ltd., Cambridge, UK.,Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea.,Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Myounghai Kwak
- National Institute of Biological Resources, Environmental Research Complex, Incheon, Korea
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Lu D, Liu B, Ren M, Wu C, Ma J, Shen Y. Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata. PLANTS (BASEL, SWITZERLAND) 2021; 10:2261. [PMID: 34834626 PMCID: PMC8618083 DOI: 10.3390/plants10112261] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/13/2021] [Accepted: 10/13/2021] [Indexed: 12/27/2022]
Abstract
The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.
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Affiliation(s)
- Danying Lu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Bin Liu
- Department of Plant Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Bellaterra, Spain;
| | - Mingjie Ren
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Chao Wu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Jingjing Ma
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Yamei Shen
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture & Forestry University, Hangzhou 311300, China; (D.L.); (M.R.); (C.W.)
- College of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
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Yokotani N, Hasegawa Y, Sato M, Hirakawa H, Kouzai Y, Nishizawa Y, Yamamoto E, Naito Y, Isobe S. Transcriptome analysis of Clavibacter michiganensis subsp. michiganensis-infected tomatoes: a role of salicylic acid in the host response. BMC PLANT BIOLOGY 2021; 21:476. [PMID: 34666675 PMCID: PMC8524973 DOI: 10.1186/s12870-021-03251-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/05/2021] [Indexed: 05/05/2023]
Abstract
Bacterial canker of tomato (Solanum lycopersicon) caused by the Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) is an economically important disease. To understand the host defense response to Cmm infection, transcriptome sequences in tomato cotyledons were analyzed by RNA-seq. Overall, 1788 and 540 genes were upregulated and downregulated upon infection, respectively. Gene Ontology enrichment analysis revealed that genes involved in the defense response, phosphorylation, and hormone signaling were over-represented by the infection. Induced expression of defense-associated genes suggested that the tomato response to Cmm showed similarities to common plant disease responses. After infection, many resistance gene analogs (RGAs) were transcriptionally upregulated, including the expressions of some receptor-like kinases (RLKs) involved in pattern-triggered immunity. The expressions of WRKYs, NACs, HSFs, and CBP60s encoding transcription factors (TFs) reported to regulate defense-associated genes were induced after infection with Cmm. Tomato genes orthologous to Arabidopsis EDS1, EDS5/SID1, and PAD4/EDS9, which are causal genes of salicylic acid (SA)-deficient mutants, were upregulated after infection with Cmm. Furthermore, Cmm infection drastically stimulated SA accumulation in tomato cotyledons. Genes involved in the phenylalanine ammonia lyase pathway were upregulated, whereas metabolic enzyme gene expression in the isochorismate synthase pathway remained unchanged. Exogenously applied SA suppressed bacterial growth and induced the expression of WRKYs, suggesting that some Cmm-responsive genes are regulated by SA signaling, and SA signaling activation should improve tomato immunity against Cmm.
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Affiliation(s)
- Naoki Yokotani
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan.
| | - Yoshinori Hasegawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Masaru Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yusuke Kouzai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Yoko Nishizawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Eiji Yamamoto
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Yoshiki Naito
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba, 292-0818, Japan
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Kourelis J, Sakai T, Adachi H, Kamoun S. RefPlantNLR is a comprehensive collection of experimentally validated plant disease resistance proteins from the NLR family. PLoS Biol 2021; 19:e3001124. [PMID: 34669691 PMCID: PMC8559963 DOI: 10.1371/journal.pbio.3001124] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 11/01/2021] [Accepted: 09/23/2021] [Indexed: 11/19/2022] Open
Abstract
Reference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant nucleotide-binding leucine-rich repeat (NLR) immune receptors. RefPlantNLR consists of 481 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark 5 NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs from protein or transcript files based on the core features found in the RefPlantNLR dataset. The RefPlantNLR dataset should also prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying understudied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.
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Affiliation(s)
- Jiorgos Kourelis
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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63
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Gottin C, Dievart A, Summo M, Droc G, Périn C, Ranwez V, Chantret N. A new comprehensive annotation of leucine-rich repeat-containing receptors in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:492-508. [PMID: 34382706 PMCID: PMC9292849 DOI: 10.1111/tpj.15456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Oryza sativa (rice) plays an essential food security role for more than half of the world's population. Obtaining crops with high levels of disease resistance is a major challenge for breeders, especially today, given the urgent need for agriculture to be more sustainable. Plant resistance genes are mainly encoded by three large leucine-rich repeat (LRR)-containing receptor (LRR-CR) families: the LRR-receptor-like kinase (LRR-RLK), LRR-receptor-like protein (LRR-RLP) and nucleotide-binding LRR receptor (NLR). Using lrrprofiler, a pipeline that we developed to annotate and classify these proteins, we compared three publicly available annotations of the rice Nipponbare reference genome. The extended discrepancies that we observed for LRR-CR gene models led us to perform an in-depth manual curation of their annotations while paying special attention to nonsense mutations. We then transferred this manually curated annotation to Kitaake, a cultivar that is closely related to Nipponbare, using an optimized strategy. Here, we discuss the breakthrough achieved by manual curation when comparing genomes and, in addition to 'functional' and 'structural' annotations, we propose that the community adopts this approach, which we call 'comprehensive' annotation. The resulting data are crucial for further studies on the natural variability and evolution of LRR-CR genes in order to promote their use in breeding future resilient varieties.
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Affiliation(s)
- Céline Gottin
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Anne Dievart
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Marilyne Summo
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Gaëtan Droc
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Christophe Périn
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
- CIRADUMR AGAP InstitutF‐34398MontpellierFrance
| | - Vincent Ranwez
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
| | - Nathalie Chantret
- UMR AGAP InstitutUniv MontpellierCIRAD, INRAEInstitut AgroF‐34398MontpellierFrance
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64
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Wang L, Zhu T, Rodriguez JC, Deal KR, Dubcovsky J, McGuire PE, Lux T, Spannagl M, Mayer KFX, Baldrich P, Meyers BC, Huo N, Gu YQ, Zhou H, Devos KM, Bennetzen JL, Unver T, Budak H, Gulick PJ, Galiba G, Kalapos B, Nelson DR, Li P, You FM, Luo MC, Dvorak J. Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation. G3-GENES GENOMES GENETICS 2021; 11:6369516. [PMID: 34515796 PMCID: PMC8664484 DOI: 10.1093/g3journal/jkab325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/31/2021] [Indexed: 01/01/2023]
Abstract
Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.
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Affiliation(s)
- Le Wang
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Juan C Rodriguez
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Karin R Deal
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Manuel Spannagl
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Munich 85764, Germany
| | - Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA.,University of Missouri, Columbia, Division of Plant Sciences, Columbia, Missouri 65211, USA
| | - Naxin Huo
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Yong Q Gu
- Crop Improvement and Genetics Research Unit, USDA-ARS, Albany, California 94710, USA
| | - Hongye Zhou
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics (Dept. of Crop & Soil Sciences) and Dept. of Plant Biology, University of Georgia, Athens, Georgia 30602, USA
| | | | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, Ankara 06374, Turkey
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, Montana 59801, USA
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, Quebec H3G 1M8, Canada
| | - Gabor Galiba
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary.,Department of Environmental Sustainability, IES, Hungarian University of Agriculture and Life Sciences, H-8360 Keszthely, Hungary
| | - Balázs Kalapos
- Department of Biological Resources, Centre for Agricultural Research, Eötvös Loránd Research Network, H-2462 Martonvásár, Hungary
| | - David R Nelson
- University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Pingchuan Li
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C5, Canada
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, Davis, California 95616, USA
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65
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Hirakawa H, Toyoda A, Itoh T, Suzuki Y, Nagano AJ, Sugiyama S, Onodera Y. A spinach genome assembly with remarkable completeness, and its use for rapid identification of candidate genes for agronomic traits. DNA Res 2021; 28:6303609. [PMID: 34142133 PMCID: PMC8231376 DOI: 10.1093/dnares/dsab004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Indexed: 01/23/2023] Open
Abstract
Spinach (Spinacia oleracea) is grown as a nutritious leafy vegetable worldwide. To accelerate spinach breeding efficiency, a high-quality reference genome sequence with great completeness and continuity is needed as a basic infrastructure. Here, we used long-read and linked-read technologies to construct a de novo spinach genome assembly, designated SOL_r1.1, which was comprised of 287 scaffolds (total size: 935.7 Mb; N50 = 11.3 Mb) with a low proportion of undetermined nucleotides (Ns = 0.34%) and with high gene completeness (BUSCO complete 96.9%). A genome-wide survey of resistance gene analogues identified 695 genes encoding nucleotide-binding site domains, receptor-like protein kinases, receptor-like proteins and transmembrane-coiled coil domains. Based on a high-density double-digest restriction-site associated DNA sequencing-based linkage map, the genome assembly was anchored to six pseudomolecules representing ∼73.5% of the whole genome assembly. In addition, we used SOL_r1.1 to identify quantitative trait loci for bolting timing and fruit/seed shape, which harbour biologically plausible candidate genes, such as homologues of the FLOWERING LOCUS T and EPIDERMAL PATTERNING FACTOR-LIKE genes. The new genome assembly, SOL_r1.1, will serve as a useful resource for identifying loci associated with important agronomic traits and for developing molecular markers for spinach breeding/selection programs.
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Affiliation(s)
- Hideki Hirakawa
- The Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Atsushi Toyoda
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Suzuki
- The Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8568, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Suguru Sugiyama
- School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yasuyuki Onodera
- The Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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66
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Park SG, Noh E, Choi S, Choi B, Shin IG, Yoo SI, Lee DJ, Ji S, Kim HS, Hwang YJ, Kim JS, Batley J, Lim YP, Edwards D, Hong CP. Draft Genome Assembly and Transcriptome Dataset for European Turnip ( Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance. Front Genet 2021; 12:651298. [PMID: 34276765 PMCID: PMC8285094 DOI: 10.3389/fgene.2021.651298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Affiliation(s)
| | - Eonji Noh
- Theragen Bio Co., Ltd., Suwon, South Korea
| | - SuRyun Choi
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - Boram Choi
- Theragen Bio Co., Ltd., Suwon, South Korea
| | | | | | | | - Sumin Ji
- Theragen Bio Co., Ltd., Suwon, South Korea
| | | | - Yoon-Jung Hwang
- Department of Chemistry Life Science, Sahmyook University, Seoul, South Korea
| | - Jung Sun Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Yong Pyo Lim
- Department of Horticulture, College of Agriculture and Life Science, Chungnam National University, Daejeon, South Korea
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
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Yang H, Mohd Saad NS, Ibrahim MI, Bayer PE, Neik TX, Severn-Ellis AA, Pradhan A, Tirnaz S, Edwards D, Batley J. Candidate Rlm6 resistance genes against Leptosphaeria. maculans identified through a genome-wide association study in Brassica juncea (L.) Czern. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2035-2050. [PMID: 33768283 DOI: 10.1007/s00122-021-03803-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
One hundred and sixty-seven B. juncea varieties were genotyped on the 90K Brassica assay (42,914 SNPs), which led to the identification of sixteen candidate genes for Rlm6. Brassica species are at high risk of severe crop loss due to pathogens, especially Leptosphaeria maculans (the causal agent of blackleg). Brassica juncea (L.) Czern is an important germplasm resource for canola improvement, due to its good agronomic traits, such as heat and drought tolerance and high blackleg resistance. The present study is the first using genome-wide association studies to identify candidate genes for blackleg resistance in B. juncea based on genome-wide SNPs obtained from the Illumina Infinium 90 K Brassica SNP array. The verification of Rlm6 in B. juncea was performed through a cotyledon infection test. Genotyping 42,914 single nucleotide polymorphisms (SNPs) in a panel of 167 B. juncea lines revealed a total of seven SNPs significantly associated with Rlm6 on chromosomes A07 and B04 in B. juncea. Furthermore, 16 candidate Rlm6 genes were found in these regions, defined as nucleotide binding site leucine-rich-repeat (NLR), leucine-rich repeat RLK (LRR-RLK) and LRR-RLP genes. This study will give insights into the blackleg resistance in B. juncea and facilitate identification of functional blackleg resistance genes which can be used in Brassica breeding.
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Affiliation(s)
- Hua Yang
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | | | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Ting Xiang Neik
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Anita A Severn-Ellis
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia.
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68
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Garcia A, Santamaria ME, Diaz I, Martinez M. Disentangling transcriptional responses in plant defense against arthropod herbivores. Sci Rep 2021; 11:12996. [PMID: 34155286 PMCID: PMC8217245 DOI: 10.1038/s41598-021-92468-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/03/2021] [Indexed: 01/21/2023] Open
Abstract
The success in the response of a plant to a pest depends on the regulatory networks that connect plant perception and plant response. Meta-analyses of transcriptomic responses are valuable tools to discover novel mechanisms in the plant/herbivore interplay. Considering the quantity and quality of available transcriptomic analyses, Arabidopsis thaliana was selected to test the ability of comprehensive meta-analyses to disentangle plant responses. The analysis of the transcriptomic data showed a general induction of biological processes commonly associated with the response to herbivory, like jasmonate signaling or glucosinolate biosynthesis. However, an uneven induction of many genes belonging to these biological categories was found, which was likely associated with the particularities of each specific Arabidopsis-herbivore interaction. A thorough analysis of the responses to the lepidopteran Pieris rapae and the spider mite Tetranychus urticae highlighted specificities in the perception and signaling pathways associated with the expression of receptors and transcription factors. This information was translated to a variable alteration of secondary metabolic pathways. In conclusion, transcriptomic meta-analysis has been revealed as a potent way to sort out relevant physiological processes in the plant response to herbivores. Translation of these transcriptomic-based analyses to crop species will permit a more appropriate design of biotechnological programs.
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Affiliation(s)
- Alejandro Garcia
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - M Estrella Santamaria
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Isabel Diaz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Manuel Martinez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.
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69
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Pavese V, Cavalet Giorsa E, Barchi L, Acquadro A, Torello Marinoni D, Portis E, James Lucas S, Botta R. Whole-genome assembly of Corylus avellana cv'Tonda Gentile delle Langhe' using linked-reads (10X Genomics). G3-GENES GENOMES GENETICS 2021; 11:6272584. [PMID: 33964151 PMCID: PMC8495946 DOI: 10.1093/g3journal/jkab152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/20/2021] [Indexed: 01/01/2023]
Abstract
The European hazelnut (Corylus avellana L.; 2n = 2x = 22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers, and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv “Tonda Gentile delle Langhe” (“TGdL”) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of “TGdL” with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv “Tombul” genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤0.4 and 92% of BUSCO completeness), whose function was analyzed with BlastP and InterProScan software. To characterize “TGdL” specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The “TGdL” genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Emile Cavalet Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Stuart James Lucas
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
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70
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Herath V, Verchot J. Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. Int J Mol Sci 2021; 22:2837. [PMID: 33799566 PMCID: PMC8001266 DOI: 10.3390/ijms22062837] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/09/2021] [Indexed: 11/16/2022] Open
Abstract
Potato virus X (PVX) belongs to genus Potexvirus. This study characterizes the cellular transcriptome responses to PVX infection in Russet potato at 2 and 3 days post infection (dpi). Among the 1242 differentially expressed genes (DEGs), 268 genes were upregulated, and 37 genes were downregulated at 2 dpi while 677 genes were upregulated, and 265 genes were downregulated at 3 dpi. DEGs related to signal transduction, stress response, and redox processes. Key stress related transcription factors were identified. Twenty-five pathogen resistance gene analogs linked to effector triggered immunity or pathogen-associated molecular pattern (PAMP)-triggered immunity were identified. Comparative analysis with Arabidopsis unfolded protein response (UPR) induced DEGs revealed genes associated with UPR and plasmodesmata transport that are likely needed to establish infection. In conclusion, this study provides an insight on major transcriptional regulatory networked involved in early response to PVX infection and establishment.
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Affiliation(s)
- Venura Herath
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA;
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA;
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71
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Zhang Y, Edwards D, Batley J. Comparison and evolutionary analysis of Brassica nucleotide binding site leucine rich repeat (NLR) genes and importance for disease resistance breeding. THE PLANT GENOME 2021; 14:e20060. [PMID: 33179454 DOI: 10.1002/tpg2.20060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
The Brassica genus contains many agriculturally significant oilseed and vegetable crops, however the crop yield is threatened by a range of fungal and bacterial pathogens. Nucleotide Binding Site Leucine Rich Repeat (NLR) genes play important roles in plant innate immunity. The evolution of NLR genes is influenced by genomic processes and pathogen selection. At the whole genome level, whole genome duplications (WGDs) generate abundant gene copies, most of which are lost during genome fractionation. At sub-genomic levels, some retained copies undergo duplication forming clusters which facilitate rapid evolution through recombination. The number, distribution and genetic variations of the NLR genes vary among Brassica species and within populations suggesting differential selection pressure exerted by pathogen populations throughout the evolutionary history. A study of the evolution of disease resistance genes in agriculturally important plants such as Brassicas helps gain insights into their function and inform the identification of resistance genes for breeding of resistant lines.
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Affiliation(s)
- Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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72
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Qin X, Zhang Z, Lou Q, Xia L, Li J, Li M, Zhou J, Zhao X, Xu Y, Li Q, Yang S, Yu X, Cheng C, Huang S, Chen J. Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber. HORTICULTURE RESEARCH 2021; 8:40. [PMID: 33642577 PMCID: PMC7917098 DOI: 10.1038/s41438-021-00475-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 05/06/2023]
Abstract
Cucumis hystrix Chakr. (2n = 2x = 24) is a wild species that can hybridize with cultivated cucumber (C. sativus L., 2n = 2x = 14), a globally important vegetable crop. However, cucumber breeding is hindered by its narrow genetic base. Therefore, introgression from C. hystrix has been anticipated to bring a breakthrough in cucumber improvement. Here, we report the chromosome-scale assembly of C. hystrix genome (289 Mb). Scaffold N50 reached 14.1 Mb. Over 90% of the sequences were anchored onto 12 chromosomes. A total of 23,864 genes were annotated using a hybrid method. Further, we conducted a comprehensive comparative genomic analysis of cucumber, C. hystrix, and melon (C. melo L., 2n = 2x = 24). Whole-genome comparisons revealed that C. hystrix is phylogenetically closer to cucumber than to melon, providing a molecular basis for the success of its hybridization with cucumber. Moreover, expanded gene families of C. hystrix were significantly enriched in "defense response," and C. hystrix harbored 104 nucleotide-binding site-encoding disease resistance gene analogs. Furthermore, 121 genes were positively selected, and 12 (9.9%) of these were involved in responses to biotic stimuli, which might explain the high disease resistance of C. hystrix. The alignment of whole C. hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C. hystrix chromosomes. Finally, we developed four cucumber-C. hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods. The assembled C. hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.
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Affiliation(s)
- Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhonghua Zhang
- College of Horticulture, Qingdao Agricultural University, 266109, Qingdao, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lei Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Mengxue Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Junguo Zhou
- College of Horticulture and Landscape, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Xiaokun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Yuanchao Xu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Qing Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Shuqiong Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China
| | - Sanwen Huang
- Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China.
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73
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Restrepo-Montoya D, McClean PE, Osorno JM. Orthology and synteny analysis of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. BMC Genomics 2021; 22:113. [PMID: 33568053 PMCID: PMC7874474 DOI: 10.1186/s12864-021-07384-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses. RESULTS Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata, two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max. CONCLUSIONS The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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74
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Wang Y, Wang P, Guo Y, Huang S, Chen Y, Xu L. prPred: A Predictor to Identify Plant Resistance Proteins by Incorporating k-Spaced Amino Acid (Group) Pairs. Front Bioeng Biotechnol 2021; 8:645520. [PMID: 33553134 PMCID: PMC7859348 DOI: 10.3389/fbioe.2020.645520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 12/31/2020] [Indexed: 11/13/2022] Open
Abstract
To infect plants successfully, pathogens adopt various strategies to overcome their physical and chemical barriers and interfere with the plant immune system. Plants deploy a large number of resistance (R) proteins to detect invading pathogens. The R proteins are encoded by resistance genes that contain cell surface-localized receptors and intracellular receptors. In this study, a new plant R protein predictor called prPred was developed based on a support vector machine (SVM), which can accurately distinguish plant R proteins from other proteins. Experimental results showed that the accuracy, precision, sensitivity, specificity, F1-score, MCC, and AUC of prPred were 0.935, 1.000, 0.806, 1.000, 0.893, 0.857, and 0.948, respectively, on an independent test set. Moreover, the predictor integrated the HMMscan search tool and Phobius to identify protein domain families and transmembrane protein regions to differentiate subclasses of R proteins. prPred is available at https://github.com/Wangys-prog/prPred. The tool requires a valid Python installation and is run from the command line.
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Affiliation(s)
- Yansu Wang
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Pingping Wang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Yingjie Guo
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Shan Huang
- Department of Neurology, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Chen
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
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75
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Yu H, Lin T, Meng X, Du H, Zhang J, Liu G, Chen M, Jing Y, Kou L, Li X, Gao Q, Liang Y, Liu X, Fan Z, Liang Y, Cheng Z, Chen M, Tian Z, Wang Y, Chu C, Zuo J, Wan J, Qian Q, Han B, Zuccolo A, Wing RA, Gao C, Liang C, Li J. A route to de novo domestication of wild allotetraploid rice. Cell 2021; 184:1156-1170.e14. [PMID: 33539781 DOI: 10.1016/j.cell.2021.01.013] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 12/02/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022]
Abstract
Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.
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Affiliation(s)
- Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tao Lin
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangdong Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuntao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Bin Han
- National Center of Plant Gene Research Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Caixia Gao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China.
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Li D, Qian J, Li W, Yu N, Gan G, Jiang Y, Li W, Liang X, Chen R, Mo Y, Lian J, Niu Y, Wang Y. A high-quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis. Mol Ecol Resour 2021; 21:1274-1286. [PMID: 33445226 DOI: 10.1111/1755-0998.13321] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 11/19/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
The eggplant (Solanum melongena L.) is one of the most important Solanaceae crops, ranking third for total production and economic value in its genus. Herein, we report a high-quality, chromosome-scale eggplant reference genome sequence of 1155.8 Mb, with an N50 of 93.9 Mb, which was assembled by combining PacBio long reads and Hi-C sequencing data. Repetitive sequences occupied 70.1% of the assembly length, and 35,018 high-confidence protein-coding genes were annotated based on multiple sources. Comparative analysis revealed 646 species-specific families and 364 positive selection genes, conferring distinguishing traits on the eggplant. We performed genome-wide comparative identification of disease resistance genes and discovered an expanded gene family of bacterial spot resistance in eggplant and pepper, but not in tomato and potato. The genes involved in chlorogenic acid synthesis were comprehensively characterized. Highly similar chromosomal distribution patterns of polyphenol oxidase genes were observed in the eggplant, tomato, and potato genomes. The eggplant reference genome sequence will not only facilitate evolutionary studies of the Solanaceae but also facilitate their breeding and improvement.
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Affiliation(s)
- Dandan Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jun Qian
- Biozeron Shenzhen, Inc, Shenzhen, China
| | - Weiliu Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Ning Yu
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guiyun Gan
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yaqin Jiang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Wenjia Li
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xuyu Liang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Riyuan Chen
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yongcheng Mo
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | | | | | - Yikui Wang
- Institute of Vegetable Research, Guangxi Academy of Agricultural Sciences, Nanning, China
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Cantila AY, Saad NSM, Amas JC, Edwards D, Batley J. Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives. Int J Mol Sci 2020; 22:E313. [PMID: 33396785 PMCID: PMC7795555 DOI: 10.3390/ijms22010313] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/29/2020] [Accepted: 12/29/2020] [Indexed: 11/20/2022] Open
Abstract
Among the Brassica oilseeds, canola (Brassica napus) is the most economically significant globally. However, its production can be limited by blackleg disease, caused by the fungal pathogen Lepstosphaeria maculans. The deployment of resistance genes has been implemented as one of the key strategies to manage the disease. Genetic resistance against blackleg comes in two forms: qualitative resistance, controlled by a single, major resistance gene (R gene), and quantitative resistance (QR), controlled by numerous, small effect loci. R-gene-mediated blackleg resistance has been extensively studied, wherein several genomic regions harbouring R genes against L. maculans have been identified and three of these genes were cloned. These studies advance our understanding of the mechanism of R gene and pathogen avirulence (Avr) gene interaction. Notably, these studies revealed a more complex interaction than originally thought. Advances in genomics help unravel these complexities, providing insights into the genes and genetic factors towards improving blackleg resistance. Here, we aim to discuss the existing R-gene-mediated resistance, make a summary of candidate R genes against the disease, and emphasise the role of players involved in the pathogenicity and resistance. The comprehensive result will allow breeders to improve resistance to L. maculans, thereby increasing yield.
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Affiliation(s)
| | | | | | | | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA 6009, Australia; (A.Y.C.); (N.S.M.S.); (J.C.A.); (D.E.)
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78
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Yang H, Bayer PE, Tirnaz S, Edwards D, Batley J. Genome-Wide Identification and Evolution of Receptor-Like Kinases (RLKs) and Receptor like Proteins (RLPs) in Brassica juncea. BIOLOGY 2020; 10:biology10010017. [PMID: 33396674 PMCID: PMC7823396 DOI: 10.3390/biology10010017] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/21/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022]
Abstract
Brassica juncea, an allotetraploid species, is an important germplasm resource for canola improvement, due to its many beneficial agronomic traits, such as heat and drought tolerance and blackleg resistance. Receptor-like kinase (RLK) and receptor-like protein (RLP) genes are two types of resistance gene analogues (RGA) that play important roles in plant innate immunity, stress response and various development processes. In this study, genome wide analysis of RLKs and RLPs is performed in B. juncea. In total, 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) are identified in the genome of B. juncea, using RGAugury. Only 13.54% RLKs and 11.79% RLPs are observed to be grouped within gene clusters. The majority of RLKs (90.17%) and RLPs (52.83%) are identified as duplicates, indicating that gene duplications significantly contribute to the expansion of RLK and RLP families. Comparative analysis between B. juncea and its progenitor species, B. rapa and B. nigra, indicate that 83.62% RLKs and 41.98% RLPs are conserved in B. juncea, and RLPs are likely to have a faster evolution than RLKs. This study provides a valuable resource for the identification and characterisation of candidate RLK and RLP genes.
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Affiliation(s)
- Hua Yang
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- School of Agriculture and Food Sciences, University of Queensland, St Lucia, QLD 4067, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia; (H.Y.); (P.E.B.); (S.T.); (D.E.)
- Correspondence: ; Tel.: +61-8-6488-5929
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Rousseau-Gueutin M, Belser C, Da Silva C, Richard G, Istace B, Cruaud C, Falentin C, Boideau F, Boutte J, Delourme R, Deniot G, Engelen S, de Carvalho JF, Lemainque A, Maillet L, Morice J, Wincker P, Denoeud F, Chèvre AM, Aury JM. Long-read assembly of the Brassica napus reference genome Darmor-bzh. Gigascience 2020; 9:giaa137. [PMID: 33319912 PMCID: PMC7736779 DOI: 10.1093/gigascience/giaa137] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus. FINDINGS Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. CONCLUSION Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
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Affiliation(s)
| | - Caroline Belser
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Corinne Cruaud
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Cyril Falentin
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Franz Boideau
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Julien Boutte
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Regine Delourme
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Stefan Engelen
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | | | - Arnaud Lemainque
- Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Loeiz Maillet
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jérôme Morice
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
| | - Anne-Marie Chèvre
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653 Le Rheu, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France
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Frontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes. Int J Mol Sci 2020; 21:ijms21238964. [PMID: 33255840 PMCID: PMC7728316 DOI: 10.3390/ijms21238964] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023] Open
Abstract
The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.
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Tirnaz S, Bayer PE, Inturrisi F, Zhang F, Yang H, Dolatabadian A, Neik TX, Severn-Ellis A, Patel DA, Ibrahim MI, Pradhan A, Edwards D, Batley J. Resistance Gene Analogs in the Brassicaceae: Identification, Characterization, Distribution, and Evolution. PLANT PHYSIOLOGY 2020; 184:909-922. [PMID: 32796089 PMCID: PMC7536671 DOI: 10.1104/pp.20.00835] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 07/21/2020] [Indexed: 05/02/2023]
Abstract
The Brassicaceae consists of a wide range of species, including important Brassica crop species and the model plant Arabidopsis (Arabidopsis thaliana). Brassica spp. crop diseases impose significant yield losses annually. A major way to reduce susceptibility to disease is the selection in breeding for resistance gene analogs (RGAs). Nucleotide binding site-leucine rich repeats (NLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are the main types of RGAs; they contain conserved domains and motifs and play specific roles in resistance to pathogens. Here, all classes of RGAs have been identified using annotation and assembly-based pipelines in all available genome annotations from the Brassicaceae, including multiple genome assemblies of the same species where available (total of 32 genomes). The number of RGAs, based on genome annotations, varies within and between species. In total 34,065 RGAs were identified, with the majority being RLKs (21,691), then NLRs (8,588) and RLPs (3,786). Analysis of the RGA protein sequences revealed a high level of sequence identity, whereby 99.43% of RGAs fell into several orthogroups. This study establishes a resource for the identification and characterization of RGAs in the Brassicaceae and provides a framework for further studies of RGAs for an ultimate goal of assisting breeders in improving resistance to plant disease.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Fabian Inturrisi
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Fangning Zhang
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Hua Yang
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland QLD 4072, Australia
| | - Aria Dolatabadian
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Ting X Neik
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Anita Severn-Ellis
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Dhwani A Patel
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Muhammad I Ibrahim
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, Western Australia WA 6009, Australia
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82
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Zhao J, Bayer PE, Ruperao P, Saxena RK, Khan AW, Golicz AA, Nguyen HT, Batley J, Edwards D, Varshney RK. Trait associations in the pangenome of pigeon pea (Cajanus cajan). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1946-1954. [PMID: 32020732 PMCID: PMC7415775 DOI: 10.1111/pbi.13354] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 12/11/2019] [Accepted: 01/14/2020] [Indexed: 05/21/2023]
Abstract
Pigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers in India and Africa. Here, we present the first pigeon pea pangenome based on 89 accessions mainly from India and the Philippines, showing that there is significant genetic diversity in Philippine individuals that is not present in Indian individuals. Annotation of variable genes suggests that they are associated with self-fertilization and response to disease. We identified 225 SNPs associated with nine agronomically important traits over three locations and two different time points, with SNPs associated with genes for transcription factors and kinases. These results will lead the way to an improved pigeon pea breeding programme.
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Affiliation(s)
- Junliang Zhao
- Rice Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Philipp E. Bayer
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Pradeep Ruperao
- National Institute of Agricultural BotanyCambridgeUK
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rachit K. Saxena
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Agnieszka A. Golicz
- Plant Molecular Biology and Biotechnology LaboratoryFaculty of Veterinary and Agricultural SciencesUniversity of MelbourneMelbourneVICAustralia
| | - Henry T. Nguyen
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Jacqueline Batley
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - David Edwards
- School of Biological Sciences and Institute of AgricultureThe University of Western AustraliaPerthWAAustralia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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Perumal S, Koh CS, Jin L, Buchwaldt M, Higgins EE, Zheng C, Sankoff D, Robinson SJ, Kagale S, Navabi ZK, Tang L, Horner KN, He Z, Bancroft I, Chalhoub B, Sharpe AG, Parkin IAP. A high-contiguity Brassica nigra genome localizes active centromeres and defines the ancestral Brassica genome. NATURE PLANTS 2020; 6:929-941. [PMID: 32782408 PMCID: PMC7419231 DOI: 10.1038/s41477-020-0735-y] [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: 02/03/2020] [Accepted: 06/28/2020] [Indexed: 05/19/2023]
Abstract
It is only recently, with the advent of long-read sequencing technologies, that we are beginning to uncover previously uncharted regions of complex and inherently recursive plant genomes. To comprehensively study and exploit the genome of the neglected oilseed Brassica nigra, we generated two high-quality nanopore de novo genome assemblies. The N50 contig lengths for the two assemblies were 17.1 Mb (12 contigs), one of the best among 324 sequenced plant genomes, and 0.29 Mb (424 contigs), respectively, reflecting recent improvements in the technology. Comparison with a de novo short-read assembly corroborated genome integrity and quantified sequence-related error rates (0.2%). The contiguity and coverage allowed unprecedented access to low-complexity regions of the genome. Pericentromeric regions and coincidence of hypomethylation enabled localization of active centromeres and identified centromere-associated ALE family retro-elements that appear to have proliferated through relatively recent nested transposition events (<1 Ma). Genomic distances calculated based on synteny relationships were used to define a post-triplication Brassica-specific ancestral genome, and to calculate the extensive rearrangements that define the evolutionary distance separating B. nigra from its diploid relatives.
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Affiliation(s)
- Sampath Perumal
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Chu Shin Koh
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lingling Jin
- Department of Computing Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Miles Buchwaldt
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Erin E Higgins
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Sateesh Kagale
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
| | - Zahra-Katy Navabi
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lily Tang
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Kyla N Horner
- Agriculture and Agri-Food Canada, Saskatoon, Saskatchewan, Canada
| | - Zhesi He
- Department of Biology, University of York, York, UK
| | - Ian Bancroft
- Department of Biology, University of York, York, UK
| | - Boulos Chalhoub
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Andrew G Sharpe
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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84
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Fu F, Zhang X, Liu F, Peng G, Yu F, Fernando D. Identification of resistance loci in Chinese and Canadian canola/rapeseed varieties against Leptosphaeria maculans based on genome-wide association studies. BMC Genomics 2020; 21:501. [PMID: 32693834 PMCID: PMC7372758 DOI: 10.1186/s12864-020-06893-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 07/07/2020] [Indexed: 01/08/2023] Open
Abstract
Background The fungal pathogen Leptosphaeria maculans (Lm). causes blackleg disease on canola/rapeseed in many parts of the world. It is important to use resistant cultivars to manage the disease and minimize yield losses. In this study, twenty-two Lm isolates were used to identify resistance genes in a collection of 243 canola/rapeseed (Brassica napus L.) accessions from Canada and China. These Lm isolates carry different compliments of avirulence genes, and the investigation was based on a genome-wide association study (GWAS) and genotype-by-sequencing (GBS). Results Using the CROP-SNP pipeline, a total of 81,471 variants, including 78,632 SNPs and 2839 InDels, were identified. The GWAS was performed using TASSEL 5.0 with GLM + Q model. Thirty-two and 13 SNPs were identified from the Canadian and Chinese accessions, respectively, tightly associated with blackleg resistance with P values < 1 × 10− 4. These SNP loci were distributed on chromosomes A03, A05, A08, A09, C01, C04, C05, and C07, with the majority of them on A08 followed by A09 and A03. The significant SNPs identified on A08 were all located in a 2010-kb region and associated with resistance to 12 of the 22 Lm isolates. Furthermore, 25 resistance gene analogues (RGAs) were identified in these regions, including two nucleotide binding site (NBS) domain proteins, fourteen RLKs, three RLPs and six TM-CCs. These RGAs can be the potential candidate genes for blackleg resistance. Conclusion This study provides insights into potentially new genomic regions for discovery of additional blackleg resistance genes. The identified regions associated with blackleg resistance in the germplasm collection may also contribute directly to the development of canola varieties with novel resistance genes against blackleg of canola.
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Affiliation(s)
- Fuyou Fu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Xuehua Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Fei Liu
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada.
| | - Dilantha Fernando
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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Restrepo-Montoya D, Brueggeman R, McClean PE, Osorno JM. Computational identification of receptor-like kinases "RLK" and receptor-like proteins "RLP" in legumes. BMC Genomics 2020; 21:459. [PMID: 32620079 PMCID: PMC7333395 DOI: 10.1186/s12864-020-06844-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Background In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant development and immunity. These plasma membrane receptors belong to large gene/protein families that are not easily classified computationally. This detailed analysis of these plasma membrane proteins brings a new source of information to the legume genetic, physiology and breeding research communities. Results A computational approach to identify and classify RLK and RLP proteins is presented. The strategy was evaluated using experimentally-validated RLK and RLP proteins and was determined to have a sensitivity of over 0.85, a specificity of 1.00, and a Matthews correlation coefficient of 0.91. The computational approach can be used to develop a detailed catalog of plasma membrane receptors (by type and domains) in several legume/crop species. The exclusive domains identified in legumes for RLKs are WaaY, APH Pkinase_C, LRR_2, and EGF, and for RLP are L-lectin LPRY and PAN_4. The RLK-nonRD and RLCK subclasses are also discovered by the methodology. In both classes, less than 20% of the total RLK predicted for each species belong to this class. Among the 10-species evaluated ~ 40% of the proteins in the kinome are RLKs. The exclusive legume domain combinations identified are B-Lectin/PR5K domains in G. max, M. truncatula, V. angularis, and V. unguiculata and a three-domain combination B-lectin/S-locus/WAK in C. cajan, M. truncatula, P. vulgaris, V. angularis. and V. unguiculata. Conclusions The analysis suggests that about 2% of the proteins of each genome belong to the RLK family and less than 1% belong to RLP family. Domain diversity combinations are greater for RLKs compared with the RLP proteins and LRR domains, and the dual domain combination LRR/Malectin were the most frequent domain for both groups of plasma membrane receptors among legume and non-legume species. Legumes exclusively show Pkinase extracellular domains, and atypical domain combinations in RLK and RLP compared with the non-legumes evaluated. The computational logic approach is statistically well supported and can be used with the proteomes of other plant species.
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Affiliation(s)
- Daniel Restrepo-Montoya
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58105-6050, USA. .,Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
| | - Robert Brueggeman
- Department of Plant Pathology, North Dakota State University, PO Box 6050, Dept. 7660, Fargo, ND, 58108, USA
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58105-6050, USA. .,Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, USA.
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Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. Sci Rep 2020; 10:9189. [PMID: 32514106 PMCID: PMC7280500 DOI: 10.1038/s41598-020-66053-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. In addition to commercial varieties and F1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many Italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('Quadrato') and protruding apex or heart shaped ('Cuneo'), elongated ('Corno') and smaller sized sub-spherical ('Tumaticot'). Each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'CM334'). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the SNP/Indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (CCS) gene. The large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.
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Liu F, Zhao Y, Beier S, Jiang Y, Thorwarth P, H. Longin CF, Ganal M, Himmelbach A, Reif JC, Schulthess AW. Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1396-1408. [PMID: 31782598 PMCID: PMC7207002 DOI: 10.1111/pbi.13303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/06/2019] [Accepted: 11/17/2019] [Indexed: 05/18/2023]
Abstract
Resistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker-assisted selection and map-based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a large hybrid wheat population of 1574 single-crosses plus their 133 parents. After imputation and quality control, exome sequencing revealed 202 875 single-nucleotide polymorphisms (SNPs) covering 19.7% of the high-confidence annotated gene space. We performed intensive data mining and found significant associations for 2171 SNPs corresponding to 50 different loci. Some of these associations mapped in the proximity of the already known resistance genes Lr21, Lr34-B, Lr1 and Lr10, while other associated genomic regions, such as those on chromosomes 1A and 3D, harboured several annotated genes putatively involved in resistance. Validation with an independent population helped to narrow down the list of putative resistance genes that should be targeted by fine-mapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.
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Affiliation(s)
- Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Patrick Thorwarth
- State Plant Breeding InstituteUniversity of HohenheimStuttgartGermany
| | | | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
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Zhang YM, Chen M, Sun L, Wang Y, Yin J, Liu J, Sun XQ, Hang YY. Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata. Front Genet 2020; 11:484. [PMID: 32457809 PMCID: PMC7224235 DOI: 10.3389/fgene.2020.00484] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/17/2020] [Indexed: 01/22/2023] Open
Abstract
Dioscorea rotundata is an important food crop that is mainly cultivated in subtropical regions of the world. D. rotundata is frequently infected by various pathogens during its lifespan, which results in a substantial economic loss in terms of yield and quality. The disease resistance gene (R gene) profile of D. rotundata is largely unknown, which has greatly hampered molecular study of disease resistance in this species. Nucleotide-binding site–leucine-rich repeat (NBS-LRR) genes are the largest group of plant R genes, and they play important roles in plant defense responses to various pathogens. In this study, 167 NBS-LRR genes were identified from the D. rotundata genome. Subsequently, one gene was assigned to the resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) subclass and the other 166 genes to the coiled coil (CC)-NBS-LRR (CNL) subclass. None of the Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes were detected in the genome. Among them, 124 genes are located in 25 multigene clusters and 43 genes are singletons. Tandem duplication serves as the major force for the cluster arrangement of NBS-LRR genes. Segmental duplication was detected for 18 NBS-LRR genes, although no whole-genome duplication has been documented for the species. Phylogenetic analysis revealed that D. rotundata NBS-LRR genes share 15 ancestral lineages with Arabidopsis thaliana genes. The NBS-LRR gene number increased by more than a factor of 10 during D. rotundata evolution. A conservatively evolved ancestral lineage was identified from D. rotundata, which is orthologs to the Arabidopsis RPM1 gene. Transcriptome analysis for four different tissues of D. rotundata revealed a low expression of most NBS-LRR genes, with the tuber and leaf displaying a relatively high NBS-LRR gene expression than the stem and flower. Overall, this study provides a complete set of NBS-LRR genes for D. rotundata, which may serve as a fundamental resource for mining functional NBS-LRR genes against various pathogens.
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Affiliation(s)
- Yan-Mei Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Ling Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yue Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jianmei Yin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jia Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Xiao-Qin Sun
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yue-Yu Hang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
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89
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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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90
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Wang H, Sun S, Ge W, Zhao L, Hou B, Wang K, Lyu Z, Chen L, Xu S, Guo J, Li M, Su P, Li X, Wang G, Bo C, Fang X, Zhuang W, Cheng X, Wu J, Dong L, Chen W, Li W, Xiao G, Zhao J, Hao Y, Xu Y, Gao Y, Liu W, Liu Y, Yin H, Li J, Li X, Zhao Y, Wang X, Ni F, Ma X, Li A, Xu SS, Bai G, Nevo E, Gao C, Ohm H, Kong L. Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science 2020; 368:science.aba5435. [PMID: 32273397 DOI: 10.1126/science.aba5435] [Citation(s) in RCA: 290] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/26/2020] [Indexed: 12/22/2022]
Abstract
Fusarium head blight (FHB), a fungal disease caused by Fusarium species that produce food toxins, currently devastates wheat production worldwide, yet few resistance resources have been discovered in wheat germplasm. Here, we cloned the FHB resistance gene Fhb7 by assembling the genome of Thinopyrum elongatum, a species used in wheat distant hybridization breeding. Fhb7 encodes a glutathione S-transferase (GST) and confers broad resistance to Fusarium species by detoxifying trichothecenes through de-epoxidation. Fhb7 GST homologs are absent in plants, and our evidence supports that Th. elongatum has gained Fhb7 through horizontal gene transfer (HGT) from an endophytic Epichloë species. Fhb7 introgressions in wheat confers resistance to both FHB and crown rot in diverse wheat backgrounds without yield penalty, providing a solution for Fusarium resistance breeding.
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Affiliation(s)
- Hongwei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
| | - Silong Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenyang Ge
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Lanfei Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Bingqian Hou
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Kai Wang
- Novogene Bioinformatics Institute, Beijing 100083, PR China
| | - Zhongfan Lyu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Liyang Chen
- Novogene Bioinformatics Institute, Beijing 100083, PR China
| | - Shoushen Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jun Guo
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, PR China
| | - Min Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Peisen Su
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xuefeng Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guiping Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Cunyao Bo
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xiaojian Fang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenwen Zhuang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xinxin Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jianwen Wu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Luhao Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wen Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Guilian Xiao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jinxiao Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yongchao Hao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Ying Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yu Gao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Wenjing Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yanhe Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Huayan Yin
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Jiazhu Li
- College of Chemistry and Chemical Engineering, Yantai University, Yantai, Shandong 264005, PR China
| | - Xiang Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Fei Ni
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Xin Ma
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Anfei Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China
| | - Steven S Xu
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, USA
| | - Guihua Bai
- USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66506, USA
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 3498838, Israel
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Herbert Ohm
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong 271018, PR China.
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91
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Dolatabadian A, Bayer PE, Tirnaz S, Hurgobin B, Edwards D, Batley J. Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:969-982. [PMID: 31553100 PMCID: PMC7061875 DOI: 10.1111/pbi.13262] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 08/30/2019] [Accepted: 09/13/2019] [Indexed: 05/18/2023]
Abstract
Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.
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Affiliation(s)
- Aria Dolatabadian
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Philipp E. Bayer
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Soodeh Tirnaz
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Bhavna Hurgobin
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - David Edwards
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
| | - Jacqueline Batley
- UWA School of Biological Sciences and the UWA Institute of AgricultureFaculty of ScienceThe University of Western AustraliaCrawleyWAAustralia
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92
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NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification. Genes (Basel) 2020; 11:genes11030333. [PMID: 32245073 PMCID: PMC7141099 DOI: 10.3390/genes11030333] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/02/2022] Open
Abstract
Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure.
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93
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Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun 2020; 11:989. [PMID: 32080174 PMCID: PMC7033125 DOI: 10.1038/s41467-020-14779-y] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies. Here, we report chromosome-level reference-quality assemblies of seven Arabidopsis thaliana accessions selected across its global range. Each genome reveals between 13–17 Mb rearranged, and 5–6 Mb non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 non-reference genes. Quantifying the collinearity between the genomes reveals ~350 euchromatic regions, where accession-specific tandem duplications destroy the collinearity between the genomes. These hotspots of rearrangements are characterized by reduced meiotic recombination in hybrids and genes implicated in biotic stress response. This suggests that hotspots of rearrangements undergo altered evolutionary dynamics, as compared to the rest of the genome, which are mostly based on the accumulation of new mutations and not on the recombination of existing variation, and thereby enable a quick response to the biotic stress. Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.
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Affiliation(s)
- Wen-Biao Jiao
- Max Planck Institute for Plant Breeding Research, Department of Chromosome Biology, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Korbinian Schneeberger
- Max Planck Institute for Plant Breeding Research, Department of Chromosome Biology, Carl-von-Linné-Weg 10, 50829, Cologne, Germany. .,Faculty of Biology, LMU Munich, Großhaderner Str. 2, 82152, Planegg-Martinsried, Germany.
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94
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Dong X, Wang Z, Tian L, Zhang Y, Qi D, Huo H, Xu J, Li Z, Liao R, Shi M, Wahocho SA, Liu C, Zhang S, Tian Z, Cao Y. De novo assembly of a wild pear (Pyrus betuleafolia) genome. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:581-595. [PMID: 31368610 PMCID: PMC6953202 DOI: 10.1111/pbi.13226] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/25/2019] [Accepted: 07/23/2019] [Indexed: 05/18/2023]
Abstract
China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
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Affiliation(s)
- Xingguang Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Luming Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Dan Qi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Hongliang Huo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Jiayu Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhe Li
- Berry Genomics CorporationBeijingChina
| | - Rui Liao
- Berry Genomics CorporationBeijingChina
| | - Miao Shi
- Berry Genomics CorporationBeijingChina
| | - Safdar Ali Wahocho
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Chao Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Simeng Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yufen Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
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95
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Tirnaz S, Zhang Y, Batley J. Genome-Wide Mining of Disease Resistance Gene Analogs Using Conserved Domains. Methods Mol Biol 2020; 2107:365-375. [PMID: 31893459 DOI: 10.1007/978-1-0716-0235-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The production of legume crop species is severely affected by disease, imposing a significant yield loss annually worldwide. Plant resistance gene analogs (RGAs) play specific roles in plant resistance responses, and their identification and subsequent application in breeding programs help to reduce this yield loss. RGAs contain conserved domains and motifs, which can be used for their identification and classification. Nucleotide-binding site-leucine-rich repeat (NLR), receptor like kinase (RLK), and receptor like protein (RLP) genes are the main types of RGAs. Computational identification and characterization of RGAs has been performed successfully among different plant species. Here, we explain the computational workflow for genome-wide RGA identification in legumes.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Yueqi Zhang
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.
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96
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Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CYL, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT. Construction and comparison of three reference-quality genome assemblies for soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1066-1082. [PMID: 31433882 DOI: 10.1111/tpj.14500] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 05/15/2023]
Abstract
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, 65101, MO, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Longhui Ren
- Interdepartmental Genetics Program, Iowa State University, Ames, 50011, IA, USA
| | - Jerry Jenkins
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Claire Y-L Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Christopher G Daum
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Christopher Plott
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | | | | | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, Ames, 50011, IA, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Haifei Hu
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Yuxuan Yuan
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Qijian Song
- Soybean Genomics and Improvement Lab, US Department of Agriculture - Agricultural Research Service, Beltsville, 20705, MD, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA
| | - David M Goodstein
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Gary Stacey
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Jane Grimwood
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
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97
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Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 2019; 17:92. [PMID: 31757219 PMCID: PMC6874827 DOI: 10.1186/s12915-019-0712-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics. RESULTS The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. CONCLUSIONS The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
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Affiliation(s)
- Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA.
| | - Rebekah Lee
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Rachel Walstead
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | - Melissa C Fogarty
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Cory R Brouwer
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Robert R Reid
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeremy J Jay
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | | | | | - Tim Langdon
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | | | - Eric N Jellen
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
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98
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Rody HVS, Bombardelli RGH, Creste S, Camargo LEA, Van Sluys MA, Monteiro-Vitorello CB. Genome survey of resistance gene analogs in sugarcane: genomic features and differential expression of the innate immune system from a smut-resistant genotype. BMC Genomics 2019; 20:809. [PMID: 31694536 PMCID: PMC6836459 DOI: 10.1186/s12864-019-6207-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Resistance genes composing the two-layer immune system of plants are thought as important markers for breeding pathogen-resistant crops. Many have been the attempts to establish relationships between the genomic content of Resistance Gene Analogs (RGAs) of modern sugarcane cultivars to its degrees of resistance to diseases such as smut. However, due to the highly polyploid and heterozygous nature of sugarcane genome, large scale RGA predictions is challenging. RESULTS We predicted, searched for orthologs, and investigated the genomic features of RGAs within a recently released sugarcane elite cultivar genome, alongside the genomes of sorghum, one sugarcane ancestor (Saccharum spontaneum), and a collection of de novo transcripts generated for six modern cultivars. In addition, transcriptomes from two sugarcane genotypes were obtained to investigate the roles of RGAs differentially expressed (RGADE) in their distinct degrees of resistance to smut. Sugarcane references lack RGAs from the TNL class (Toll-Interleukin receptor (TIR) domain associated to nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains) and harbor elevated content of membrane-associated RGAs. Up to 39% of RGAs were organized in clusters, and 40% of those clusters shared synteny. Basically, 79% of predicted NBS-encoding genes are located in a few chromosomes. S. spontaneum chromosome 5 harbors most RGADE orthologs responsive to smut in modern sugarcane. Resistant sugarcane had an increased number of RGAs differentially expressed from both classes of RLK (receptor-like kinase) and RLP (receptor-like protein) as compared to the smut-susceptible. Tandem duplications have largely contributed to the expansion of both RGA clusters and the predicted clades of RGADEs. CONCLUSIONS Most of smut-responsive RGAs in modern sugarcane were potentially originated in chromosome 5 of the ancestral S. spontaneum genotype. Smut resistant and susceptible genotypes of sugarcane have a distinct pattern of RGADE. TM-LRR (transmembrane domains followed by LRR) family was the most responsive to the early moment of pathogen infection in the resistant genotype, suggesting the relevance of an innate immune system. This work can help to outline strategies for further understanding of allele and paralog expression of RGAs in sugarcane, and the results should help to develop a more applied procedure for the selection of resistant plants in sugarcane.
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Affiliation(s)
- Hugo V S Rody
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Renato G H Bombardelli
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Silvana Creste
- Centro de Cana, IAC-Apta, Ribeirão Preto, Av. Pádua Dias n11, CEP 13418-900, Piracicaba, São Paulo, Brazil
| | - Luís E A Camargo
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânia, Universidade de São Paulo, Instituto de Biociências, São Paulo, Brazil
| | - Claudia B Monteiro-Vitorello
- Escola Superior de Agricultura "Luiz de Queiroz", Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brazil.
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99
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Fu F, Liu X, Wang R, Zhai C, Peng G, Yu F, Fernando WGD. Fine mapping of Brassica napus blackleg resistance gene Rlm1 through bulked segregant RNA sequencing. Sci Rep 2019; 9:14600. [PMID: 31601933 PMCID: PMC6787231 DOI: 10.1038/s41598-019-51191-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 09/26/2019] [Indexed: 01/02/2023] Open
Abstract
The fungal pathogen Leptosphaeria maculans causes blackleg disease on canola and rapeseed (Brassica napus) in many parts of the world. A B. napus cultivar, ‘Quinta’, has been widely used for the classification of L. maculans into pathogenicity groups. In this study, we confirmed the presence of Rlm1 in a DH line (DH24288) derived from B. napus cultivar ‘Quinta’. Rlm1 was located on chromosome A07, between 13.07 to 22.11 Mb, using a BC1 population made from crosses of F1 plants of DH16516 (a susceptible line) x DH24288 with bulked segregant RNA Sequencing (BSR-Seq). Rlm1 was further fine mapped in a 100 kb region from 19.92 to 20.03 Mb in the BC1 population consisting of 1247 plants and a F2 population consisting of 3000 plants using SNP markers identified from BSR-Seq through Kompetitive Allele-Specific PCR (KASP). A potential resistance gene, BnA07G27460D, was identified in this Rlm1 region. BnA07G27460D encodes a serine/threonine dual specificity protein kinase, catalytic domain and is homologous to STN7 in predicted genes of B. rapa and B. oleracea, and A. thaliana. Robust SNP markers associated with Rlm1 were developed, which can assist in introgression of Rlm1 and confirm the presence of Rlm1 gene in canola breeding programs.
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Affiliation(s)
- Fuyou Fu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada.,Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Xunjia Liu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Rui Wang
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada.,Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Chun Zhai
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Gary Peng
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada
| | - Fengqun Yu
- Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, S7N 0X2, Canada.
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100
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Lantican DV, Strickler SR, Canama AO, Gardoce RR, Mueller LA, Galvez HF. De Novo Genome Sequence Assembly of Dwarf Coconut ( Cocos nucifera L. 'Catigan Green Dwarf') Provides Insights into Genomic Variation Between Coconut Types and Related Palm Species. G3 (BETHESDA, MD.) 2019; 9:2377-2393. [PMID: 31167834 PMCID: PMC6686914 DOI: 10.1534/g3.119.400215] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 05/31/2019] [Indexed: 11/23/2022]
Abstract
We report the first whole genome sequence (WGS) assembly and annotation of a dwarf coconut variety, 'Catigan Green Dwarf' (CATD). The genome sequence was generated using the PacBio SMRT sequencing platform at 15X coverage of the expected genome size of 2.15 Gbp, which was corrected with assembled 50X Illumina paired-end MiSeq reads of the same genome. The draft genome was improved through Chicago sequencing to generate a scaffold assembly that results in a total genome size of 2.1 Gbp consisting of 7,998 scaffolds with N50 of 570,487 bp. The final assembly covers around 97.6% of the estimated genome size of coconut 'CATD' based on homozygous k-mer peak analysis. A total of 34,958 high-confidence gene models were predicted and functionally associated to various economically important traits, such as pest/disease resistance, drought tolerance, coconut oil biosynthesis, and putative transcription factors. The assembled genome was used to infer the evolutionary relationship within the palm family based on genomic variations and synteny of coding gene sequences. Data show that at least three (3) rounds of whole genome duplication occurred and are commonly shared by these members of the Arecaceae family. A total of 7,139 unique SSR markers were designed to be used as a resource in marker-based breeding. In addition, we discovered 58,503 variants in coconut by aligning the Hainan Tall (HAT) WGS reads to the non-repetitive regions of the assembled CATD genome. The gene markers and genome-wide SSR markers established here will facilitate the development of varieties with resilience to climate change, resistance to pests and diseases, and improved oil yield and quality.
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Affiliation(s)
- Darlon V Lantican
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Philippine Genome Center, University of the Philippines System, Diliman, Quezon City, Philippines
| | | | - Alma O Canama
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | - Roanne R Gardoce
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Hayde F Galvez
- Genetics Laboratory, Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
- Institute of Crop Science, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Laguna, Philippines 4031
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