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Luo W, Gonzalez E, Zarei A, Calleja S, Rozzi B, Demieville J, Li H, Truco MJ, Lavelle D, Michelmore R, Dyer JM, Jenks MA, Pauli D. Leaf cuticular wax composition of a genetically diverse collection of lettuce ( Lactuca sativa L.) cultivars evaluated under field conditions. Heliyon 2024; 10:e27226. [PMID: 38463774 PMCID: PMC10923717 DOI: 10.1016/j.heliyon.2024.e27226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/15/2023] [Accepted: 02/26/2024] [Indexed: 03/12/2024] Open
Abstract
Cuticular waxes of plants impart tolerance to many forms of environmental stress and help shed dangerous human pathogens on edible plant parts. Although the chemical composition of waxes on a wide variety of important crops has been described, a detailed wax compositional analysis has yet to be reported for lettuce (Lactuca sativa L.), one of the most widely consumed vegetables. We present herein the leaf wax content and composition of 12 genetically diverse lettuce cultivars sampled across five time points during their vegetative growth phase in the field. Mean total leaf wax amounts across all cultivars varied little over 28 days of vegetative growth, except for a notable decrease in total waxes following a major precipitation event, presumably due to wax degradation from wind and rain. All lettuce cultivars were found to contain a unique wax composition highly enriched in 22- and 24-carbon length 1-alcohols (docosanol and tetracosanol, respectively). In our report, the dominance of these shorter chain length 1-alcohols as wax constituents represents a relatively rare phenotype in plants. The ecological significance of these dominant and relatively short 1-alcohols is still unknown. Although waxes have been a target for improvement of various crops, no such work has been reported for lettuce. This study lays the groundwork for future research that aims to integrate cuticular wax characteristics of field grown plants into the larger context of lettuce breeding and cultivar development.
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Affiliation(s)
- Wenting Luo
- Departments of Mathematics and Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Emmanuel Gonzalez
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Ariyan Zarei
- Department of Computer Science, University of Arizona, Tucson, AZ, 85721, USA
| | - Sebastian Calleja
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Bruno Rozzi
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jeffrey Demieville
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Haiquan Li
- Department of Biosystems Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Maria-Jose Truco
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Dean Lavelle
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Richard Michelmore
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - John M. Dyer
- U.S. Department of Agriculture, Agricultural Research Service, Albany, CA, 94710, USA
| | - Matthew A. Jenks
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Duke Pauli
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
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2
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Xiong W, van Workum DJM, Berke L, Bakker LV, Schijlen E, Becker FFM, van de Geest H, Peters S, Michelmore R, van Treuren R, Jeuken M, Smit S, Schranz ME. Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding. G3 (Bethesda) 2023; 13:jkad204. [PMID: 37740775 PMCID: PMC10627274 DOI: 10.1093/g3journal/jkad204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 09/25/2023]
Abstract
Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. To breed resilient and resistant lettuce in the future, valuable genetic variation found in close relatives could be further exploited. Lactuca virosa (2x = 2n = 18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the 3 Lactuca species as core, accessory, and unique. In addition, we identified 3 interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using 3-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicated the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Dirk-Jan M van Workum
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Frank F M Becker
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
- Laboratory of Genetics, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Henri van de Geest
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Richard Michelmore
- The Genome Center, Genome & Biomedical Sciences Facility, University of California, Davis, 451 East Health Sciences Drive, Davis, CA 95616-8816, USA
| | - Rob van Treuren
- Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
| | - Marieke Jeuken
- Plant Breeding Group, Wageningen University & Research, P.O. Box 386, Wageningen, 6700 AJ, The Netherlands
| | - Sandra Smit
- Bioinformatics Group, Wageningen University & Research, P.O. Box 633, Wageningen, 6700 AP, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, P.O. Box 16, Wageningen, 6700 AA, The Netherlands
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3
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Fletcher K, Michelmore R. Genome-Enabled Insights into Downy Mildew Biology and Evolution. Annu Rev Phytopathol 2023; 61:165-183. [PMID: 37268005 DOI: 10.1146/annurev-phyto-021622-103440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Oomycetes that cause downy mildew diseases are highly specialized, obligately biotrophic phytopathogens that can have major impacts on agriculture and natural ecosystems. Deciphering the genome sequence of these organisms provides foundational tools to study and deploy control strategies against downy mildew pathogens (DMPs). The recent telomere-to-telomere genome assembly of the DMP Peronospora effusa revealed high levels of synteny with distantly related DMPs, higher than expected repeat content, and previously undescribed architectures. This provides a road map for generating similar high-quality genome assemblies for other oomycetes. This review discusses biological insights made using this and other assemblies, including ancestral chromosome architecture, modes of sexual and asexual variation, the occurrence of heterokaryosis, candidate gene identification, functional validation, and population dynamics. We also discuss future avenues of research likely to be fruitful in studies of DMPs and highlight resources necessary for advancing our understanding and ability to forecast and control disease outbreaks.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, California, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, California, USA
- Department of Plant Sciences; Department of Molecular and Cellular Biology; Department of Medical Microbiology and Immunology, University of California, Davis, California, USA;
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4
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Sheikhi A, Arab MM, Davis M, Palmer WJ, Michelmore R, Brown PJ. Contrasting allelic effects for pistachio salinity tolerance in juvenile and mature trees. Sci Rep 2023; 13:14391. [PMID: 37658100 PMCID: PMC10474094 DOI: 10.1038/s41598-023-41195-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/23/2023] [Indexed: 09/03/2023] Open
Abstract
Breeding perennial tree crops often requires prediction of mature performance from juvenile data. To assess the utility of juvenile screens to predict salinity tolerance of mature pistachio trees, we compared performance of 3-month ungrafted seedlings and 4-year-old grafted rootstocks under salinity stress. The QTL allele associated with higher salt exclusion from seedling leaves conferred lower growth in saline field conditions, suggesting that mapping QTL in seedlings may be easier than discerning the optimal allele for field performance.
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Affiliation(s)
| | - Mohammad M Arab
- Department of Plant Sciences, University of California, Davis, USA
| | - Matthew Davis
- Department of Plant Sciences, University of California, Davis, USA
| | - William J Palmer
- The Genome Center, University of California, Davis, USA
- Gencove Inc, New York, USA
| | - Richard Michelmore
- Department of Plant Sciences, University of California, Davis, USA
- The Genome Center, University of California, Davis, USA
| | - Pat J Brown
- Department of Plant Sciences, University of California, Davis, USA.
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5
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Nur M, Wood K, Michelmore R. EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage Specificity. Mol Plant Microbe Interact 2023; 36:397-410. [PMID: 36853198 DOI: 10.1094/mpmi-11-22-0236-ta] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Oomycete plant pathogens cause a wide variety of diseases, including late blight of potato, sudden oak death, and downy mildews of plants. These pathogens are major contributors to loss in numerous food crops. Oomycetes secrete effector proteins to manipulate their hosts to the advantage of the pathogen. Plants have evolved to recognize effectors, resulting in an evolutionary cycle of defense and counter-defense in plant-microbe interactions. This selective pressure results in highly diverse effector sequences that can be difficult to computationally identify using only sequence similarity. We developed a novel effector prediction tool, EffectorO, that uses two complementary approaches to predict effectors in oomycete pathogen genomes: i) a machine learning-based pipeline that predicts effector probability based on the biochemical properties of the N-terminal amino-acid sequence of a protein and ii) a pipeline based on lineage specificity to find proteins that are unique to one species or genus, a sign of evolutionary divergence due to adaptation to the host. We tested EffectorO on Bremia lactucae, which causes lettuce downy mildew, and Phytophthora infestans, which causes late blight of potato and tomato, and predicted many novel effector candidates while recovering the majority of known effector candidates. EffectorO will be useful for discovering novel families of oomycete effectors without relying on sequence similarity to known effectors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Munir Nur
- The Genome Center, University of California, Davis, CA, U.S.A
| | - Kelsey Wood
- The Genome Center, University of California, Davis, CA, U.S.A
- Integrative Genetics & Genomics Graduate Group, University of California, Davis, CA, U.S.A
| | - Richard Michelmore
- The Genome Center, University of California, Davis, CA, U.S.A
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
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6
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Xiong W, Berke L, Michelmore R, van Workum DJM, Becker FFM, Schijlen E, Bakker LV, Peters S, van Treuren R, Jeuken M, Bouwmeester K, Schranz ME. The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae. Plant J 2023; 115:108-126. [PMID: 36987839 DOI: 10.1111/tpj.16212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibility (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad-spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen recognition receptors, including nucleotide-binding leucine-rich repeat (NLR) proteins and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia-infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidates for determinants of the NHR phenotype of L. saligna.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Frank F M Becker
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rob van Treuren
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University and Research, Wageningen, The Netherlands
| | - Marieke Jeuken
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
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7
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Kafkas S, Ma X, Zhang X, Topçu H, Navajas-Pérez R, Wai CM, Tang H, Xu X, Khodaeiaminjan M, Güney M, Paizila A, Karcı H, Zhang X, Lin J, Lin H, Herrán RDL, Rejón CR, García-Zea JA, Robles F, Muñoz CDV, Hotz-Wagenblatt A, Min XJ, Özkan H, Motalebipour EZ, Gozel H, Çoban N, Kafkas NE, Kilian A, Huang H, Lv X, Liu K, Hu Q, Jacygrad E, Palmer W, Michelmore R, Ming R. Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution. Plant Commun 2023; 4:100497. [PMID: 36435969 DOI: 10.1016/j.xplc.2022.100497] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 10/01/2022] [Accepted: 11/23/2022] [Indexed: 05/11/2023]
Abstract
Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.
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Affiliation(s)
- Salih Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey.
| | - Xiaokai Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hayat Topçu
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuming Xu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Mortaza Khodaeiaminjan
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Murat Güney
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Aibibula Paizila
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Harun Karcı
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Xiaodan Zhang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jing Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Lin
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | | | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Campus de Fuentenueva s/n, 18071 Granada, Spain
| | - Coral Del Val Muñoz
- Department of Computer Science, University of Granada, Granada, Spain; Andalusian Research Institute in Data Science and Computational Intelligence (DaSCI Institute), 18014 Granada, Spain
| | - Agnes Hotz-Wagenblatt
- German Cancer Research Center, Omics IT and Data Management Core Facility, Heidelberg, Germany
| | - Xiangjia Jack Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | | | - Hatice Gozel
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nergiz Çoban
- Pistachio Research Institute, Şahinbey, Gaziantep 27060, Turkey
| | - Nesibe Ebru Kafkas
- Department of Horticulture, Faculty of Agriculture, University of Çukurova, Adana 01330, Turkey
| | - Andrej Kilian
- Diversity Arrays Technology, University of Canberra, Canberra, ACT, Australia
| | - HuaXing Huang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuanrui Lv
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kunpeng Liu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qilin Hu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ewelina Jacygrad
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - William Palmer
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Richard Michelmore
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Fletcher K, Martin F, Isakeit T, Cavanaugh K, Magill C, Michelmore R. The genome of the oomycete Peronosclerospora sorghi, a cosmopolitan pathogen of maize and sorghum, is inflated with dispersed pseudogenes. G3 (Bethesda) 2023; 13:jkac340. [PMID: 36592124 PMCID: PMC9997571 DOI: 10.1093/g3journal/jkac340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/14/2022] [Accepted: 12/05/2022] [Indexed: 01/03/2023]
Abstract
Several species in the oomycete genus Peronosclerospora cause downy mildew on maize and can result in significant yield losses in Asia. Bio-surveillance of these pathogens is a high priority to prevent epidemics on maize in the United States and consequent damage to the US economy. The unresolved taxonomy and dearth of molecular resources for Peronosclerospora spp. hinder these efforts. P. sorghi is a pathogen of sorghum and maize with a global distribution, for which limited diversity has been detected in the southern USA. We characterized the genome, transcriptome, and mitogenome of an isolate, representing the US pathotype 6. The highly homozygous genome was assembled using 10× Genomics linked reads and scaffolded using Hi-C into 13 chromosomes. The total assembled length was 303.2 Mb, larger than any other oomycete previously assembled. The mitogenome was 38 kb, similar in size to other oomycetes, although it had a unique gene order. Nearly 20,000 genes were annotated in the nuclear genome, more than described for other downy mildew causing oomycetes. The 13 chromosomes of P. sorghi were highly syntenic with the 17 chromosomes of Peronospora effusa with conserved centromeric regions and distinct chromosomal fusions. The increased assembly size and gene count of P. sorghi is due to extensive retrotransposition, resulting in putative pseudogenization. Ancestral genes had higher transcript abundance and were enriched for differential expression. This study provides foundational resources for analysis of Peronosclerospora and comparisons to other oomycete genera. Further genomic studies of global Peronosclerospora spp. will determine the suitability of the mitogenome, ancestral genes, and putative pseudogenes for marker development and taxonomic relationships.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Frank Martin
- U.S. Department of Agriculture–Agriculture Research Service, Salinas, CA, 93905, USA
| | - Thomas Isakeit
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Keri Cavanaugh
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, CA 95616, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, CA 95616, USA
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9
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Bull T, Debernardi J, Reeves M, Hill T, Bertier L, Van Deynze A, Michelmore R. GRF-GIF chimeric proteins enhance in vitro regeneration and Agrobacterium-mediated transformation efficiencies of lettuce (Lactuca spp.). Plant Cell Rep 2023; 42:629-643. [PMID: 36695930 PMCID: PMC10042933 DOI: 10.1007/s00299-023-02980-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
KEY MESSAGE GRF-GIF chimeric proteins from multiple source species enhance in vitro regeneration in both wild and cultivated lettuce. In addition, they enhance regeneration in multiple types of lettuce including butterheads, romaines, and crispheads. The ability of plants to regenerate in vitro has been exploited for use in tissue culture systems for plant propagation, plant transformation, and genome editing. The success of in vitro regeneration is often genotype dependent and continues to be a bottleneck for Agrobacterium-mediated transformation and its deployment for improvement of some crop species. Manipulation of transcription factors that play key roles in plant development such as BABY BOOM, WUSCHEL, and GROWTH-REGULATING FACTORs (GRFs) has improved regeneration and transformation efficiencies in several plant species. Here, we compare the efficacy of GRF-GIF gene fusions from multiple species to boost regeneration efficiency and shooting frequency in four genotypes of wild and cultivated lettuce (Lactuca spp. L.). In addition, we show that GRF-GIFs with mutated miRNA 396 binding sites increase regeneration efficiency and shooting frequency when compared to controls. We also present a co-transformation strategy for increased transformation efficiency and recovery of transgenic plants harboring a gene of interest. This strategy will enhance the recovery of transgenic plants of other lettuce genotypes and likely other crops in the Compositae family.
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Affiliation(s)
- Tawni Bull
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, USA
- The Genome Center, University of California, Davis, Davis, CA, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Juan Debernardi
- Plant Transformation Facility, University of California, Davis, CA, USA
| | - Megan Reeves
- The Genome Center, University of California, Davis, Davis, CA, USA
| | - Theresa Hill
- The Seed Biotechnology Center, University of California, Davis, Davis, CA, USA
| | - Lien Bertier
- The Genome Center, University of California, Davis, Davis, CA, USA
- Ohalo Genetics, Inc., Aptos, CA, USA
| | - Allen Van Deynze
- The Seed Biotechnology Center, University of California, Davis, Davis, CA, USA
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, USA.
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.
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10
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Davis JT, Li R, Kim S, Michelmore R, Kim S, Maloof JN. Whole genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae. G3 (Bethesda) 2023; 13:7022186. [PMID: 36724115 PMCID: PMC10085753 DOI: 10.1093/g3journal/jkad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/04/2021] [Accepted: 12/21/2022] [Indexed: 02/02/2023]
Abstract
Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from B. rapa and B. oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high quality draft genomes of this species have been released. Using third generation sequencing and assembly technologies, we generated a new genome assembly for the synthetic Brassica napus cultivar Da-Ae. Through the use of long reads, linked-reads, and Hi-C proximity data, we assembled a new draft genome that provides a high quality reference genome of a synthetic Brassica napus. In addition, we identified potential hotspots of homoeologous exchange between subgenomes within Da-Ae, based on their presence in other independently-derived lines. The occurrence of these hotspots may provide insight into the genetic rearrangements required for B. napus to be viable following the hybridization of B. rapa and B. oleracea.
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Affiliation(s)
- John T Davis
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Ruijuan Li
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Seungmo Kim
- FnP Co., Ltd., Jeungpyeong-gun, Chungbuk-do 27903, South Korea
| | - Richard Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Shinje Kim
- FnP Co., Ltd., Jeungpyeong-gun, Chungbuk-do 27903, South Korea
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
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11
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Palmer W, Jacygrad E, Sagayaradj S, Cavanaugh K, Han R, Bertier L, Beede B, Kafkas S, Golino D, Preece J, Michelmore R. Genome assembly and association tests identify interacting loci associated with vigor, precocity, and sex in interspecific pistachio rootstocks. G3 (Bethesda) 2022; 13:6861913. [PMID: 36454230 PMCID: PMC9911073 DOI: 10.1093/g3journal/jkac317] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Understanding the basis of hybrid vigor remains a key question in crop breeding and improvement, especially for rootstock development where F1 hybrids are extensively utilized. Full-sibling UCB-1 F1 seedling rootstocks are widely planted in commercial pistachio orchards that are generated by crossing 2 highly heterozygous outbreeding parental trees of Pistacia atlantica (female) and P. integerrima (male). This results in extensive phenotypic variability, prompting costly removal of low-yielding small trees. To identify the genetic basis of this variability, we assembled chromosome-scale genome assemblies of the parental trees of UCB-1. We genotyped 960 UCB-1 trees in an experimental orchard for which we also collected multiyear phenotypes. We genotyped an additional 1,358 rootstocks in 6 commercial pistachio orchards and collected single-year tree-size data. Genome-wide single marker association tests identified loci associated with tree size and shape, sex, and precocity. In the experimental orchard, we identified multiple trait-associated loci and a strong candidate for ZZ/ZW sex chromosomes. We found significant marker associations unique to different traits and to early vs late phenotypic measures of the same trait. We detected 2 loci strongly associated with rootstock size in commercial orchards. Pseudo-testcross classification of markers demonstrated that the trait-associated alleles for each locus were segregating in the gametes of opposite parents. These 2 loci interact epistatically to generate the bimodal distribution of tree size with undesirable small trees observed by growers. We identified candidate genes within these regions. These findings provide a foundational resource for marker development and genetic selection of vigorous pistachio UCB-1 rootstock.
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Affiliation(s)
- William Palmer
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA,Present address: Gencove, 30-02 48th Avenue, Suite 370, Long Island City, NY 11101, USA
| | - Ewelina Jacygrad
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sagayamary Sagayaradj
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Keri Cavanaugh
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Rongkui Han
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Lien Bertier
- Genome Center, University of California, Davis, One Shields Ave, Davis, CA 95616, USA,Present address: Ohalo Genetics, 9565 Soquel Dr. Suite 101, Aptos, CA 95003, USA
| | - Bob Beede
- UC Cooperative Extension, 680 North Campus Dr., Hanford, CA 93230, USA
| | - Salih Kafkas
- Department of Horticulture, University of Çukurova, 01330 Adana, Turkey
| | - Deborah Golino
- Foundation Plant Services, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - John Preece
- National Clonal Germplasm Repository, University of California, Davis, One Shields Ave, Davis, CA 95616, USA
| | - Richard Michelmore
- Corresponding author: Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA.
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12
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Pink H, Talbot A, Graceson A, Graham J, Higgins G, Taylor A, Jackson AC, Truco M, Michelmore R, Yao C, Gawthrop F, Pink D, Hand P, Clarkson JP, Denby K. Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens. Theor Appl Genet 2022; 135:2481-2500. [PMID: 35674778 PMCID: PMC9271113 DOI: 10.1007/s00122-022-04129-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.
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Affiliation(s)
- Harry Pink
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Adam Talbot
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Abi Graceson
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Juliane Graham
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Gill Higgins
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Andrew Taylor
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Alison C Jackson
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Maria Truco
- Genome Center, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Richard Michelmore
- Genome Center, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Chenyi Yao
- A. L. Tozer Ltd., Pyports, Downside Road, Cobham, Surrey, KT11 3EH, UK
| | - Frances Gawthrop
- A. L. Tozer Ltd., Pyports, Downside Road, Cobham, Surrey, KT11 3EH, UK
| | - David Pink
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - Paul Hand
- Department of Agriculture and Environment, Harper Adams University, Newport, Shropshire, TF10 8NB, UK
| | - John P Clarkson
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Katherine Denby
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK.
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13
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Bull T, Michelmore R. Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce ( Lactuca sativa L.). Front Plant Sci 2022; 13:888425. [PMID: 35615120 PMCID: PMC9125155 DOI: 10.3389/fpls.2022.888425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/31/2022] [Indexed: 05/12/2023]
Abstract
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
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Affiliation(s)
- Tawni Bull
- The Genome Center, University of California, Davis, Davis, CA, United States
- Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States
| | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, CA, United States
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
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14
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Acharya CB, Schrom J, Mitchell AM, Coil DA, Marquez C, Rojas S, Wang CY, Liu J, Pilarowski G, Solis L, Georgian E, Belafsky S, Petersen M, DeRisi J, Michelmore R, Havlir D. Viral Load Among Vaccinated and Unvaccinated, Asymptomatic and Symptomatic Persons Infected With the SARS-CoV-2 Delta Variant. Open Forum Infect Dis 2022; 9:ofac135. [PMID: 35479304 PMCID: PMC8992250 DOI: 10.1093/ofid/ofac135] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/16/2022] [Indexed: 07/21/2023] Open
Abstract
We found no significant difference in cycle threshold values between vaccinated and unvaccinated persons infected with severe acute respiratory syndrome coronavirus 2 Delta, overall or stratified by symptoms. Given the substantial proportion of asymptomatic vaccine breakthrough cases with high viral levels, interventions, including masking and testing, should be considered in settings with elevated coronavirus disease 2019 transmission.
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Affiliation(s)
| | - John Schrom
- Unidos en Salud, San Francisco, California, USA
| | - Anthea M Mitchell
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - David A Coil
- Genome Center, University of California, Davis, Davis, California, USA
| | - Carina Marquez
- Unidos en Salud, San Francisco, California, USA
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | | | - Chung Yu Wang
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Jamin Liu
- Joint UCB/UCSF Bioengineering Program, University of California, Berkeley, and University of California, San Francisco, San Francisco, California, USA
| | - Genay Pilarowski
- Unidos en Salud, San Francisco, California, USA
- The Public Health Company, Oakland, California, USA
| | - Leslie Solis
- Genome Center, University of California, Davis, Davis, California, USA
| | | | - Sheri Belafsky
- Department of Public Health Sciences, University of California, Davis, Davis, California, USA
| | - Maya Petersen
- Unidos en Salud, San Francisco, California, USA
- School of Public Health, University of California, Berkeley, Berkeley, California, USA
| | - Joseph DeRisi
- Chan Zuckerberg Biohub and Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
| | | | - Diane Havlir
- Unidos en Salud, San Francisco, California, USA
- Division of HIV, Infectious Disease and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
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15
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Fletcher K, Han R, Smilde D, Michelmore R. Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state. BMC Bioinformatics 2022; 23:150. [PMID: 35468720 PMCID: PMC9040317 DOI: 10.1186/s12859-022-04685-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 03/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Polyploidy and heterokaryosis are common and consequential genetic phenomena that increase the number of haplotypes in an organism and complicate whole-genome sequence analysis. Allele balance has been used to infer polyploidy and heterokaryosis in diverse organisms using read sets sequenced to greater than 50× whole-genome coverage. However, sequencing to adequate depth is costly if applied to multiple individuals or large genomes. Results We developed VCFvariance.pl to utilize the variance of allele balance to infer polyploidy and/or heterokaryosis at low sequence coverage. This analysis requires as little as 10× whole-genome coverage and reduces the allele balance profile down to a single value, which can be used to determine if an individual has two or more haplotypes. This approach was validated using simulated, synthetic, and authentic read sets from the oomycete species Bremia lactucae and Phytophthora infestans, the fungal species Saccharomyces cerevisiae, and the plant species Arabidopsis arenosa. This approach was deployed to determine that nine of 21 genotyped European race-type isolates of Bremia lactucae were inconsistent with diploidy and therefore likely heterokaryotic. Conclusions Variance of allele balance is a reliable metric to detect departures from a diploid state, including polyploidy, heterokaryosis, a mixed sample, or chromosomal copy number variation. Deploying this strategy is computationally inexpensive, can reduce the cost of sequencing by up to 80%, and used to test any organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04685-z.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, USA.,The Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Diederik Smilde
- Naktuinbouw, Postbus 40, Sotaweg 22, 2370 AA, Roelofarendsveen, The Netherlands
| | - Richard Michelmore
- The Genome Center, University of California, Davis, USA. .,Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, USA.
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16
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Crouch J, Davis W, Shishkoff N, Castroagudín V, Martin F, Michelmore R, Thines M. Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources. Fungal Syst Evol 2022; 9:43-86. [PMID: 35978987 PMCID: PMC9355112 DOI: 10.3114/fuse.2022.09.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/20/2022] [Indexed: 11/29/2022] Open
Abstract
Downy mildew pathogens of graminicolous hosts (Poaceae) are members of eight morphologically and phylogenetically distinct genera in the Peronosporaceae (Oomycota,Peronosporales). Graminicolous downy mildews (GDMs) cause severe losses in crops such as maize, millets, sorghum, and sugarcane in many parts of the world, especially in tropical climates. In countries where the most destructive GDMs are not endemic, these organisms are often designated as high-risk foreign pathogens and subject to oversight and quarantine by regulatory officials. Thus, there is a need to reliably and accurately identify the causal organisms. This paper provides an overview of the Peronosporaceae species causing graminicolous downy mildew diseases, with a description of their impact on agriculture and the environment, along with brief summaries of the nomenclatural and taxonomic issues surrounding these taxa. Key diagnostic characters are summarized, including DNA sequence data for types and/or voucher specimens, morphological features, and new illustrations. New sequence data for cox2 and 28S rDNA markers are provided from the type specimens of three species, Peronosclerospora philippinensis, Sclerospora iseilematis, and Sclerospora northii. Thirty-nine species of graminicolous downy mildews are accepted, and seven previously invalidly published taxa are validated. Fifty-five specimens are formally designated as types, including lectotypification of 10 species, neotypification of three species, and holotype designation for Sclerophthora cryophila. Citation: Crouch JA, Davis WJ, Shishkoff N, Castroagudín VL, Martin F, Michelmore R, Thines M (2022). Peronosporaceae species causing downy mildew diseases of Poaceae, including nomenclature revisions and diagnostic resources. Fungal Systematics and Evolution9: 43–86. doi: 10.3114/fuse.2022.09.05
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Affiliation(s)
- J.A. Crouch
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
| | - W.J. Davis
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge Tennessee, USA
| | - N. Shishkoff
- USDA-ARS, Foreign Disease Weed Science Research Unit, Frederick, MD, USA
| | - V.L. Castroagudín
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD, USA
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge Tennessee, USA
| | - F. Martin
- USDA-ARS, Crop Improvement and Protection Research, Salinas, CA, USA
| | - R. Michelmore
- The Genome Center and Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - M. Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
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17
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Han R, Lavelle D, Truco MJ, Michelmore R. Quantitative Trait Loci and Candidate Genes Associated with Photoperiod Sensitivity in Lettuce (Lactuca spp.). Theor Appl Genet 2021; 134:3473-3487. [PMID: 34245320 PMCID: PMC8440299 DOI: 10.1007/s00122-021-03908-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/02/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE A population of lettuce that segregated for photoperiod sensitivity was planted under long-day and short-day conditions. Genetic mapping revealed two distinct sets of QTLs controlling daylength-independent and photoperiod-sensitive flowering time. The molecular mechanism of flowering time regulation in lettuce is of interest to both geneticists and breeders because of the extensive impact of this trait on agricultural production. Lettuce is a facultative long-day plant which changes in flowering time in response to photoperiod. Variations exist in both flowering time and the degree of photoperiod sensitivity among accessions of wild (Lactuca serriola) and cultivated (L. sativa) lettuce. An F6 population of 236 recombinant inbred lines (RILs) was previously developed from a cross between a late-flowering, photoperiod-sensitive L. serriola accession and an early-flowering, photoperiod-insensitive L. sativa accession. This population was planted under long-day (LD) and short-day (SD) conditions in a total of four field and screenhouse trials; the developmental phenotype was scored weekly in each trial. Using genotyping-by-sequencing (GBS) data of the RILs, quantitative trait loci (QTL) mapping revealed five flowering time QTLs that together explained more than 20% of the variation in flowering time under LD conditions. Using two independent statistical models to extract the photoperiod sensitivity phenotype from the LD and SD flowering time data, we identified an additional five QTLs that together explained more than 30% of the variation in photoperiod sensitivity in the population. Orthology and sequence analysis of genes within the nine QTLs revealed potential functional equivalents in the lettuce genome to the key regulators of flowering time and photoperiodism, FD and CONSTANS, respectively, in Arabidopsis.
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Affiliation(s)
- Rongkui Han
- The Plant Biology Graduate Group, University of California, Davis, 95616, USA
- The Genome Center, University of California, Davis, 95616, USA
| | - Dean Lavelle
- The Genome Center, University of California, Davis, 95616, USA
| | | | - Richard Michelmore
- The Genome Center, University of California, Davis, 95616, USA.
- Department of Plant Sciences, University of California, Davis, 95616, USA.
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18
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Fletcher K, Zhang L, Gil J, Han R, Cavanaugh K, Michelmore R. AFLAP: assembly-free linkage analysis pipeline using k-mers from genome sequencing data. Genome Biol 2021; 22:115. [PMID: 33883006 PMCID: PMC8061198 DOI: 10.1186/s13059-021-02326-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/25/2021] [Indexed: 11/20/2022] Open
Abstract
Our assembly-free linkage analysis pipeline (AFLAP) identifies segregating markers as k-mers in the raw reads without using a reference genome assembly for calling variants and provides genotype tables for the construction of unbiased, high-density genetic maps without a genome assembly. AFLAP is validated and contrasted to a conventional workflow using simulated data. AFLAP is applied to whole genome sequencing and genotype-by-sequencing data of F1, F2, and recombinant inbred populations of two different plant species, producing genetic maps that are concordant with genome assemblies. The AFLAP-based genetic map for Bremia lactucae enables the production of a chromosome-scale genome assembly.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, University of California, Davis, USA
| | - Lin Zhang
- The Genome Center, University of California, Davis, USA
| | - Juliana Gil
- The Genome Center, University of California, Davis, USA
| | - Rongkui Han
- The Genome Center, University of California, Davis, USA
| | | | - Richard Michelmore
- The Genome Center, University of California, Davis, USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, USA
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19
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Parra L, Nortman K, Sah A, Truco MJ, Ochoa O, Michelmore R. Identification and mapping of new genes for resistance to downy mildew in lettuce. Theor Appl Genet 2021; 134:519-528. [PMID: 33128618 PMCID: PMC7843477 DOI: 10.1007/s00122-020-03711-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/16/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE Eleven new major resistance genes for lettuce downy mildew were introgressed from wild Lactuca species and mapped to small regions in the lettuce genome. Downy mildew, caused by the oomycete pathogen Bremia lactucae Regel, is the most important disease of lettuce (Lactuca sativa L.). The most effective method to control this disease is by using resistant cultivars expressing dominant resistance genes (Dm genes). In order to counter changes in pathogen virulence, multiple resistance genes have been introgressed from wild species by repeated backcrosses to cultivated lettuce, resulting in numerous near-isogenic lines (NILs) only differing for small chromosome regions that are associated with resistance. Low-pass, whole genome sequencing of 11 NILs was used to identify the chromosome segments introgressed from the wild donor species. This located the candidate chromosomal positions for resistance genes as well as additional segments. F2 segregating populations derived from these NILs were used to genetically map the resistance genes to one or two loci in the lettuce reference genome. Precise knowledge of the location of new Dm genes provides the foundation for marker-assisted selection to breed cultivars with multiple genes for resistance to downy mildew.
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Affiliation(s)
- Lorena Parra
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kazuko Nortman
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Anil Sah
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Maria Jose Truco
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Oswaldo Ochoa
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Richard Michelmore
- The Genome Center, Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
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20
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Wood KJ, Nur M, Gil J, Fletcher K, Lakeman K, Gann D, Gothberg A, Khuu T, Kopetzky J, Naqvi S, Pandya A, Zhang C, Maisonneuve B, Pel M, Michelmore R. Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif. PLoS Pathog 2020; 16:e1009012. [PMID: 33104763 PMCID: PMC7644090 DOI: 10.1371/journal.ppat.1009012] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 11/05/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors that has been implicated in immune suppression as well as effector recognition by host resistance proteins. We predicted 55 WY domain containing proteins in the genome of B. lactucae and found substantial variation in both sequence and domain architecture. These candidate effectors exhibit several characteristics of pathogen effectors, including an N-terminal signal peptide, lineage specificity, and expression during infection. Unexpectedly, only a minority of B. lactucae WY effectors contain the canonical N-terminal RXLR motif, which is a conserved feature in the majority of cytoplasmic effectors reported in Phytophthora spp. Functional analysis of 21 effectors containing WY domains revealed 11 that elicited cell death on wild accessions and domesticated lettuce lines containing resistance genes, indicative of recognition of these effectors by the host immune system. Only two of the 11 recognized effectors contained the canonical RXLR motif, suggesting that there has been an evolutionary divergence in sequence motifs between genera; this has major consequences for robust effector prediction in oomycete pathogens.
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Affiliation(s)
- Kelsey J. Wood
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Integrative Genetics & Genomics Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Munir Nur
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Juliana Gil
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Plant Pathology Graduate Group, University of California, Davis, Davis, California, United States of America
| | - Kyle Fletcher
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | - Dasan Gann
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Ayumi Gothberg
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Tina Khuu
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Jennifer Kopetzky
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Sanye Naqvi
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Archana Pandya
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | - Chi Zhang
- The Genome Center, University of California, Davis, Davis, California, United States of America
| | | | | | - Richard Michelmore
- The Genome Center, University of California, Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, Davis, California, United States of America
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21
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Fletcher K, Gil J, Bertier LD, Kenefick A, Wood KJ, Zhang L, Reyes-Chin-Wo S, Cavanaugh K, Tsuchida C, Wong J, Michelmore R. Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae. Nat Commun 2019; 10:2645. [PMID: 31201315 PMCID: PMC6570648 DOI: 10.1038/s41467-019-10550-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/14/2019] [Indexed: 12/26/2022] Open
Abstract
Lettuce downy mildew caused by Bremia lactucae is the most important disease of lettuce globally. This oomycete is highly variable and rapidly overcomes resistance genes and fungicides. The use of multiple read types results in a high-quality, near-chromosome-scale, consensus assembly. Flow cytometry plus resequencing of 30 field isolates, 37 sexual offspring, and 19 asexual derivatives from single multinucleate sporangia demonstrates a high incidence of heterokaryosis in B. lactucae. Heterokaryosis has phenotypic consequences on fitness that may include an increased sporulation rate and qualitative differences in virulence. Therefore, selection should be considered as acting on a population of nuclei within coenocytic mycelia. This provides evolutionary flexibility to the pathogen enabling rapid adaptation to different repertoires of host resistance genes and other challenges. The advantages of asexual persistence of heterokaryons may have been one of the drivers of selection that resulted in the loss of uninucleate zoospores in multiple downy mildews.
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Affiliation(s)
- Kyle Fletcher
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Juliana Gil
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lien D Bertier
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Aubrey Kenefick
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Kelsey J Wood
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
| | - Lin Zhang
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Sebastian Reyes-Chin-Wo
- Genome Center, University of California, Davis, CA, 95616, USA
- Integrated Genetics and Genomics Graduate Group, University of California, Davis, CA, 95616, USA
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, USA
| | - Keri Cavanaugh
- Genome Center, University of California, Davis, CA, 95616, USA
| | - Cayla Tsuchida
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Pathology Graduate Group, University of California, Davis, CA, 95616, USA
- Arcadia Biosciences, Davis, CA, 95616, USA
| | - Joan Wong
- Genome Center, University of California, Davis, CA, 95616, USA
- Plant Biology Graduate Group, University of California, Davis, CA, 95616, USA
- Pacific Biosciences of California, Inc., Menlo Park, CA, 94025, USA
| | - Richard Michelmore
- Genome Center, University of California, Davis, CA, 95616, USA.
- Departments of Plant Sciences, Molecular and Cellular Biology, Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA.
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22
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Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 2019; 51:877-884. [PMID: 31043755 DOI: 10.1038/s41588-019-0405-z] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/28/2019] [Indexed: 12/24/2022]
Abstract
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
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Affiliation(s)
- David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Josh Clevenger
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Longhui Ren
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, USA
| | | | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sergio S Samoluk
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | | | | | | | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Moaine El Baidouri
- UMR5096, Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France.,UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture, Agricultural Research Service, Tifton, GA, USA
| | - Wei Huang
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Walid Korani
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Sophie Lanciano
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | - Christopher G Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Marie Mirouze
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | | | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Jin Hee Shin
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | | | | | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Xinyou Zhang
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Zheng Zheng
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Ziqi Sun
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Lutz Froenicke
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Erez L Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Corley Holbrook
- Crop Genetics and Breeding Research Unit, US Department of Agriculture Agricultural Research Service, Tifton, GA, USA
| | | | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, US Department of Agriculture Agricultural Research Service, Stoneville, MS, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA. .,Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
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23
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Fletcher K, Klosterman SJ, Derevnina L, Martin F, Bertier LD, Koike S, Reyes-Chin-Wo S, Mou B, Michelmore R. Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics 2018; 19:851. [PMID: 30486780 PMCID: PMC6264045 DOI: 10.1186/s12864-018-5214-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/31/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. RESULTS We virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp. CONCLUSIONS We present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven J. Klosterman
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lida Derevnina
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Present Address: The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH UK
| | - Frank Martin
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Lien D. Bertier
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Steven Koike
- UC Davis Cooperative Extension Monterey County, Salinas, CA 93901 USA
- Present Address: TriCal Diagnostics, Hollister, CA 95023 USA
| | - Sebastian Reyes-Chin-Wo
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
| | - Beiquan Mou
- United States Department of Agriculture, Agricultural Research Service, Salinas, CA 93905 USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, 451 East Health Sciences Drive, Davis, CA 95616 USA
- Departments of Plant Sciences, Molecular & Cellular Biology, Medical Microbiology & Immunology, University of California, Davis, 95616 USA
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24
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Abstract
A high-quality, annotated genome assembly is the foundation for many downstream studies. However, obtaining such an assembly is a complex, reiterative process that requires the assimilation of high-quality data and combines different approaches and data types. While some software packages incorporating multiple steps of genome assembly are commercially available, they may not be flexible enough to be routinely applied to all organisms, particularly to nonmodel species such as pathogenic oomycetes and fungi. If researchers understand and apply the most appropriate, currently available tools for each step, it is possible to customize parameters and optimize results for their organism of study. Based on our experience of de novo assembly and annotation of several oomycete species, this chapter provides a modular workflow from processing of raw reads, to initial assembly generation, through optimization, chromosome-scale scaffolding and annotation, outlining input and output data as well as examples and alternative software used for each step. The accompanying Notes provide background information for each step as well as alternative options. The final result of this workflow could be an annotated, high-quality, validated, chromosome-scale assembly or a draft assembly of sufficient quality to meet specific needs of a project.
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Affiliation(s)
- Kyle Fletcher
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA
| | - Richard Michelmore
- The Genome Center, Genome and Biomedical Sciences Facility, University of California, Davis, CA, USA.
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25
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Michelmore R, Coaker G, Bart R, Beattie G, Bent A, Bruce T, Cameron D, Dangl J, Dinesh-Kumar S, Edwards R, Eves-van den Akker S, Gassmann W, Greenberg JT, Hanley-Bowdoin L, Harrison RJ, Harvey J, He P, Huffaker A, Hulbert S, Innes R, Jones JDG, Kaloshian I, Kamoun S, Katagiri F, Leach J, Ma W, McDowell J, Medford J, Meyers B, Nelson R, Oliver R, Qi Y, Saunders D, Shaw M, Smart C, Subudhi P, Torrance L, Tyler B, Valent B, Walsh J. Foundational and Translational Research Opportunities to Improve Plant Health. Mol Plant Microbe Interact 2017; 30:515-516. [PMID: 28398839 PMCID: PMC5810936 DOI: 10.1094/mpmi-01-17-0010-cr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reader Comments | Submit a Comment The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.
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Affiliation(s)
- Richard Michelmore
- 1 The Genome Center and Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
| | - Gitta Coaker
- 2 Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | | | | | - Andrew Bent
- 5 University of Wisconsin, Madison, WI, U.S.A
| | | | | | - Jeffery Dangl
- 8 University of North Carolina, Chapel Hill, NC, U.S.A
| | | | - Rob Edwards
- 10 University of Newcastle, Newcastle upon Tyne, U.K
| | | | | | | | | | | | | | - Ping He
- 17 Texas A&M University, College Station, TX, U.S.A
| | | | - Scot Hulbert
- 19 Washington State University, Pullman, WA, U.S.A
| | - Roger Innes
- 20 Indiana University, Bloomigton, IN, U.S.A
| | | | | | | | | | - Jan Leach
- 24 Colorado State University, Fort Collins, CO, U.S.A
| | - Wenbo Ma
- 22 University of California, Riverside, CA, U.S.A
| | | | | | | | | | | | - Yiping Qi
- 29 East Carolina University, Greenville, NC, U.S.A
| | | | | | | | | | - Lesley Torrance
- 33 University of St. Andrews and James Hutton Institute, Fife, U.K
| | - Bret Tyler
- 34 Oregon State University, Corvallis, OR, U.S.A.; and
| | | | - John Walsh
- 35 University of Warwick, Wellesbourne, U.K
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26
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Scaglione D, Reyes-Chin-Wo S, Acquadro A, Froenicke L, Portis E, Beitel C, Tirone M, Mauro R, Lo Monaco A, Mauromicale G, Faccioli P, Cattivelli L, Rieseberg L, Michelmore R, Lanteri S. Corrigendum: The genome sequence of the outbreeding globe artichoke constructed de novo incorporating a phase-aware low-pass sequencing strategy of F1 progeny. Sci Rep 2016; 6:25323. [PMID: 27212460 PMCID: PMC4876515 DOI: 10.1038/srep25323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
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27
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Derevnina L, Chin-Wo-Reyes S, Martin F, Wood K, Froenicke L, Spring O, Michelmore R. Genome Sequence and Architecture of the Tobacco Downy Mildew Pathogen Peronospora tabacina. Mol Plant Microbe Interact 2015; 28:1198-215. [PMID: 26196322 DOI: 10.1094/mpmi-05-15-0112-r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N50 = 79 kb) and 3,245 (55.3 Mb, N50 = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain-containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.
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Affiliation(s)
- Lida Derevnina
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | | | - Frank Martin
- 2 United States Department of Agriculture-Agricultural Research Service, Salinas, CA U.S.A
| | - Kelsey Wood
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Lutz Froenicke
- 1 Genome Center, University of California Davis, Davis, CA, U.S.A
| | - Otmar Spring
- 3 Institute of Botany, University of Hohenheim, Germany
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Muñoz-Bodnar A, Perez-Quintero AL, Gomez-Cano F, Gil J, Michelmore R, Bernal A, Szurek B, Lopez C. RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis. Plant Cell Rep 2014; 33:1901-12. [PMID: 25120000 DOI: 10.1007/s00299-014-1667-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 06/25/2014] [Accepted: 07/23/2014] [Indexed: 05/28/2023]
Abstract
An RNAseq-based analysis of the cassava plants inoculated with Xam allowed the identification of transcriptional upregulation of genes involved in jasmonate metabolism, phenylpropanoid biosynthesis and putative targets for a TALE. Cassava bacterial blight, a disease caused by the gram-negative bacterium Xanthomonas axonopodis pv. manihotis (Xam), is a major limitation to cassava production worldwide and especially in developing countries. The molecular mechanisms underlying cassava susceptibility to Xam are currently unknown. To identify host genes and pathways leading to plant susceptibility, we analyzed the transcriptomic responses occurring in cassava plants challenged with either the non-pathogenic Xam strain ORST4, or strain ORST4(TALE1 Xam ) which is pathogenic due to the major virulence transcription activator like effector TALE1 Xam . Both strains triggered similar responses, i.e., induction of genes related to photosynthesis and phenylpropanoid biosynthesis, and repression of genes related to jasmonic acid signaling. Finally, to search for TALE1 Xam virulence targets, we scanned the list of cassava genes induced upon inoculation of ORST4(TALE1 Xam ) for candidates harboring a predicted TALE1 Xam effector binding element in their promoter. Among the six genes identified as potential candidate targets of TALE1 Xam a gene coding for a heat shock transcription factor stands out as the best candidate based on their induction in presence of TALE1 Xam and contain a sequence putatively recognized by TALE1 Xam .
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Affiliation(s)
- Alejandra Muñoz-Bodnar
- Manihot Biotec Group, Department of Biology, Universidad Nacional de Colombia, Bogotá, Colombia
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Matvienko M, Kozik A, Froenicke L, Lavelle D, Martineau B, Perroud B, Michelmore R. Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One 2013; 8:e55913. [PMID: 23409088 PMCID: PMC3568094 DOI: 10.1371/journal.pone.0055913] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 01/04/2013] [Indexed: 12/22/2022] Open
Abstract
Several applications of high throughput genome and transcriptome sequencing would benefit from a reduction of the high-copy-number sequences in the libraries being sequenced and analyzed, particularly when applied to species with large genomes. We adapted and analyzed the consequences of a method that utilizes a thermostable duplex-specific nuclease for reducing the high-copy components in transcriptomic and genomic libraries prior to sequencing. This reduces the time, cost, and computational effort of obtaining informative transcriptomic and genomic sequence data for both fully sequenced and non-sequenced genomes. It also reduces contamination from organellar DNA in preparations of nuclear DNA. Hybridization in the presence of 3 M tetramethylammonium chloride (TMAC), which equalizes the rates of hybridization of GC and AT nucleotide pairs, reduced the bias against sequences with high GC content. Consequences of this method on the reduction of high-copy and enrichment of low-copy sequences are reported for Arabidopsis and lettuce.
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Affiliation(s)
- Marta Matvienko
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Alexander Kozik
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Lutz Froenicke
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Dean Lavelle
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Belinda Martineau
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Bertrand Perroud
- Genome Center, University of California Davis, Davis, California, United States of America
| | - Richard Michelmore
- Genome Center, University of California Davis, Davis, California, United States of America
- Departments of Plant Sciences, Molecular and Cellular Biology, and Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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31
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Strasburg JL, Kane NC, Raduski AR, Bonin A, Michelmore R, Rieseberg LH. Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Mol Biol Evol 2011; 28:1569-80. [PMID: 20952500 PMCID: PMC3080132 DOI: 10.1093/molbev/msq270] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, with high levels of adaptive evolution in Drosophila, bacteria, and viruses but very little evidence of widespread adaptive evolution in hominids. Although estimates in plants are more limited, some recent work has suggested that rates of adaptive evolution in a range of plant taxa are surprisingly low and that there is little association between adaptive evolution and effective population size in contrast to patterns seen in other taxa. Here, we analyze data from 35 loci for six sunflower species that vary dramatically in effective population size. We find that rates of adaptive evolution are positively correlated with effective population size in these species, with a significant fraction of amino acid substitutions driven by positive selection in the species with the largest effective population sizes but little or no evidence of adaptive evolution in species with smaller effective population sizes. Although other factors likely contribute as well, in sunflowers effective population size appears to be an important determinant of rates of adaptive evolution.
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Cui X, You N, Girke T, Michelmore R, Van Deynze A. Single feature polymorphism detection using recombinant inbred line microarray expression data. Bioinformatics 2010; 26:1983-9. [PMID: 20576626 DOI: 10.1093/bioinformatics/btq316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The Affymetrix GeneChip microarray is currently providing a high-density and economical platform for discovery of genetic polymorphisms. Microarray data for single feature polymorphism (SFP) detection in recombinant inbred lines (RILs) can capitalize on the high level of replication available for each locus in the RIL population. It was suggested that the binding affinities from all of the RILs would form a multimodal distribution for a SFP. This motivated us to estimate the binding affinities from the robust multi-array analysis (RMA) method and formulate the SFP detection problem as a hypothesis testing problem, i.e. testing whether the underlying distribution of the estimated binding affinity (EBA) values of a probe is unimodal or multimodal. RESULTS We developed a bootstrap-based hypothesis testing procedure using the 'dip' statistic. Our simulation studies show that the proposed procedure can reach satisfactory detection power with false discovery rate controlled at a desired level and is robust to the unimodal distribution assumption, which facilitates wide application of the proposed procedure. Our analysis of the real data identified more than four times the SFPs compared to the previous studies, covering 96% of their findings. The constructed genetic map using the SFP markers predicted from our procedure shows over 99% concordance of the genetic orders of these markers with their known physical locations on the genome sequence. AVAILABILITY The R package 'dipSFP' can be downloaded from http://sites.google.com/a/bioinformatics.ucr.edu/xinping-cui/home/software.
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Affiliation(s)
- Xinping Cui
- Department of Statistics, University of California, Riverside, CA, USA.
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33
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Abstract
Species of Orobanchaceae parasitize the roots of nearby host plants to rob them of water and other nutrients. Parasitism can be debilitating to the host plant, and some of the world's most pernicious agricultural pests are parasitic weeds. We demonstrate here that interfering hairpin constructs transformed into host plants can silence expression of the targeted genes in the parasite. Transgenic roots of the hemi-parasitic plant Triphysaria versicolor expressing the GUS reporter gene were allowed to parasitize transgenic lettuce roots expressing a hairpin RNA containing a fragment of the GUS gene (hpGUS). When stained for GUS activity, Triphysaria roots attached to non-transgenic lettuce showed full GUS activity, but those parasitizing transgenic hpGUS lettuce lacked activity in root tissues distal to the haustorium. Transcript quantification indicated a reduction in the steady-state level of GUS mRNA in Triphysaria when they were attached to hpGUS lettuce. These results demonstrate that the GUS silencing signal generated by the host roots was translocated across the haustorium interface and was functional in the parasite. Movement across the haustorium was bi-directional, as demonstrated in double-junction experiments in which non-transgenic Triphysaria concomitantly parasitized two hosts, one transgenic for hpGUS and the other transgenic for a functional GUS gene. Observation of GUS silencing in the second host demonstrated that the silencing trigger could be moved from one host to another using the parasite as a physiological bridge. Silencing of parasite genes by generating siRNAs in the host provides a novel strategy for controlling parasitic weeds.
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Affiliation(s)
- Alexey A Tomilov
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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Kuang H, van Eck HJ, Sicard D, Michelmore R, Nevo E. Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster. Genetics 2008; 178:1547-58. [PMID: 18385115 PMCID: PMC2278093 DOI: 10.1534/genetics.107.080796] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 12/23/2007] [Indexed: 12/15/2022] Open
Abstract
Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern Turkish and Armenian populations were the most diverse populations and might be located in the origin and center of diversity of L. serriola. Screening 709 accessions using the microsatellite MSATE6 that is located in the coding region of most RGC2 homologs detected 366 different haplotypes. Again, the eastern Turkish and Armenian populations had the highest diversities at the RGC2 cluster. The diversities at the RGC2 cluster in different populations were significantly correlated with their genomewide diversities. There was significant variation of copy number of RGC2 homologs in different populations, ranging from 12 to 22 copies per genome. The nucleotide diversities of two conserved lineages (type II) of RGC2 genes (K and L) were not correlated with diversities calculated using the MSATE6 or AFLP data. We hypothesize that the high genomewide diversity and diversity of the RGC2 cluster in eastern Turkish and Armenian populations resulted from high abiotic and biotic stresses in the regions of origin of L. serriola.
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Affiliation(s)
- Hanhui Kuang
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel
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35
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Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R. Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 2006; 173:2227-35. [PMID: 16783026 PMCID: PMC1569713 DOI: 10.1534/genetics.105.049205] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 06/07/2006] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of <5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.
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Affiliation(s)
- Lee Timms
- Biology Department, University of Massachusetts, Boston 02125, USA
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Wroblewski T, Tomczak A, Michelmore R. Optimization of Agrobacterium-mediated transient assays of gene expression in lettuce, tomato and Arabidopsis. Plant Biotechnol J 2005; 3:259-73. [PMID: 17173625 DOI: 10.1111/j.1467-7652.2005.00123.x] [Citation(s) in RCA: 183] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Agrobacterium-mediated transient assays for gene function are increasingly being used as alternatives to genetic complementation and stable transformation. However, such assays are variable and not equally successful in different plant species. We analysed a range of genetic and physiological factors affecting transient expression following agroinfiltration, and developed a protocol for efficient and routine transient assays in several plant species. Lettuce exhibited high levels of transient expression and was at least as easy to work with as Nicotiana benthamiana. Transient expression occurred in the majority of cells within the infiltrated tissue and approached 100% in some regions. High levels of transient expression were obtained in some ecotypes of Arabidopsis; however, Arabidopsis remains recalcitrant to routine, genotype-independent transient assays. Transient expression levels often exceeded those observed in stably transformed plants. The laboratory Agrobacterium tumefaciens strain C58C1 was the best strain for use in plant species that did not elicit a necrotic response to A. tumefaciens. A wild A. tumefaciens strain, 1D1246, was identified that provided high levels of transient expression in solanaceous plants without background necrosis, enabling routine transient assays in these species.
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Affiliation(s)
- Tadeusz Wroblewski
- The Genome Center, University of California, Davis, 1 Shiels Ave., Davis, CA 95616, USA
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Cannon SB, Kozik A, Chan B, Michelmore R, Young ND. DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol 2003; 4:R68. [PMID: 14519203 PMCID: PMC328457 DOI: 10.1186/gb-2003-4-10-r68] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2003] [Revised: 06/19/2003] [Accepted: 08/08/2003] [Indexed: 11/10/2022] Open
Abstract
The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity. The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity.
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Affiliation(s)
- Steven B Cannon
- Plant Biology Department, University of Minnesota, St Paul, MN 55108, USA.
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Abstract
GenomePixelizer is a visualization tool that generates custom images of the physical or genetic positions of specified sets of genes in whole genomes or parts of genomes. Multiple sets of genes can be shown simultaneously with user-defined characteristics displayed. It allows the analysis of duplication events within and between species based on sequence similarities. The program is written in Tcl/Tk and works on any platform that supports the Tcl/Tk toolkit. GenomePixelizer generates HTML ImageMap tags for each gene in the image allowing links to databases. Images can be saved and presented on web pages.
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Affiliation(s)
- A Kozik
- Department of Vegetable Crops, University of California, Davis, CA 95616, USA.
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Gedil MA, Slabaugh MB, Berry S, Johnson R, Michelmore R, Miller J, Gulya T, Knapp SJ. Candidate disease resistance genes in sunflower cloned using conserved nucleotide-binding site motifs: genetic mapping and linkage to the downy mildew resistance gene Pl1. Genome 2001; 44:205-12. [PMID: 11341730 DOI: 10.1139/g00-110] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Disease resistance gene candidates (RGCs) belonging to the nucleotide-binding site (NBS) superfamily have been cloned from numerous crop plants using highly conserved DNA sequence motifs. The aims of this research were to (i) isolate genomic DNA clones for RGCs in cultivated sunflower (Helianthus annuus L.) and (ii) map RGC markers and Pl1, a gene for resistance to downy mildew (Plasmopara halstedii (Farl.) Berl. & de Toni) race 1. Degenerate oligonucleotide primers targeted to conserved NBS DNA sequence motifs were used to amplify RGC fragments from sunflower genomic DNA. PCR products were cloned, sequenced, and assigned to 11 groups. RFLP analyses mapped six RGC loci to three linkage groups. One of the RGCs (Ha-4W2) was linked to Pl1, a downy mildew resistance gene. A cleaved amplified polymorphic sequence (CAPS) marker was developed for Ha-4W2 using gene-specific oligonucleotide primers. Downy mildew susceptible lines (HA89 and HA372) lacked a 276-bp Tsp5091 restriction fragment that was present in downy mildew resistant lines (HA370, 335, 336, 337, 338, and 339). HA370 x HA372 F2 progeny were genotyped for the Ha-4W2 CAPS marker and phenotyped for resistance to downy mildew race 1. The CAPS marker was linked to but did not completely cosegregate with Pl1 on linkage group 8. Ha-4W2 was found to comprise a gene family with at least five members. Although genetic markers for Ha-4W2 have utility for marker-assisted selection, the RGC detected by the CAPS marker has been ruled out as a candidate gene for Pl1. Three of the RGC probes were monomorphic between HA370 and HA372 and still need to be mapped and screened for linkage to disease resistance loci.
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Affiliation(s)
- M A Gedil
- Department of Crop and Soil Science, Oregon State University, Corvallis 97331-3002, USA
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40
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Gedil MA, Slabaugh MB, Berry S, Johnson R, Michelmore R, Miller J, Gulya T, Knapp SJ. Candidate disease resistance genes in sunflower cloned using conserved nucleotide-binding site motifs: Genetic mapping and linkage to the downy mildew resistance gene Pl1. Genome 2001. [DOI: 10.1139/gen-44-2-205] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Abstract
Genomic approaches are beginning to revolutionize our understanding of plant disease resistance. Large-scale sequencing will reveal the detailed organization of resistance-gene clusters and the genetic mechanisms involved in generating new resistance specificities. Global functional analyses will elucidate the complex regulatory networks and the diversity of proteins involved in resistance and susceptibility.
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Affiliation(s)
- R Michelmore
- Department of Vegetable Crops, University of California, Davis 95616, USA.
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Sicard D, Woo SS, Arroyo-Garcia R, Ochoa O, Nguyen D, Korol A, Nevo E, Michelmore R. Molecular diversity at the major cluster of disease resistance genes in cultivated and wild Lactuca spp. Theor Appl Genet 1999; 99:405-418. [PMID: 22665172 DOI: 10.1007/s001220051251] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Diversity was analyzed in wild and cultivated Lactuca germplasm using molecular markers derived from resistance genes of the NBS-LRR type. Three molecular markers, one microsatellite marker and two SCAR markers that amplified LRR-encoding regions, were developed from sequences of resistance gene homologs at the main resistance gene cluster in lettuce. Variation for these markers were assessed in germplasm including accessions of cultivated lettuce, Lactuca sativa L. and three wild Lactuca spp., L. serriola L., L. saligna and L. virosa L. Diversity was also studied within and between natural populations of L. serriola from Israel and California; the former is close to the center of diversity for Lactuca spp. while the latter is an area of more recent colonization. Large numbers of haplotypes were detected indicating the presence of numerous resistance genes in wild species. The diversity in haplotypes provided evidence for gene duplication and unequal crossing-over during the evolution of this cluster of resistance genes. However, there was no evidence for duplications and deletions within the LRR-encoding regions studied. The three markers were highly correlated with resistance phenotypes in L. sativa. They were able to discriminate between accessions that had previously been shown to be resistant to all known isolates of Bremia lactucae. Therefore, these markers will be highly informative for the establishment of core collections and marker-aided selection. A hierarchical analysis of the population structure of L. serriola showed that countries, as well as locations, were significantly differentiated. These differences may reflect local founder effects and/or divergent selection.
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Affiliation(s)
- D Sicard
- Department of Vegetable Crops, University of California, Davis, CA 95616, USA , US
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43
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Shiue YL, Bickel LA, Caetano AR, Millon LV, Clark RS, Eggleston ML, Michelmore R, Bailey E, Guérin G, Godard S, Mickelson JR, Valberg SJ, Murray JD, Bowling AT. A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. Anim Genet 1999; 30:1-9. [PMID: 10050277 DOI: 10.1046/j.1365-2052.1999.00377.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic groups were defined, comprised of two to 26 markers with correlation coefficient (r) values ranging from 0.70 to 1.0. Based on significant correlation values with physically mapped microsatellite (type II) or gene (type I) markers, 22 syntenic groups were assigned to horse chromosomes (1, 2, 3, 4, 6, 9, 10, 11, 12, 13, 15, 18, 19, 20, 21, 22, 23, 24, 26, 30, X and Y). The other 11 syntenic groups were provisionally assigned to the remaining chromosomes based on information provided by heterologous species painting probes and work in progress with type I markers.
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Affiliation(s)
- Y L Shiue
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis 95616-8744, USA
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Hill M, Witsenboer H, Zabeau M, Vos P, Kesseli R, Michelmore R. PCR-based fingerprinting using AFLPs as a tool for studying genetic relationships in Lactuca spp. Theor Appl Genet 1996; 93:1202-10. [PMID: 24162531 DOI: 10.1007/bf00223451] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/1995] [Accepted: 02/23/1996] [Indexed: 05/14/2023]
Abstract
AFLP markers were evaluated for determining the phylogenetic relationships Lactuca spp. Genetic distances based on AFLP data were estimated for 44 morphologically diverse lines of cultivated L. sativa and 13 accessions of the wild species L. serriola, L. saligna, L. virosa, L. perennis, and L. indica. The same genotypes were analyzed as in a previous study that had utilized RFLP markers. The phenetic tree based on AFLP data was consistent with known taxonomic relationships and similar to a tree developed with RFLP data. The genetic distance matrices derived from AFLP and RFLP data were compared using least squares regression analysis and, for the cultivar data, by principal component analysis. There was also a positive linear relationship between distance estimates based on AFLP data and kinship coefficients calculated from pedigree data. AFLPs represent reliable PCR-based markers for studies of genetic relationships at a variety of taxonomic levels.
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Affiliation(s)
- M Hill
- Department of Biology, University of Massachusetts, 02125-3393, Boston, MA, USA
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Yang CH, Carroll B, Scofield S, Jones J, Michelmore R. Transactivation of Ds elements in plants of lettuce (Lactuca sativa). Mol Gen Genet 1993; 241:389-98. [PMID: 8246892 DOI: 10.1007/bf00284692] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The maize transposable element, Activator (Ac), is being used to develop a transposon mutagenesis system in lettuce, Lactuca sativa. In this paper, we describe somatic and germinal transactivation of Ds by chimeric transposase genes in whole plants. Constructs containing either the Ds element or the Ac transposase open reading frame (ORF) were introduced into lettue. The Ds element was located between either the 35S or the Nos promoter and a chimeric spectinomycin resistance gene (which included a transit peptide), preventing expression of spectinomycin resistance. The genomic coding region of the Ac transposase was expressed from the 35S promoter. Crosses were made between 104 independent R1 plants containing Ds and three independent R1 plants expressing transposase. The excision of Ds in F1 progenies was monitored using a phenotypic assay on spectinomycin-containing medium. Green sectors in one-third of the F1 families indicated transactivation of Ds by the transposase at different developmental stages and at different frequencies in lettuce plants. Excision was confirmed using PCR and by Southern analysis. The lack of green sectors in the majority of F1 families suggest that the majority of T-DNA insertion sites are not conducive to excision. In subsequent experiments, the F1 plants containing both Ds and the transposase were grown to maturity and the F2 seeds screened on medium containing spectinomycin. Somatic excision was again observed in several F2 progeny; however, evidence for germinal excision was observed in only one F2 family.
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Affiliation(s)
- C H Yang
- Department of Vegetable Crops, University of California, Davis 95616
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Paran I, Kesseli R, Michelmore R. Identification of restriction fragment length polymorphism and random amplified polymorphic DNA markers linked to downy mildew resistance genes in lettuce, using near-isogenic lines. Genome 1991; 34:1021-7. [PMID: 1685721 DOI: 10.1139/g91-157] [Citation(s) in RCA: 130] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Near-isogenic lines were used to identify restriction fragment length polymorphism (RFLP) and random amplified polymorphic DNA (RAPD) markers linked to genes for resistance to downy mildew (Dm) in lettuce. Two pairs of near-isogenic lines that differed for Dm1 plus Dm3 and one pair of near-isogenic lines that differed for Dm11 were used as sources of DNA. Over 500 cDNAs and 212 arbitrary 10-mer oligonucleotide primers were screened for their ability to detect polymorphism between the near-isogenic lines. Four RFLP markers and four RAPD markers were identified as linked to the Dm1 and Dm3 region. Dm1 and Dm3 are members of a cluster of seven Dm genes. Marker CL922 was absolutely linked to Dm15 and Dm16, which are part of this cluster. Six RAPD markers were identified as linked to the Dm11 region. The use of RAPD markers allowed us to increase the density of markers in the two Dm regions in a short time. These regions were previously only sparsely populated with RFLP markers. The rapid screening and identification of tightly linked markers to the target genes demonstrated the potential of RAPD markers for saturating genetic maps.
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Affiliation(s)
- I Paran
- Department of Vegetable Crops, University of California, Davis 95616
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Abstract
We have examined 67 accessions of Lactuca sativa L. and five related species for variation at restriction fragment length polymorphism loci. Fifty-five clones were used to probe genomic DNA digested separately with three restriction endonucleases; this defined 143 loci. Variation in L. sativa was sampled in detail. Lactuca sativa is closely related to L. serriola but not to any of the other species in this survey: L. saligna, L. virosa, L. perennis, and L. indica. However, Lactuca sativa is not a direct extraction from the sampled populations of L. serriola; other L. serriola populations or some other unknown entities were involved in the evolution of cultivated lettuce. Numerous genetic differences characterized each cultivated type, suggesting a polyphyletic origin for L. sativa.Key words: Lactuca sativa, lettuce, genetic variation, phylogeny, restriction fragment length polymorphism.
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