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Barro-Trastoy D, Köhler C. Helitrons: genomic parasites that generate developmental novelties. Trends Genet 2024; 40:437-448. [PMID: 38429198 DOI: 10.1016/j.tig.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
Abstract
Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.
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Affiliation(s)
- Daniela Barro-Trastoy
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Claudia Köhler
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden.
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2
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Hu J, Liu C, Du Z, Guo F, Song D, Wang N, Wei Z, Jiang J, Cao Z, Shi C, Zhang S, Zhu C, Chen P, Larkin RM, Lin Z, Xu Q, Ye J, Deng X, Bosch M, Franklin‐Tong VE, Chai L. Transposable elements cause the loss of self-incompatibility in citrus. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1113-1131. [PMID: 38038155 PMCID: PMC11022811 DOI: 10.1111/pbi.14250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/25/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
Self-incompatibility (SI) is a widespread prezygotic mechanism for flowering plants to avoid inbreeding depression and promote genetic diversity. Citrus has an S-RNase-based SI system, which was frequently lost during evolution. We previously identified a single nucleotide mutation in Sm-RNase, which is responsible for the loss of SI in mandarin and its hybrids. However, little is known about other mechanisms responsible for conversion of SI to self-compatibility (SC) and we identify a completely different mechanism widely utilized by citrus. Here, we found a 786-bp miniature inverted-repeat transposable element (MITE) insertion in the promoter region of the FhiS2-RNase in Fortunella hindsii Swingle (a model plant for citrus gene function), which does not contain the Sm-RNase allele but are still SC. We demonstrate that this MITE plays a pivotal role in the loss of SI in citrus, providing evidence that this MITE insertion prevents expression of the S-RNase; moreover, transgenic experiments show that deletion of this 786-bp MITE insertion recovers the expression of FhiS2-RNase and restores SI. This study identifies the first evidence for a role for MITEs at the S-locus affecting the SI phenotype. A family-wide survey of the S-locus revealed that MITE insertions occur frequently adjacent to S-RNase alleles in different citrus genera, but only certain MITEs appear to be responsible for the loss of SI. Our study provides evidence that insertion of MITEs into a promoter region can alter a breeding strategy and suggests that this phenomenon may be broadly responsible for SC in species with the S-RNase system.
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Affiliation(s)
- Jianbing Hu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Chenchen Liu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zezhen Du
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Furong Guo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Dan Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Nan Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zhuangmin Wei
- Guangxi Subtropical Crops Research InstituteNanningP. R. China
| | - Jingdong Jiang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Zonghong Cao
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chunmei Shi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Siqi Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Chenqiao Zhu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Peng Chen
- Horticultural Institute, Hunan Academy of Agricultural SciencesChangshaChina
| | - Robert M. Larkin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Zongcheng Lin
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Qiang Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Junli Ye
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
| | - Xiuxin Deng
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Lijun Chai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanP. R. China
- Hubei Hongshan LaboratoryWuhanP. R. China
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Goeckeritz CZ, Rhoades KE, Childs KL, Iezzoni AF, VanBuren R, Hollender CA. Genome of tetraploid sour cherry (Prunus cerasus L.) 'Montmorency' identifies three distinct ancestral Prunus genomes. HORTICULTURE RESEARCH 2023; 10:uhad097. [PMID: 37426879 PMCID: PMC10323630 DOI: 10.1093/hr/uhad097] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/04/2023] [Indexed: 07/11/2023]
Abstract
Sour cherry (Prunus cerasus L.) is a valuable fruit crop in the Rosaceae family and a hybrid between progenitors closely related to extant Prunus fruticosa (ground cherry) and Prunus avium (sweet cherry). Here we report a chromosome-scale genome assembly for sour cherry cultivar Montmorency, the predominant cultivar grown in the USA. We also generated a draft assembly of P. fruticosa to use alongside a published P. avium sequence for syntelog-based subgenome assignments for 'Montmorency' and provide compelling evidence P. fruticosa is also an allotetraploid. Using hierarchal k-mer clustering and phylogenomics, we show 'Montmorency' is trigenomic, containing two distinct subgenomes inherited from a P. fruticosa-like ancestor (A and A') and two copies of the same subgenome inherited from a P. avium-like ancestor (BB). The genome composition of 'Montmorency' is AA'BB and little-to-no recombination has occurred between progenitor subgenomes (A/A' and B). In Prunus, two known classes of genes are important to breeding strategies: the self-incompatibility loci (S-alleles), which determine compatible crosses, successful fertilization, and fruit set, and the Dormancy Associated MADS-box genes (DAMs), which strongly affect dormancy transitions and flowering time. The S-alleles and DAMs in 'Montmorency' and P. fruticosa were manually annotated and support subgenome assignments. Lastly, the hybridization event 'Montmorency' is descended from was estimated to have occurred less than 1.61 million years ago, making sour cherry a relatively recent allotetraploid. The 'Montmorency' genome highlights the evolutionary complexity of the genus Prunus and will inform future breeding strategies for sour cherry, comparative genomics in the Rosaceae, and questions regarding neopolyploidy.
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Affiliation(s)
- Charity Z Goeckeritz
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Kathleen E Rhoades
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA
| | - Amy F Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
| | - Courtney A Hollender
- Department of Horticulture, Michigan State University, 1066 Bogue St, East Lansing, MI 48824, USA
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Li C, Cong C, Liu F, Yu Q, Zhan Y, Zhu L, Li Y. Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize. Int J Mol Sci 2023; 24:ijms24076574. [PMID: 37047545 PMCID: PMC10095026 DOI: 10.3390/ijms24076574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023] Open
Abstract
Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of Helitrons transposition in plants. Here, by constructing several artificial defective Helitron (dHel) reporter systems, we aim to identify the autonomous Helitrons (aHel) in maize genetically and to demonstrate the transposition and repair mechanisms of Helitrons upon the dHel-GFP excision in maize. When crossing with various inbred lines, several transgenic lines produced progeny of segregated, purple-blotched kernels, resulting from a leaky expression of the C1 gene driven by the dHel-interrupted promoter. Transcription analysis indicated that the insertion of different dHels into the C1 promoter or exon would lead to multiple distinct mRNA transcripts corresponding to transgenes in the host genome. Simple excision products and circular intermediates of dHel-GFP transposition have been detected from the leaf tissue of the seedlings in F1 hybrids of transgenic lines with corresponding c1 tester, although they failed to be detected in all primary transgenic lines. These results revealed the transposition and repair mechanism of Helitrons in maize. It is strongly suggested that this reporter system can detect the genetic activity of autonomic Helitron at the molecular level. Sequence features of dHel itself, together with the flanking regions, impact the excision activity of dHel and the regulation of the dHel on the transcription level of the host gene.
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Affiliation(s)
- Chuxi Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunsheng Cong
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fangyuan Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qian Yu
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Yuan Zhan
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yubin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
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Xu Y, Zhang Q, Zhang X, Wang J, Ayup M, Yang B, Guo C, Gong P, Dong W. The proteome reveals the involvement of serine/threonine kinase in the recognition of self- incompatibility in almond. J Proteomics 2022; 256:104505. [PMID: 35123051 DOI: 10.1016/j.jprot.2022.104505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/15/2022] [Accepted: 01/25/2022] [Indexed: 10/19/2022]
Abstract
The self-incompatibility recognition mechanism determines whether the gametophyte is successfully fertilized between pollen tube SCF (SKP1-CUL1-F-box-RBX1) protein and pistil S-RNase protein during fertilization is unclear. In this study, the pistils of two almond cultivars 'Wanfeng' and 'Nonpareil' were used as the experimental materials after self- and nonself/cross-pollination, and pistils from the stamen-removed flowers were used as controls. We used fluorescence microscopy to observe the development of pollen tubes after pollination and 4D-LFQ to detect the protein expression profiles of 'Wanfeng' and 'Nonpareil' pistils and in controls. The results showed that it took 24-36 h for the development of the pollen tube to 1/3 of the pistil, and a total of 7684 differentially accumulated proteins (DAPs) were identified in the pistil after pollinating for 36 h, of which 7022 were quantifiable. Bioinformatics analysis based on the function of DAPs, identified RNA polymerases (4 DAPs), autophagy (3 DAPs), oxidative phosphorylation (3 DAPs), and homologous recombination (2 DAPs) pathways associated with the self-incompatibility process. These results were confirmed by parallel reaction monitoring (PRM), protein interaction and bioinformatics analysis. Taken together, these results provide the involvement of serine/threonine kinase protein in the reaction of pollen tube recognition the nonself- and the self-S-RNase protein. SIGNIFICANCE: Gametophytic self-incompatibility (GSI) is controlled by the highly polymorphic S locus or S haplotype, with two linked self-incompatibility genes, one encoding the S-RNase protein of the pistil S-determinant and the other encoding the F-box/SLF/SFB (S haplotype-specific F-box protein) protein of the pollen S-determinant. The recognition mechanism between pollen tube SCF protein and pistil S-RNase protein is divided into nonself- and self-recognition hypothesis mechanisms. At present, two hypothetical mechanisms cannot explain the recognition between pollen and pistil well, so the mechanism of gametophytic self-incompatibility recognition is still not fully revealed. In this experiment, we investigated the molecular mechanism of pollen-pistil recognition in self-incompatibility using self- and nonself-pollinated pistils of almond cultivars 'Wanfeng' and 'Nonpareil'. Based on our results, we proposed a potential involvement of the MARK2 (serine/threonine kinase) protein in the reaction of pollen tube recognition of the nonself- and the self-S-RNase protein. It provides a new way to reveal how almond pollen tubes recognize the self and nonself S-RNase enzyme protein.
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Affiliation(s)
- Yeting Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China; Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Qiuping Zhang
- Liaoning Institute of Pomology, Xiongyue 115009, Liaoning, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China
| | - Jian Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China
| | - Mubarek Ayup
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Bo Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Chunmiao Guo
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China
| | - Peng Gong
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi 830091, China.
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang 11086, Liaoning, China.
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Simple Sequence Repeat and S-Locus Genotyping to Assist the Genetic Characterization and Breeding of Polyploid Prunus Species, P. spinosa and P. domestica subsp. insititia. Biochem Genet 2021; 59:1065-1087. [PMID: 34132957 PMCID: PMC8249305 DOI: 10.1007/s10528-021-10090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/28/2021] [Indexed: 11/18/2022]
Abstract
Polyploid Prunus spinosa (2n = 4 ×) and P. domestica subsp. insititia (2n = 6 ×) represent enormous genetic potential in Central Europe, which can be exploited in breeding programs. In Hungary, 16 cultivar candidates and a recognized cultivar ‘Zempléni’ were selected from wild-growing populations including ten P. spinosa, four P. domestica subsp. insititia and three P. spinosa × P. domestica hybrids (2n = 5 ×) were also created. Genotyping in eleven simple sequence repeat (SSR) loci and the multiallelic S-locus was used to characterize genetic variability and achieve a reliable identification of tested accessions. Nine SSR loci proved to be polymorphic and eight of those were highly informative (PIC values ˃ 0.7). A total of 129 SSR alleles were identified, which means 14.3 average allele number per locus and all accessions but two clones could be discriminated based on unique SSR fingerprints. A total of 23 S-RNase alleles were identified and the complete and partial S-genotype was determined for 10 and 7 accessions, respectively. The DNA sequence was determined for a total of 17 fragments representing 11 S-RNase alleles. ‘Zempléni’ was confirmed to be self-compatible carrying at least one non-functional S-RNase allele (SJ). Our results indicate that the S-allele pools of wild-growing P. spinosa and P. domestica subsp. insititia are overlapping in Hungary. Phylogenetic and principal component analyses confirmed the high level of diversity and genetic differentiation present within the analysed accessions and indicated putative ancestor–descendant relationships. Our data confirm that S-locus genotyping is suitable for diversity studies in polyploid Prunus species but non-related accessions sharing common S-alleles may distort phylogenetic inferences.
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Vieira J, Pimenta J, Gomes A, Laia J, Rocha S, Heitzler P, Vieira CP. The identification of the Rosa S-locus and implications on the evolution of the Rosaceae gametophytic self-incompatibility systems. Sci Rep 2021; 11:3710. [PMID: 33580108 PMCID: PMC7881130 DOI: 10.1038/s41598-021-83243-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 01/19/2021] [Indexed: 12/19/2022] Open
Abstract
In Rosaceae species, two gametophytic self-incompatibility (GSI) mechanisms are described, the Prunus self-recognition system and the Maleae (Malus/Pyrus/Sorbus) non-self- recognition system. In both systems the pistil component is a S-RNase gene, but from two distinct phylogenetic lineages. The pollen component, always a F-box gene(s), in the case of Prunus is a single gene, and in Maleae there are multiple genes. Previously, the Rosa S-locus was mapped on chromosome 3, and three putative S-RNase genes were identified in the R. chinensis ‘Old Blush’ genome. Here, we show that these genes do not belong to the S-locus region. Using R. chinensis and R. multiflora genomes and a phylogenetic approach, we identified the S-RNase gene, that belongs to the Prunus S-lineage. Expression patterns support this gene as being the S-pistil. This gene is here also identified in R. moschata, R. arvensis, and R. minutifolia low coverage genomes, allowing the identification of positively selected amino acid sites, and thus, further supporting this gene as the S-RNase. Furthermore, genotype–phenotype association experiments also support this gene as the S-RNase. For the S-pollen GSI component we find evidence for multiple F-box genes, that show the expected expression pattern, and evidence for diversifying selection at the F-box genes within an S-haplotype. Thus, Rosa has a non-self-recognition system, like in Maleae species, despite the S-pistil gene belonging to the Prunus S-RNase lineage. These findings are discussed in the context of the Rosaceae GSI evolution. Knowledge on the Rosa S-locus has practical implications since genes controlling floral and other ornamental traits are in linkage disequilibrium with the S-locus.
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Affiliation(s)
- J Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - J Pimenta
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - A Gomes
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - J Laia
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - S Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - P Heitzler
- Institut de Biologie Moléculaire Des Plantes, CNRS, Université de Strasbourg, UPR 2357, 67000, Strasbourg, France
| | - C P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal. .,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
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8
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Vieira J, Rocha S, Vázquez N, López-Fernández H, Fdez-Riverola F, Reboiro-Jato M, Vieira CP. Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model. FRONTIERS IN PLANT SCIENCE 2019; 10:879. [PMID: 31379893 PMCID: PMC6649718 DOI: 10.3389/fpls.2019.00879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 06/10/2023]
Abstract
Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S-locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insight on how this recognition mechanism works. In this system, each of the encoded S-pollen proteins (called SLFs in Solanaceae and Plantaginaceae /SFBBs in Maleae) recognizes and interacts with a sub-set of non-self S-pistil proteins, called S-RNases, mediating their ubiquitination and degradation. In Petunia there are 17 SLF genes per S-haplotype, making impossible to determine experimentally each SLF specificity. Moreover, domain -swapping experiments are unlikely to be performed in large scale to determine S-pollen and S-pistil specificities. Phylogenetic analyses of the Petunia SLFs and those from two Solanum genomes, suggest that diversification of SLFs predate the two genera separation. Here we first identify putative SLF genes from nine Solanum and 10 Nicotiana genomes to determine how many gene lineages are present in the three genera, and the rate of origin of new SLF gene lineages. The use of multiple genomes per genera precludes the effect of incompleteness of the genome at the S-locus. The similar number of gene lineages in the three genera implies a comparable effective population size for these species, and number of specificities. The rate of origin of new specificities is one per 10 million years. Moreover, here we determine the amino acids positions under positive selection, those involved in SLF specificity recognition, using 10 Petunia S-haplotypes with more than 11 SLF genes. These 16 amino acid positions account for the differences of self-incompatible (SI) behavior described in the literature. When SLF and S-RNase proteins are divided according to the SI behavior, and the positively selected amino acids classified according to hydrophobicity, charge, polarity and size, we identified fixed differences between SI groups. According to the in silico 3D structure of the two proteins these amino acid positions interact. Therefore, this methodology can be used to infer SLF/S-RNase specificity recognition.
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Affiliation(s)
- Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Sara Rocha
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Noé Vázquez
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
| | - Hugo López-Fernández
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Miguel Reboiro-Jato
- Escuela Superior de Ingeniería Informática (ESEI), Edificio Politécnico, Universidad de Vigo, Ourense, Spain
- Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia), Vigo, Spain
- SING Research Group, Instituto de Investigación Sanitaria Galicia Sur (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Cristina P. Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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9
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Han G, Zhang N, Xu J, Jiang H, Ji C, Zhang Z, Song Q, Stanley D, Fang J, Wang J. Characterization of a novel Helitron family in insect genomes: insights into classification, evolution and horizontal transfer. Mob DNA 2019; 10:25. [PMID: 31164927 PMCID: PMC6544945 DOI: 10.1186/s13100-019-0165-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/30/2019] [Indexed: 01/09/2023] Open
Abstract
Background Helitrons play an important role in shaping eukaryotic genomes due to their ability to transfer horizontally between distantly related species and capture gene fragments during the transposition. However, the mechanisms of horizontal transfer (HT) and the process of gene fragment capturing of Helitrons still remain to be further clarified. Results Here, we characterized a novel Helitron family discontinuously distributed in 27 out of 256 insect genomes. The most prominent characteristic of Hel1 family is its high sequence similarity among species of different insect orders. Related elements were also identified in two spiders, representing the first report of spider Helitrons. All these elements were classified into 2 families, 9 subfamilies and 35 exemplars based on our new classification criteria. Autonomous partners of Helitron were reconstructed in the genomes of three insects and one spider. Integration pattern analysis showed that majority of Hel1A elements in Papilio xuthus and Pieris rapae inserted into introns. Consistent with filler DNA model, stepwise sequence acquisition was observed in Sfru_Hel1Aa, Sfru_Hel1Ab and Sfru_Hel1Ac in Spodoptera frugiperda. Remarkably, the evidence that Prap_Hel1Aa in a Lepdidoptera insect, Pieris rapae, was derived from Cves_Hel1Aa in a parasitoid wasp, Cotesia vestalis, suggested the role of nonregular host-parasite interactions in HT of Helitrons. Conclusions We proposed a modified classification criteria of Helitrons based on the important role of the 5′-end of Helitrons in transposition, and provided evidence for stepwise sequence acquisition and recurrent HT of a novel Helitron family. Our findings of the nonregular host-parasite interactions may be more conducive to the HT of transposons. Electronic supplementary material The online version of this article (10.1186/s13100-019-0165-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guangjie Han
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China.,Jiangsu Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Nan Zhang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Jian Xu
- Jiangsu Lixiahe Institute of Agricultural Sciences, Yangzhou, 225007 China
| | - Heng Jiang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Caihong Ji
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
| | - Ze Zhang
- 3School of Life Sciences, Chongqing University, Chongqing, 400044 China
| | - Qisheng Song
- 4Division of Plant Sciences, University of Missouri, Columbia, MO USA
| | - David Stanley
- 5USDA/Agricultural Research Service, Biological Control of Insects Research Laboratory, Columbia, MO USA
| | - Jichao Fang
- 6Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Jianjun Wang
- 1College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
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10
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Pontier D, Picart C, El Baidouri M, Roudier F, Xu T, Lahmy S, Llauro C, Azevedo J, Laudié M, Attina A, Hirtz C, Carpentier MC, Shen L, Lagrange T. The m 6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci Alliance 2019; 2:2/3/e201900393. [PMID: 31142640 PMCID: PMC6545605 DOI: 10.26508/lsa.201900393] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/24/2022] Open
Abstract
This study reveals that an m6A-assisted polyadenylation pathway comprising conserved m6A writer proteins and a plant-specific m6A reader contributes to transcriptome integrity in Arabidopsis thaliana by restricting RNA chimera formation at rearranged loci. Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.
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Affiliation(s)
- Dominique Pontier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Claire Picart
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Moaine El Baidouri
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Lyon, France
| | - Tao Xu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sylvie Lahmy
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Christel Llauro
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Jacinthe Azevedo
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Michèle Laudié
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Aurore Attina
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Christophe Hirtz
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Marie-Christine Carpentier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore
| | - Thierry Lagrange
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France .,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
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11
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Fujii S, Kubo KI, Takayama S. Non-self- and self-recognition models in plant self-incompatibility. NATURE PLANTS 2016; 2:16130. [PMID: 27595657 DOI: 10.1038/nplants.2016.130] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 07/22/2016] [Indexed: 05/25/2023]
Abstract
The mechanisms by which flowering plants choose their mating partners have interested researchers for a long time. Recent findings on the molecular mechanisms of non-self-recognition in some plant species have provided new insights into self-incompatibility (SI), the trait used by a wide range of plant species to avoid self-fertilization and promote outcrossing. In this Review, we compare the known SI systems, which can be largely classified into non-self- or self-recognition systems with respect to their molecular mechanisms, their evolutionary histories and their modes of evolution. We review previous controversies on haplotype evolution in the gametophytic SI system of Solanaceae species in light of a recently elucidated non-self-recognition model. In non-self-recognition SI systems, the transition from self-compatibility (SC) to SI may be more common than previously thought. Reversible transition between SI and SC in plants may have contributed to their adaptation to diverse and fluctuating environments.
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Affiliation(s)
- Sota Fujii
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Ken-Ichi Kubo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Seiji Takayama
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
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12
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Abstract
Helitrons, the eukaryotic rolling-circle transposable elements, are widespread but most prevalent among plant and animal genomes. Recent studies have identified three additional coding and structural variants of Helitrons called Helentrons, Proto-Helentron, and Helitron2. Helitrons and Helentrons make up a substantial fraction of many genomes where nonautonomous elements frequently outnumber the putative autonomous partner. This includes the previously ambiguously classified DINE-1-like repeats, which are highly abundant in Drosophila and many other animal genomes. The purpose of this review is to summarize what we have learned about Helitrons in the decade since their discovery. First, we describe the history of autonomous Helitrons, and their variants. Second, we explain the common coding features and difference in structure of canonical Helitrons versus the endonuclease-encoding Helentrons. Third, we review how Helitrons and Helentrons are classified and discuss why the system used for other transposable element families is not applicable. We also touch upon how genome-wide identification of candidate Helitrons is carried out and how to validate candidate Helitrons. We then shift our focus to a model of transposition and the report of an excision event. We discuss the different proposed models for the mechanism of gene capture. Finally, we will talk about where Helitrons are found, including discussions of vertical versus horizontal transfer, the propensity of Helitrons and Helentrons to capture and shuffle genes and how they impact the genome. We will end the review with a summary of open questions concerning the biology of this intriguing group of transposable elements.
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13
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Zhao D, Ferguson AA, Jiang N. What makes up plant genomes: The vanishing line between transposable elements and genes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1859:366-80. [PMID: 26709091 DOI: 10.1016/j.bbagrm.2015.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/09/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023]
Abstract
The ultimate source of evolution is mutation. As the largest component in plant genomes, transposable elements (TEs) create numerous types of mutations that cannot be mimicked by other genetic mechanisms. When TEs insert into genomic sequences, they influence the expression of nearby genes as well as genes unlinked to the insertion. TEs can duplicate, mobilize, and recombine normal genes or gene fragments, with the potential to generate new genes or modify the structure of existing genes. TEs also donate their transposase coding regions for cellular functions in a process called TE domestication. Despite the host defense against TE activity, a subset of TEs survived and thrived through discreet selection of transposition activity, target site, element size, and the internal sequence. Finally, TEs have established strategies to reduce the efficacy of host defense system by increasing the cost of silencing TEs. This review discusses the recent progress in the area of plant TEs with a focus on the interaction between TEs and genes.
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Affiliation(s)
- Dongyan Zhao
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ann A Ferguson
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824, USA.
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14
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Hanada T, Watari A, Kibe T, Yamane H, Wünsch A, Gradziel TM, Sasabe Y, Yaegaki H, Yamaguchi M, Tao R. Two Novel Self-compatible S Haplotypes in Peach (Prunus persica). ACTA ACUST UNITED AC 2014. [DOI: 10.2503/jjshs1.ch-099] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Peace C, Bassil N, Main D, Ficklin S, Rosyara UR, Stegmeir T, Sebolt A, Gilmore B, Lawley C, Mockler TC, Bryant DW, Wilhelm L, Iezzoni A. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry. PLoS One 2012; 7:e48305. [PMID: 23284615 PMCID: PMC3527432 DOI: 10.1371/journal.pone.0048305] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/17/2012] [Indexed: 11/19/2022] Open
Abstract
High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb) of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome) and P. fruticosa (fruticosa subgenome). Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269) and sour (n = 330) cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery, genome structure investigation, and genetic diversity assessment in this diploid-tetraploid crop group.
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Affiliation(s)
- Cameron Peace
- Department of Horticulture, Washington State University, Pullman, Washington, United States of America.
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17
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Matsumoto D, Yamane H, Abe K, Tao R. Identification of a Skp1-like protein interacting with SFB, the pollen S determinant of the gametophytic self-incompatibility in Prunus. PLANT PHYSIOLOGY 2012; 159:1252-62. [PMID: 22548785 PMCID: PMC3387707 DOI: 10.1104/pp.112.197343] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 04/26/2012] [Indexed: 05/23/2023]
Abstract
Many species in Rosaceae, Solanaceae, and Plantaginaceae exhibit S-RNase-based self-incompatibility (SI). In this system, the pistil and pollen specificities are determined by S-RNase and the S locus F-box protein, respectively. The pollen S determinant F-box protein in Prunus (Rosaceae) is referred to by two different terms, SFB (for S-haplotype-specific F-box protein) and SLF (for S locus F box), whereas it is called SLF in Solanaceae and Plantaginaceae. Prunus SFB is thought to be a molecule indispensable for its cognate S-RNase to exert cytotoxicity and to arrest pollen tube growth in incompatible reactions. Although recent studies have demonstrated the molecular function of SCF(SLF) in the SI reaction of Solanaceae and Plantaginaceae, how SFB participates in the Prunus SI mechanism remains to be elucidated. Here we report the identification of sweet cherry (Prunus avium) SFB (PavSFB)-interacting Skp1-like1 (PavSSK1) using a yeast (Saccharomyces cerevisiae) two-hybrid screening against the pollen cDNA library. Phylogenetic analysis showed that PavSSK1 belongs to the same clade as Antirrhinum hispanicum SLF-interacting Skp1-like1 and Petunia hybrida SLF-interacting Skp1-like1 (PhSSK1). In yeast, PavSSK1 interacted not only with PavSFBs from different S haplotypes and Cullin1-likes (PavCul1s), but also with S-locus F-box-likes. A pull-down assay confirmed the interactions between PavSSK1 and PavSFB and between PavSSK1 and PavCul1s. These results collectively indicate that PavSSK1 could be a functional component of the SCF complex and that PavSFB may function as a component of the SCF complex. We discuss the molecular function of PavSFB in self-/nonself-recognition in the gametophytic SI of Prunus.
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