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Miniature inverted-repeat transposable elements (MITEs), derived insertional polymorphism as a tool of marker systems for molecular plant breeding. Mol Biol Rep 2020; 47:3155-3167. [PMID: 32162128 DOI: 10.1007/s11033-020-05365-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/29/2020] [Indexed: 12/20/2022]
Abstract
Plant molecular breeding is expected to give significant gains in cultivar development through development and utilization of suitable molecular marker systems for genetic diversity analysis, rapid DNA fingerprinting, identification of true hybrids, trait mapping and marker-assisted selection. Transposable elements (TEs) are the most abundant component in a genome and being used as genetic markers in the plant molecular breeding. Here, we review on the high copious transposable element belonging to class-II DNA TEs called "miniature inverted-repeat transposable elements" (MITEs). MITEs are ubiquitous, short and non-autonomous DNA transposable elements which have a tendency to insert into genes and genic regions have paved a way for the development of functional DNA marker systems in plant genomes. This review summarises the characteristics of MITEs, principles and methodologies for development of MITEs based DNA markers, bioinformatics tools and resources for plant MITE discovery and their utilization in crop improvement.
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52
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Monshi FI, Khan N, Kimura K, Suzuki S, Yamamoto Y, Katsube-Tanaka T. Structure and diversity of 13S globulin zero-repeat subunit, the trypsin-resistant storage protein of common buckwheat ( Fagopyrum esculentum M.) seeds. BREEDING SCIENCE 2020; 70:118-127. [PMID: 32351311 PMCID: PMC7180142 DOI: 10.1270/jsbbs.19017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 08/25/2019] [Indexed: 06/11/2023]
Abstract
The zero-repeat subunit of 13S globulin, which lacks tandem repeat inserts, is trypsin-resistant and suggested to show higher allergenicity than the other subunits in common buckwheat (Fagopyrum esculentum Moench). To evaluate allelic variations and find novel alleles, the diversity of the zero-repeat genes was examined for two Japanese elite cultivars and 15 Pakistani landraces. The results demonstrated that two new alleles GlbNA1 and GlbNC1, plus three additional new alleles GlbNA2, GlbNA3, and GlbND, were identified besides the already-known GlbNA, GlbNB, and GlbNC alleles. In the Pakistani landraces, GlbNA was the most dominant allele (0.60-0.88 of allele frequency) in all except one landrace, where GlbNB was the most dominant allele (0.50 of allele frequency). Similar to GlbNC, the alleles GlbNA2 and GlbNA3 had extra ~200 bp MITE-like sequences around the stop codon. Secondary structure predictions of a sense strand demonstrated that the extra ~200 bp sequences of GlbNC, GlbNA2, and GlbNA3 can form rigid hairpin structures with free energies of -78.95, -67.06, and -29.90 kcal/mol, respectively. These structures may affect proper transcription and/or translation. In the GlbNC homozygous line, no transcript of a zero-repeat gene was detected, suggesting the material would be useful for developing hypoallergenic buckwheat.
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Affiliation(s)
- Fakhrul Islam Monshi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
- Faculty of Agriculture, Sylhet Agricultural University, Sylhet-3100, Bangladesh
| | - Nadar Khan
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Kohtaro Kimura
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Seita Suzuki
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Yuka Yamamoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
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53
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Espinas NA, Tu LN, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H. Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome. PLoS Genet 2020; 16:e1008637. [PMID: 32187179 PMCID: PMC7145194 DOI: 10.1371/journal.pgen.1008637] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 04/09/2020] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Intronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.
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Affiliation(s)
- Nino A. Espinas
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama city, Kanagawa, Japan
| | - Le Ngoc Tu
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Yasuka Shimajiri
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- EditForce, Fukuoka, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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54
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Bhat RS, Shirasawa K, Monden Y, Yamashita H, Tahara M. Developing Transposable Element Marker System for Molecular Breeding. Methods Mol Biol 2020; 2107:233-251. [PMID: 31893450 DOI: 10.1007/978-1-0716-0235-5_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Transposable element (TE) marker system was developed considering the useful properties of the transposable elements such as their large number in the animal and plant genomes, high rate of insertion polymorphism, and ease of detection. Various methods have been employed for developing a large number of TE markers in several crop plants for genomics studies. Here we describe some of these methods including the recent whole genome search. We also review the application of TE markers in molecular breeding.
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Affiliation(s)
- R S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, Karnataka, India.
| | - K Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Y Monden
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - H Yamashita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - M Tahara
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
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Mohan A, Dhaliwal AK, Nagarajan R, Gill KS. Molecular Characterization of Auxin Efflux Carrier- ABCB1 in hexaploid wheat. Sci Rep 2019; 9:17327. [PMID: 31757978 PMCID: PMC6874703 DOI: 10.1038/s41598-019-51482-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/29/2019] [Indexed: 11/09/2022] Open
Abstract
Auxin is an important phytohormone that regulates response, differentiation, and development of plant cell, tissue, and organs. Along with its local production, long-distance transport coordinated by the efflux/influx membrane transporters is instrumental in plant development and architecture. In the present study, we cloned and characterized a wheat (Triticum aestivum) auxin efflux carrier ABCB1. The TaABCB1 was physically localized to the proximal 15% of the short arm of wheat homoeologous group 7 chromosomes. Size of the Chinese spring (CS) homoeologs genomic copies ranged from 5.3–6.2 kb with the 7A copy being the largest due to novel insertions in its third intron. The three homoeologous copies share 95–97% sequence similarity at the nucleotide, 98–99% amino acid, and overall Q-score of 0.98 at 3-D structure level. Though detected in all analyzed tissues, TaABCB1 predominantly expressed in the meristematic tissues likely due to the presence of meristem-specific activation regulatory element identified in the promoter region. RNAi plants of TaABCB1 gene resulted in reduced plant height and increased seed width. Promoter analysis revealed several responsive elements detected in the promoter region including that for different hormones as auxin, gibberellic acid, jasmonic acid and abscisic acid, light, and circadian regulated elements.
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Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Amandeep K Dhaliwal
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Ragupathi Nagarajan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
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56
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Chang W, Li H, Chen H, Qiao F, Zeng H. Identification of mimp-associated effector genes in Fusarium oxysporum f. sp. cubense race 1 and race 4 and virulence confirmation of a candidate effector gene. Microbiol Res 2019; 232:126375. [PMID: 31783262 DOI: 10.1016/j.micres.2019.126375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022]
Abstract
Effectors secreted by microbes contribute to pathogen virulence and/or avirulence on host plants in the interaction of plants and microbes. Also, the effector repertoire determines the host specificity of a pathogen. Fusarium oxysporum f. sp. cubense (Foc) is the causal agent of banana wilt; however, knowledge about Foc effector genes is very limited. In this study, genome-wide effector gene identification was performed in Foc race 1 (Foc 1) and Foc race 4 (Foc 4) based on the context association between the effector genes and the transposable element mimp. A total of 20 candidate effector genes were identified, of which 3 were Foc 1-specific, 6 were Foc 4-specific, and 11 were present in both Foc 1 and Foc 4. Most genes (14 out of 20) showed a significant transcriptional burst in planta compared with in-culture conditions, from more than 10-fold to 1,617-fold, and at the highest 32,725-fold. In addition to Foc 1- and Foc 4-specific genes, the genes Foc 283, Foc 495, and Foc 594 also exhibited transcriptional race specificity. Sixteen of the twenty genes were predicted to have a signal peptide, nine genes might encode real effectors predicted by EffectorP 2.0, and eight genes had predicted motifs. To validate the pathogenicity of the candidate effector genes, we generated knockout mutant and complementants of the gene Foc 1324 and tested their virulence on banana plants. The results showed that Foc 1324 was a virulent factor and required for the pathogenicity of Foc 4.
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Affiliation(s)
- Wenjun Chang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China.
| | - Heng Li
- College of Tropical Agriculture and Forestry, Hainan University, Renmin Avenue 58, Haikou 570208, China
| | - Hanqing Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China
| | - Fan Qiao
- College of Tropical Agriculture and Forestry, Hainan University, Renmin Avenue 58, Haikou 570208, China
| | - Huicai Zeng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Longhua District, Haikou 571101, China
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57
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Dynamic regulation of chromatin topology and transcription by inverted repeat-derived small RNAs in sunflower. Proc Natl Acad Sci U S A 2019; 116:17578-17583. [PMID: 31409706 DOI: 10.1073/pnas.1903131116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Transposable elements (TEs) are extremely abundant in complex plant genomes. siRNAs of 24 nucleotides in length control transposon activity in a process that involves de novo methylation of targeted loci. Usually, these epigenetic modifications trigger nucleosome condensation and a permanent silencing of the affected loci. Here, we show that a TE-derived inverted repeat (IR) element, inserted near the sunflower HaWRKY6 locus, dynamically regulates the expression of the gene by altering chromatin topology. The transcripts of this IR element are processed into 24-nt siRNAs, triggering DNA methylation on its locus. These epigenetic marks stabilize the formation of tissue-specific loops in the chromatin. In leaves, an intragenic loop is formed, blocking HaWRKY6 transcription. While in cotyledons (Cots), formation of an alternative loop, encompassing the whole HaWRKY6 gene, enhances transcription of the gene. The formation of this loop changes the promoter directionality, reducing IR transcription, and ultimately releasing the loop. Our results provide evidence that TEs can act as active and dynamic regulatory elements within coding loci in a mechanism that combines RNA silencing, epigenetic modification, and chromatin remodeling machineries.
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58
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Shi J, Liang C. Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection. PLANT PHYSIOLOGY 2019; 180:1803-1815. [PMID: 31152127 PMCID: PMC6670090 DOI: 10.1104/pp.19.00386] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 05/17/2019] [Indexed: 05/25/2023]
Abstract
Comprehensive and accurate annotation of the repeatome, including transposons, is critical for deepening our understanding of repeat origins, biogenesis, regulatory mechanisms, and roles. Here, we developed Generic Repeat Finder (GRF), a tool for genome-wide repeat detection based on fast, exhaustive numerical calculation algorithms integrated with optimized dynamic programming strategies. GRF sensitively identifies terminal inverted repeats (TIRs), terminal direct repeats (TDRs), and interspersed repeats that bear both inverted and direct repeats. GRF also detects DNA or RNA transposable elements characterized by these repeats in plant and animal genomes. For TIRs and TDRs, GRF identifies spacers in the middle and mismatches/insertions or deletions in terminal repeats, showing their alignment or base-pairing information. GRF helps improve the annotation for various DNA transposons and retrotransposons, such as miniature inverted-repeat transposable elements (MITEs), long terminal repeat (LTR) retrotransposons, and non-LTR retrotransposons, including long interspersed nuclear elements and short interspersed nuclear elements in plants. We used GRF to perform TIR/TDR, interspersed-repeat, and MITE detection in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and mouse (Mus musculus). As a generic bioinformatics tool in repeat finding implemented as a parallelized C++ program, GRF was faster and more sensitive than the existing inverted repeat/MITE detection tools based on numerical approaches (i.e. detectIR and detectMITE) in Arabidopsis and mouse. GRF is more sensitive than Inverted Repeat Finder in TIR detection, LTR_FINDER in short TDR detection (≤1,000 nt), and phRAIDER in interspersed repeat detection in Arabidopsis and rice. GRF is an open source available from Github.
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Affiliation(s)
- Jieming Shi
- Department of Biology, Miami University, Oxford, Ohio 45056
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056
- Department of Computer Science and Software Engineering, Miami University, Oxford, Ohio 45056
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59
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Xin Y, Ma B, Xiang Z, He N. Amplification of miniature inverted-repeat transposable elements and the associated impact on gene regulation and alternative splicing in mulberry ( Morus notabilis). Mob DNA 2019; 10:27. [PMID: 31289464 PMCID: PMC6593561 DOI: 10.1186/s13100-019-0169-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
Background Miniature inverted-repeat transposable elements (MITEs) are common in eukaryotic genomes, and are important for genomic evolution. Results In the present study, the identification of MITEs in the mulberry genome revealed 286,122 MITE-related sequences, including 90,789 full-length elements. The amplification of mulberry MITEs and the influence of MITEs on the evolution of the mulberry genome were analyzed. The timing of MITE amplifications varied considerably among the various MITE families. Fifty-one MITE families have undergone a single round of amplification, while the other families developed from multiple amplifications. Most mulberry MITEs were inserted near genes and some could regulate gene expression through small RNAs. An analysis of transgenic plants indicated that MITE insertions can upregulate the expression of a target gene. Moreover, MITEs are frequently associated with alternative splicing events (exonizations). Conclusion The data presented herein provide insights into the generation of MITEs as well as their impact on gene regulation and evolution in mulberry. Electronic supplementary material The online version of this article (10.1186/s13100-019-0169-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Youchao Xin
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Beibei, Chongqing, 400715 China
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60
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Tang Y, Ma X, Zhao S, Xue W, Zheng X, Sun H, Gu P, Zhu Z, Sun C, Liu F, Tan L. Identification of an active miniature inverted-repeat transposable element mJing in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:639-653. [PMID: 30689248 PMCID: PMC6850418 DOI: 10.1111/tpj.14260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/01/2019] [Accepted: 01/18/2019] [Indexed: 05/27/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are structurally homogeneous non-autonomous DNA transposons with high copy numbers that play important roles in genome evolution and diversification. Here, we analyzed the rice high-tillering dwarf (htd) mutant in an advanced backcross population between cultivated and wild rice, and identified an active MITE named miniature Jing (mJing). The mJing element belongs to the PIF/Harbinger superfamily. japonica rice var. Nipponbare and indica var. 93-11 harbor 72 and 79 mJing family members, respectively, have undergone multiple rounds of amplification bursts during the evolution of Asian cultivated rice (Oryza sativa L.). A heterologous transposition experiment in Arabidopsis thaliana indicated that the autonomous element Jing is likely to have provides the transposase needed for mJing mobilization. We identified 297 mJing insertion sites and their presence/absence polymorphism among 71 rice samples through targeted high-throughput sequencing. The results showed that the copy number of mJing varies dramatically among Asian cultivated rice (O. sativa), its wild ancestor (O. rufipogon), and African cultivated rice (O. glaberrima) and that some mJing insertions are subject to directional selection. These findings suggest that the amplification and removal of mJing elements have played an important role in rice genome evolution and species diversification.
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Affiliation(s)
- Yanyan Tang
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xin Ma
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Wei Xue
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Hongying Sun
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Ping Gu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Zuofeng Zhu
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Fengxia Liu
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- National Center for Evaluation of Agricultural Wild Plants (Rice)MOE Laboratory of Crop Heterosis and UtilizationDepartment of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
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61
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Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, Wing RA, McNally KL, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N. Structural variants in 3000 rice genomes. Genome Res 2019; 29:870-880. [PMID: 30992303 PMCID: PMC6499320 DOI: 10.1101/gr.241240.118] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/11/2019] [Indexed: 12/24/2022]
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5′ UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
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Affiliation(s)
- Roven Rommel Fuentes
- International Rice Research Institute, Laguna 4031, Philippines.,Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | | | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia.,Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Sean Smith
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Juan Fernando De la Hoz
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Rod A Wing
- International Rice Research Institute, Laguna 4031, Philippines.,Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA.,King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Tatiana Tatarinova
- Department of Biology, University of La Verne, La Verne, California 91750, USA.,Vavilov Institute of General Genetics, Moscow 119333, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia.,Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey Grigoriev
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Ramil Mauleon
- International Rice Research Institute, Laguna 4031, Philippines
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62
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Liu Y, Tahir Ul Qamar M, Feng JW, Ding Y, Wang S, Wu G, Ke L, Xu Q, Chen LL. Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species. BMC PLANT BIOLOGY 2019; 19:140. [PMID: 30987586 PMCID: PMC6466647 DOI: 10.1186/s12870-019-1757-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 04/04/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons are ubiquitous in plants genomes, and highly important in their evolution and diversity. However, their mechanisms of insertion/amplification and roles in Citrus genome's evolution/diversity are still poorly understood. RESULTS To address this knowledge gap, we developed different computational pipelines to analyze, annotate and classify MITEs and LTR retrotransposons in six different sequenced Citrus species. We identified 62,010 full-length MITEs from 110 distinguished families. We observed MITEs tend to insert in gene related regions and enriched in promoters. We found that DTM63 is possibly an active Mutator-like MITE family in the traceable past and may still be active in Citrus. The insertion of MITEs resulted in massive polymorphisms and played an important role in Citrus genome diversity and gene structure variations. In addition, 6630 complete LTR retrotransposons and 13,371 solo-LTRs were identified. Among them, 12 LTR lineages separated before the differentiation of mono- and dicotyledonous plants. We observed insertion and deletion of LTR retrotransposons was accomplished with a dynamic balance, and their half-life in Citrus was ~ 1.8 million years. CONCLUSIONS These findings provide insights into MITEs and LTR retrotransposons and their roles in genome diversity in different Citrus genomes.
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Affiliation(s)
- Yan Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muhammad Tahir Ul Qamar
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yuduan Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Guizhi Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lingjun Ke
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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Su W, Gu X, Peterson T. TIR-Learner, a New Ensemble Method for TIR Transposable Element Annotation, Provides Evidence for Abundant New Transposable Elements in the Maize Genome. MOLECULAR PLANT 2019; 12:447-460. [PMID: 30802553 DOI: 10.1016/j.molp.2019.02.008] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 05/21/2023]
Abstract
Transposable elements (TEs) make up a large and rapidly evolving proportion of plant genomes. Among Class II DNA TEs, TIR elements are flanked by characteristic terminal inverted repeat sequences (TIRs). TIR TEs may play important roles in genome evolution, including generating allelic diversity, inducing structural variation, and regulating gene expression. However, TIR TE identification and annotation has been hampered by the lack of effective tools, resulting in erroneous TE annotations and a significant underestimation of the proportion of TIR elements in the maize genome. This problem has largely limited our understanding of the impact of TIR elements on plant genome structure and evolution. In this paper, we propose a new method of TIR element detection and annotation. This new pipeline combines the advantages of current homology-based annotation methods with powerful de novo machine-learning approaches, resulting in greatly increased efficiency and accuracy of TIR element annotation. The results show that the copy number and genome proportion of TIR elements in maize is much larger than that of current annotations. In addition, the distribution of some TIR superfamily elements is reduced in centromeric and pericentromeric positions, while others do not show a similar bias. Finally, the incorporation of machine-learning techniques has enabled the identification of large numbers of new DTA (hAT) family elements, which have all the hallmarks of bona fide TEs yet which lack high homology with currently known DTA elements. Together, these results provide new tools for TE research and new insight into the impact of TIR elements on maize genome diversity.
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Affiliation(s)
- Weijia Su
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA
| | - Thomas Peterson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011-3260, USA; Department of Agronomy, Iowa State University, Ames, IA 50011-3260, USA.
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64
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Choi JY, Purugganan MD. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. Mol Biol Evol 2019; 35:365-382. [PMID: 29126199 PMCID: PMC5850837 DOI: 10.1093/molbev/msx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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65
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Hassing B, Winter D, Becker Y, Mesarich CH, Eaton CJ, Scott B. Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne. PLoS One 2019; 14:e0209463. [PMID: 30759164 PMCID: PMC6374014 DOI: 10.1371/journal.pone.0209463] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - David Winter
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Yvonne Becker
- Institute for Epidemiology and Pathogen Diagnostics, Julius Küehn-Institute, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Carl H. Mesarich
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Carla J. Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
- Bio-Protection Research Centre, Massey University, Palmerston North, New Zealand
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66
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Grativol C, Thiebaut F, Sangi S, Montessoro P, Santos WDS, Hemerly AS, Ferreira PC. A miniature inverted-repeat transposable element, AddIn-MITE, located inside a WD40 gene is conserved in Andropogoneae grasses. PeerJ 2019; 7:e6080. [PMID: 30648010 PMCID: PMC6331000 DOI: 10.7717/peerj.6080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 11/07/2018] [Indexed: 11/25/2022] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) have been associated with genic regions in plant genomes and may play important roles in the regulation of nearby genes via recruitment of small RNAs (sRNA) to the MITEs loci. We identified eight families of MITEs in the sugarcane genome assembly with MITE-Hunter pipeline. These sequences were found to be upstream, downstream or inserted into 67 genic regions in the genome. The position of the most abundant MITE (Stowaway-like) in genic regions, which we call AddIn-MITE, was confirmed in a WD40 gene. The analysis of four monocot species showed conservation of the AddIn-MITE sequence, with a large number of copies in their genomes. We also investigated the conservation of the AddIn-MITE’ position in the WD40 genes from sorghum, maize and, in sugarcane cultivars and wild Saccharum species. In all analyzed plants, AddIn-MITE has located in WD40 intronic region. Furthermore, the role of AddIn-MITE-related sRNA in WD40 genic region was investigated. We found sRNAs preferentially mapped to the AddIn-MITE than to other regions in the WD40 gene in sugarcane. In addition, the analysis of the small RNA distribution patterns in the WD40 gene and the structure of AddIn-MITE, suggests that the MITE region is a proto-miRNA locus in sugarcane. Together, these data provide insights into the AddIn-MITE role in Andropogoneae grasses.
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Affiliation(s)
- Clicia Grativol
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Flavia Thiebaut
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Sara Sangi
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Patricia Montessoro
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Walaci da Silva Santos
- Laboratório de Química e Função de Proteínas e Peptídeos/Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo C.G. Ferreira
- Laboratório de Biologia Molecular de Plantas/Instituto de Bioquímica Médica Leopoldo De Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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67
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Keidar-Friedman D, Bariah I, Kashkush K. Genome-wide analyses of miniature inverted-repeat transposable elements reveals new insights into the evolution of the Triticum-Aegilops group. PLoS One 2018; 13:e0204972. [PMID: 30356268 PMCID: PMC6200218 DOI: 10.1371/journal.pone.0204972] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 09/08/2018] [Indexed: 11/19/2022] Open
Abstract
The sequence drafts of wild emmer and bread wheat facilitated high resolution, genome-wide analysis of transposable elements (TEs), which account for up to 90% of the wheat genome. Despite extensive studies, the role of TEs in reshaping nascent polyploid genomes remains to be fully understood. In this study, we retrieved miniature inverted-repeat transposable elements (MITEs) from the recently published genome drafts of Triticum aestivum, Triticum turgidum ssp. dicoccoides, Aegilops tauschii and the available genome draft of Triticum urartu. Overall, 239,126 MITE insertions were retrieved, including 3,874 insertions of a newly identified, wheat-unique MITE family that we named "Inbar". The Stowaway superfamily accounts for ~80% of the retrieved MITE insertions, while Thalos is the most abundant family. MITE insertions are distributed in the seven homologous chromosomes of the wild emmer and bread wheat genomes. The remarkably high level of insertions in the B sub-genome (~59% of total retrieved MITE insertions in the wild emmer genome draft, and ~41% in the bread wheat genome draft), emphasize its highly repetitive nature. Nearly 52% of all MITE insertions were found within or close (less than 100bp) to coding genes, and ~400 MITE sequences were found in the bread wheat transcriptome, indicating that MITEs might have a strong impact on wheat genome expression. In addition, ~40% of MITE insertions were found within TE sequences, and remarkably, ~90% of Inbar insertions were located in retrotransposon sequences. Our data thus shed new light on the role of MITEs in the diversification of allopolyploid wheat species.
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Affiliation(s)
| | - Inbar Bariah
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
| | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beer-Sheva, Israel
- * E-mail:
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68
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Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 2018; 10:304-318. [PMID: 29281015 PMCID: PMC5786231 DOI: 10.1093/gbe/evx276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 01/05/2023] Open
Abstract
Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, California
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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69
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Crescente JM, Zavallo D, Helguera M, Vanzetti LS. MITE Tracker: an accurate approach to identify miniature inverted-repeat transposable elements in large genomes. BMC Bioinformatics 2018; 19:348. [PMID: 30285604 PMCID: PMC6171319 DOI: 10.1186/s12859-018-2376-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/18/2018] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Miniature inverted-repeat transposable elements (MITEs) are short, non-autonomous class II transposable elements present in a high number of conserved copies in eukaryote genomes. An accurate identification of these elements can help to shed light on the mechanisms controlling genome evolution and gene regulation. The structure and distribution of these elements are well-defined and therefore computational approaches can be used to identify MITEs sequences. RESULTS Here we describe MITE Tracker, a novel, open source software program that finds and classifies MITEs using an efficient alignment strategy to retrieve nearby inverted-repeat sequences from large genomes. This program groups them into high sequence homology families using a fast clustering algorithm and finally filters only those elements that were likely transposed from different genomic locations because of their low scoring flanking sequence alignment. CONCLUSIONS Many programs have been proposed to find MITEs hidden in genomes. However, none of them are able to process large-scale genomes such as that of bread wheat. Furthermore, in many cases the existing methods perform high false-positive rates (or miss rates). The rice genome was used as reference to compare MITE Tracker against known tools. Our method turned out to be the most reliable in our tests. Indeed, it revealed more known elements, presented the lowest false-positive number and was the only program able to run with the bread wheat genome as input. In wheat, MITE Tracker discovered 6013 MITE families and allowed the first structural exploration of MITEs in the complete bread wheat genome.
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Affiliation(s)
- Juan Manuel Crescente
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Zavallo
- Instituto de Biotecnología, CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA) Castelar, Los Reseros y Nicolas Repeto, Hurlingham, Buenos Aires, Argentina
| | - Marcelo Helguera
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
| | - Leonardo Sebastián Vanzetti
- Grupo Biotecnología y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Shimada T, Endo T, Fujii H, Nakano M, Sugiyama A, Daido G, Ohta S, Yoshioka T, Omura M. MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues. BMC PLANT BIOLOGY 2018; 18:166. [PMID: 30103701 PMCID: PMC6090715 DOI: 10.1186/s12870-018-1369-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/24/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic 'Hamlin' sweet orange by antisense-overexpression. RESULTS The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain-containing protein. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryonic type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T1 plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds. CONCLUSION CitRKD1 at the polyembryonic locus plays a principal role in regulating citrus somatic embryogenesis. CitRKD1 comprised multiple alleles that were divided into two types, polyembryonic alleles with a MITE insertion in the upstream region and monoembryonic alleles without it. CitRKD1 was transcribed in reproductive tissues of polyembryonic varieties with the polyembryonic allele. The MITE insertion in the upstream region of CitRKD1 might be involved in regulating the transcription of CitRKD1.
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Affiliation(s)
- Takehiko Shimada
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, 424-0292 Japan
| | - Tomoko Endo
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, 424-0292 Japan
| | - Hiroshi Fujii
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, 424-0292 Japan
| | - Michiharu Nakano
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, 422-8529 Japan
| | - Aiko Sugiyama
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, 422-8529 Japan
| | - Genya Daido
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, 422-8529 Japan
| | - Satoshi Ohta
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, 424-0292 Japan
| | - Terutaka Yoshioka
- National Agriculture and Food Research Organization, Institute of Fruit and Tea Tree Science, Shimizu, Shizuoka, 424-0292 Japan
| | - Mitsuo Omura
- Faculty of Agriculture, Shizuoka University, Suruga, Shizuoka, 422-8529 Japan
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Odonkor S, Choi S, Chakraborty D, Martinez-Bello L, Wang X, Bahri BA, Tenaillon MI, Panaud O, Devos KM. QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica. FRONTIERS IN PLANT SCIENCE 2018; 9:918. [PMID: 30073004 PMCID: PMC6060267 DOI: 10.3389/fpls.2018.00918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/11/2018] [Indexed: 05/13/2023]
Abstract
Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5'UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.
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Affiliation(s)
- Sandra Odonkor
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA, United States
| | | | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Xuewen Wang
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Bochra A. Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Laboratory of Bioagressors and Integrated Protection in Agriculture (LR14AGR02), The National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
| | - Maud I. Tenaillon
- UMR8120 Génétique Quantitative et Evolution Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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Amorim IC, Costa RGC, Xavier C, de Moura RDC. Characterization and chromosomal mapping of the DgmarMITE transposon in populations of Dichotomius (Luederwaldtinia) sericeus species complex (Coleoptera: Scarabaeidae). Genet Mol Biol 2018; 41:419-425. [PMID: 29870572 PMCID: PMC6082228 DOI: 10.1590/1678-4685-gmb-2017-0230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/23/2017] [Indexed: 01/01/2023] Open
Abstract
Transposable elements are dispersed repetitive DNA sequences that can move within the genome and are related to genome and chromosome evolution, adaptation, and speciation. The aim of this study was to characterize and determine the chromosomal location and accumulation of a Mariner-like element in populations of four phylogenetically related species of the Dichotomius (Luederwaldtinia) sericeus complex. Mapping of the isolated element was performed by fluorescent in situ hybridization in different populations of analyzed species. Characterization of the isolated element revealed a degenerated transposon, named DgmarMITE. This transposon is 496-bp-long, AT rich (57%), and contains 24 bp terminal inverted repeats. In situ mapping revealed presence of this element only in two out of four species analyzed. DgmarMITE sites were located in heterochromatic and euchromatic regions and varied in location and number on the karyotypes of Dichotomius (L.) gilletti and D. (L.) guaribensis across different populations. These results demonstrate differential accumulation of the DgmarMITE in genomes of these species, which is probably due to the occurrence of ectopic recombination and cross-mobilization of the element mediated by the transposase of closely related or unrelated transposable elements.
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Affiliation(s)
- Igor Costa Amorim
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoCentro de BiociênciasDepartamento de GenéticaRecifePEBrazilDepartamento de Genética, Centro de
Biociências, Universidade Federal de Pernambuco, Recife, PE,
Brazil
| | - Rafaelle Grazielle Coelho Costa
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
| | - Crislaine Xavier
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
- Universidade Federal de
PernambucoUniversidade Federal de
PernambucoCentro de BiociênciasDepartamento de GenéticaRecifePEBrazilDepartamento de Genética, Centro de
Biociências, Universidade Federal de Pernambuco, Recife, PE,
Brazil
| | - Rita de Cássia de Moura
- Universidade de PernambucoUniversidade de PernambucoInstituto de Ciências
BiológicasLaboratório de Biodiversidade e Genética de
InsetosRecifePEBrazilLaboratório de Biodiversidade e Genética de
Insetos, Instituto de Ciências Biológicas, Universidade de Pernambuco,
Recife, PE, Brazil
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73
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Wang L, Yuan J, Ma Y, Jiao W, Ye W, Yang DL, Yi C, Chen ZJ. Rice Interploidy Crosses Disrupt Epigenetic Regulation, Gene Expression, and Seed Development. MOLECULAR PLANT 2018; 11:300-314. [PMID: 29269023 DOI: 10.1016/j.molp.2017.12.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/01/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
Seed development in angiosperms requires a 2:1 maternal-to-paternal genome ratio (2m:1p) in the endosperm. When the ratio is disrupted, the seed development is impaired. Rice interploidy crosses result in endosperm failures, but the underlying molecular mechanisms remain unclear. Here, we report that the defective endosperm in rice interploidy crosses was associated with nonadditive expression of small RNAs and protein-coding genes. Interestingly, 24-nt small interfering RNAs were enriched in the 5' and 3' flanking sequences of nonadditively expressed genes in the interploidy crosses and were negatively associated with the expression of imprinted genes. Furthermore, some PRC2 family genes and DNA methylation-related genes including OsMET1b and OsCMT3a were upregulated in the 2×4 cross (pollinating a diploid "mother" with a tetraploid "father") but repressed in the reciprocal cross. These different epigenetic effects could lead to precocious or delayed cellularization during endosperm development. Notably, many endosperm-preferred genes, including starch metabolic and storage protein genes during grain filling, were found to be associated with DNA methylation or H3K27me3, which are repressed in both 2×4 and 4×2 crosses. WUSCHEL homeobox2 (WOX2)-like (WOX2L), an endosperm-preferred gene, was expressed specifically in the rice endosperm, in contrast to WOX2 expression in the Arabidopsis embryo. Disruption of WOX2L in transgenic rice by CRISPR/Cas9-mediated gene editing blocked starch and protein accumulation, resulting in seed abortion. In addition to gene repression, disrupting epigenetic process in the interploidy crosses also induced expression of stress-responsive genes. Thus, maintaining the 2m:1p genome ratio in the endosperm is essential for normal grain development in rice and other cereal crops.
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Affiliation(s)
- Limei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Yujie Ma
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
| | - Chuandeng Yi
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou 225009, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China; Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
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74
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Gayathri M, Shirasawa K, Varshney RK, Pandey MK, Bhat RS. Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.). BMC Res Notes 2018; 11:10. [PMID: 29310707 PMCID: PMC5759262 DOI: 10.1186/s13104-017-3121-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/29/2017] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVE In peanut, the DNA polymorphism is very low despite enormous phenotypic variations. This limits the use of genomics-assisted breeding to enhance peanut productivity. This study aimed to develop and validate new AhMITE1 and cleaved amplified polymorphic sequences (CAPS) markers. RESULTS In total, 2957 new AhMITE1 markers were developed in addition to identifying 465 already reported markers from the whole genome re-sequencing data (WGRS) of 33 diverse genotypes of peanut. The B sub-genome (1620) showed more number of markers than the A sub-genome (1337). Distribution also varied among the chromosomes of both the sub-genomes. Further, 52.6% of the markers were from genic regions; where 31.0% were from intronic regions and 5.2% were from exonic regions. Of the 343 randomly selected markers, 82.2% showed amplification validation, with up to 35.5% polymorphism. From the SNPs on the A03, B01, B02 and B03 chromosomes, 11,730 snip-SNPs (potential CAPS sites) were identified, and 500 CAPS markers were developed from chromosome A03. Of these markers, 30.0% showed validation and high polymorphism. This study demonstrated the potential of the WGRS data to develop AhMITE1 and CAPS markers, which showed high level of validation and polymorphism. These marker resources will be useful for various genetic studies and mapping in peanut.
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Affiliation(s)
- M. Gayathri
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
| | - Kenta Shirasawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, 292-0818 Japan
| | - R. K. Varshney
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324 India
| | - M. K. Pandey
- Center of Excellence in Genomics (CEG), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502 324 India
| | - R. S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, 580 005 India
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75
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Tracking the genome-wide outcomes of a transposable element burst over decades of amplification. Proc Natl Acad Sci U S A 2017; 114:E10550-E10559. [PMID: 29158416 PMCID: PMC5724284 DOI: 10.1073/pnas.1716459114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rice (Oryza sativa) has a unique combination of attributes that made it an ideal host to track the natural behavior of very active transposable elements (TEs) over generations. In this study, we have exploited its small genome and propagation by self or sibling pollination to identify and characterize two strain pairs, EG4/HEG4 and A119/A123, undergoing bursts of the nonautonomous miniature inverted repeat transposable element mPing. Comparative sequence analyses of these strains have advanced our understanding of (i) factors that contribute to sustaining a TE burst for decades, (ii) features that distinguish a natural TE burst from bursts in cell culture or mutant backgrounds, and (iii) the extent to which TEs can rapidly diversify the genome of an inbred organism. To understand the success strategies of transposable elements (TEs) that attain high copy numbers, we analyzed two pairs of rice (Oryza sativa) strains, EG4/HEG4 and A119/A123, undergoing decades of rapid amplification (bursts) of the class 2 autonomous Ping element and the nonautonomous miniature inverted repeat transposable element (MITE) mPing. Comparative analyses of whole-genome sequences of the two strain pairs validated that each pair has been maintained for decades as inbreds since divergence from their respective last common ancestor. Strains EG4 and HEG4 differ by fewer than 160 SNPs and a total of 264 new mPing insertions. Similarly, strains A119 and A123 exhibited about half as many SNPs (277) as new mPing insertions (518). Examination of all other potentially active TEs in these genomes revealed only a single new insertion out of ∼40,000 loci surveyed. The virtual absence of any new TE insertions in these strains outside the mPing bursts demonstrates that the Ping/mPing family gradually attains high copy numbers by maintaining activity and evading host detection for dozens of generations. Evasion is possible because host recognition of mPing sequences appears to have no impact on initiation or maintenance of the burst. Ping is actively transcribed, and both Ping and mPing can transpose despite methylation of terminal sequences. This finding suggests that an important feature of MITE success is that host recognition does not lead to the silencing of the source of transposase.
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76
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Wang PH, Wittmeyer KT, Lee TF, Meyers BC, Chopra S. Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1. PLoS One 2017; 12:e0187157. [PMID: 29112965 PMCID: PMC5675401 DOI: 10.1371/journal.pone.0187157] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 10/14/2017] [Indexed: 11/18/2022] Open
Abstract
Allelic variation at the Zea mays (maize) pericarp color1 (p1) gene has been attributed to epigenetic gene regulation. A p1 distal enhancer, 5.2 kb upstream of the transcriptional start site, has demonstrated variation in DNA methylation in different p1 alleles/epialleles. In addition, DNA methylation of sequences within the 3’ end of intron 2 also plays a role in tissue-specific expression of p1 alleles. We show here a direct evidence for small RNAs’ involvement in regulating p1 that has not been demonstrated previously. The role of mediator of paramutation1 (mop1) was tested in the maintenance of somatic silencing at distinct p1 alleles: the non-paramutagenic P1-wr allele and paramutagenic P1-rr’ epiallele. The mop1-1 mutation gradually relieves the silenced phenotype after multiple generations of exposure; P1-wr;mop1-1 plants display a loss of 24-nt small RNAs and DNA methylation in the 3’ end of the intron 2, a region close to a Stowaway transposon. In addition, a MULE sequence within the proximal promoter of P1-wr shows depletion of 24nt siRNAs in mop1-1 plants. Release of silencing was not correlated with small RNAs at the distal enhancer region of the P1-wr allele. We found that the somatic silencing of the paramutagenic P1-rr’ is correlated with significantly reduced H3K9me2 in the distal enhancer of P1-rr’; mop1-1 plants, while symmetric DNA methylation is not significantly different. This study highlights that the epigenetic regulation of p1 alleles is controlled both via RdDM as well as non-RdDM mechanisms.
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Affiliation(s)
- Po-Hao Wang
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Kameron T. Wittmeyer
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Plant Biology Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tzuu-fen Lee
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Blake C. Meyers
- Department of Plant & Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Surinder Chopra
- Department of Plant Science, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Plant Biology Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
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77
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Hake AA, Shirasawa K, Yadawad A, Sukruth M, Patil M, Nayak SN, Lingaraju S, Patil PV, Nadaf HL, Gowda MVC, Bhat RS. Mapping of important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut (Arachis hypogaea L.). PLoS One 2017; 12:e0186113. [PMID: 29040293 PMCID: PMC5645101 DOI: 10.1371/journal.pone.0186113] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/25/2017] [Indexed: 12/30/2022] Open
Abstract
A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.
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Affiliation(s)
- Anil A Hake
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Kenta Shirasawa
- Department of Frontier Research, Kazusa DNA Research Institute, Chiba, Japan
| | - Arati Yadawad
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - M Sukruth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Malagouda Patil
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Spurthi N Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - S Lingaraju
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad, India
| | - P V Patil
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad, India
| | - H L Nadaf
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - M V C Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - R S Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
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78
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Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion. Curr Genet 2017; 64:405-412. [DOI: 10.1007/s00294-017-0765-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
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79
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Yuan J, Chen S, Jiao W, Wang L, Wang L, Ye W, Lu J, Hong D, You S, Cheng Z, Yang DL, Chen ZJ. Both maternally and paternally imprinted genes regulate seed development in rice. THE NEW PHYTOLOGIST 2017; 216:373-387. [PMID: 28295376 DOI: 10.1111/nph.14510] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/01/2017] [Indexed: 05/20/2023]
Abstract
Genetic imprinting refers to the unequal expression of paternal and maternal alleles of a gene in sexually reproducing organisms, including mammals and flowering plants. Although many imprinted genes have been identified in plants, the functions of these imprinted genes have remained largely uninvestigated. We report genome-wide analysis of gene expression, DNA methylation and small RNAs in the rice endosperm and functional tests of five imprinted genes during seed development using Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated gene9 (CRISPR/Cas9) gene editing technology. In the rice endosperm, we identified 162 maternally expressed genes (MEGs) and 95 paternally expressed genes (PEGs), which were associated with miniature inverted-repeat transposable elements, imprinted differentially methylated loci and some 21-22 small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs). Remarkably, one-third of MEGs and nearly one-half of PEGs were associated with grain yield quantitative trait loci. Most MEGs and some PEGs were expressed specifically in the endosperm. Disruption of two MEGs increased the amount of small starch granules and reduced grain and embryo size, whereas mutation of three PEGs reduced starch content and seed fertility. Our data indicate that both MEGs and PEGs in rice regulate nutrient metabolism and endosperm development, which optimize seed development and offspring fitness to facilitate parental-offspring coadaptation. These imprinted genes and mechanisms could be used to improve the grain yield of rice and other cereal crops.
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Affiliation(s)
- Jingya Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Sushu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wu Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Longfei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Limei Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Wenxue Ye
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Jie Lu
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Delin Hong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Siliang You
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Zhukuan Cheng
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 1 West Beichen Road, Beijing, 100101, China
| | - Dong-Lei Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Z Jeffrey Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA
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80
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Ganie SA, Debnath AB, Gumi AM, Mondal TK. Comprehensive survey and evolutionary analysis of genome-wide miRNA genes from ten diploid Oryza species. BMC Genomics 2017; 18:711. [PMID: 28893199 PMCID: PMC5594537 DOI: 10.1186/s12864-017-4089-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species. Analysis of the nucleotide substitution rates indicated that the mature sequences show the least substitution rates among the different regions of miRNA genes, and also show a very much less substitution rates as compared to that of all protein-coding genes across the Oryza species. Evolution of miRNA genes was also found to be contributed by transposons. A non-neutral selection was observed at 80 different miRNA loci across Oryza species which were estimated to have lost ~87% of the sequence diversity during the domestication. The phylogenetic analysis revealed that O. longistaminata diverged first among the AA-genomes, whereas O. brachyantha and O. punctata appeared as the eminent out-groups. The miR1861 family organised into nine distinct compact clusters in the studied Oryza species except O. brachyantha. Further, the expression analysis showed that 11 salt-responsive miRNAs were differentially regulated between O. coarctata and O. glaberrima. CONCLUSION Our study provides the evolutionary dynamics in the miRNA genes of 10 different Oryza species which will support more investigations about the structural and functional organization of miRNA genes of Oryza species.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Ananda Bhusan Debnath
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Abubakar Mohammad Gumi
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa, IARI Campus, New Delhi, 110012, India.
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81
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Xu J, Wang Q, Freeling M, Zhang X, Xu Y, Mao Y, Tang X, Wu F, Lan H, Cao M, Rong T, Lisch D, Lu Y. Natural antisense transcripts are significantly involved in regulation of drought stress in maize. Nucleic Acids Res 2017; 45:5126-5141. [PMID: 28175341 PMCID: PMC5435991 DOI: 10.1093/nar/gkx085] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/30/2017] [Indexed: 01/02/2023] Open
Abstract
Natural antisense transcripts (NATs) are a prominent and complex class of regulatory RNAs. Using strand-specific RNA sequencing, we identified 1769 sense and antisense transcript pairs (NAT pairs) in two maize inbreds with different sensitivity to drought, as well as in two derivative recombination inbred lines (RILs). A significantly higher proportion of NATs relative to non-NATs are specifically expressed under water stress (WS). Surprisingly, expression of sense and antisense transcripts produced by NAT pairs is significantly correlated, particularly under WS. We found an unexpected large proportion of NATs with protein coding potential, as estimated by ribosome release scores. Small RNAs significantly accumulate within NAT pairs, with 21 nt smRNA particularly enriched in overlapping regions of these pairs of genes. The abundance of these smRNAs is significantly altered in the leafbladeless1 mutant, suggesting that these genes may be regulated by the tasiRNA pathway. Further, NATs are significantly hypomethylated and include fewer transposable element sequences relative to non-NAT genes. NAT gene regions also exhibit higher levels of H3K36me3, H3K9ac, and H3K4me3, but lower levels of H3K27me3, indicating that NAT gene pairs generally exhibit an open chromatin configuration. Finally, NAT pairs in 368 diverse maize inbreds and 19 segregating populations were specifically enriched for polymorphisms associated with drought tolerance. Taken together, the data highlight the potential impact of that small RNAs and histone modifications have in regulation of NAT expression, and the significance of NATs in response to WS.
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Affiliation(s)
- Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China.,Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Micheal Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94703, USA
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130, Texcoco, Mexico.,Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian, Beijing 100081, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Hai Lan
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Moju Cao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.,Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
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82
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Guo C, Spinelli M, Ye C, Li QQ, Liang C. Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions. Sci Rep 2017; 7:2634. [PMID: 28572566 PMCID: PMC5454002 DOI: 10.1038/s41598-017-02855-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes. They are known to critically influence the process of genome evolution and play a role in gene regulation. As the first study concentrated in the transposition activities of MITEs among different ecotype accessions within a species, we conducted a genome-wide comparative analysis by characterizing and comparing MITEs in 19 Arabidopsis thaliana accessions. A total of 343485 MITE putative sequences, including canonical, diverse and partial ones, were delineated from all 19 accessions. Within the entire population of MITEs sequences, 80.7% of them were previously unclassified MITEs, demonstrating a different genomic distribution and functionality compared to the classified MITEs. The interactions between MITEs and homologous genes across 19 accessions provided a fine source for analyzing MITE transposition activities and their impacts on genome evolution. Moreover, a significant proportion of MITEs were found located in the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of genes. Finally, analysis of the impact of MITEs on gene expression suggests that migrations of MITEs have no detectable effect on the expression level for host genes across accessions.
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Affiliation(s)
- Cheng Guo
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | | | - Congting Ye
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, 91766, USA.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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83
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Song X, Cao X. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:111-118. [PMID: 28273484 DOI: 10.1016/j.pbi.2017.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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84
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Bewick AJ, Schmitz RJ. Gene body DNA methylation in plants. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:103-110. [PMID: 28258985 PMCID: PMC5413422 DOI: 10.1016/j.pbi.2016.12.007] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/29/2016] [Indexed: 05/19/2023]
Abstract
The type, amount, and location of DNA methylation within a gene provides pivotal information on the enzymatic pathway by which it was achieved and its functional consequences. In plants (angiosperms specifically), gene body methylation (gbM) refers to genes with an enrichment of CG DNA methylation within the transcribed regions and depletion at the transcriptional start and termination sites. GbM genes often compose the bulk of methylated genes within angiosperm genomes and are enriched for housekeeping functions. Contrary to the transcriptionally repressive effects of other chromatin modifications within gene bodies, gbM genes are constitutively expressed. GbM has intrigued researchers since its discovery, and much effort has been placed on identifying its functional role. Here, we highlight the recent findings on the evolutionary origin and molecular mechanism of gbM and synthesize studies describing the possible roles for this enigmatic epigenetic phenotype.
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Affiliation(s)
- Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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85
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Translational repression by a miniature inverted-repeat transposable element in the 3' untranslated region. Nat Commun 2017; 8:14651. [PMID: 28256530 PMCID: PMC5338036 DOI: 10.1038/ncomms14651] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/18/2017] [Indexed: 12/18/2022] Open
Abstract
Transposable elements constitute a substantial portion of eukaryotic genomes and contribute to genomic variation, function, and evolution. Miniature inverted-repeat transposable elements (MITEs), as DNA transposons, are widely distributed in plant and animal genomes. Previous studies have suggested that retrotransposons act as translational regulators; however, it remains unknown how host mRNAs are influenced by DNA transposons. Here we report a translational repression mechanism mediated by a stowaway-like MITE (sMITE) embedded in the 3'-untranslated region (3'-UTR) of Ghd2, a member of the CCT (CONSTANS [CO], CO-LIKE and TIMING OF CAB1) gene family in rice. Ghd2 regulates important agronomic traits, including grain number, plant height and heading date. Interestingly, the translational repression of Ghd2 by the sMITE mainly relies on Dicer-like 3a (OsDCL3a). Furthermore, other MITEs in the 3'-UTRs of different rice genes exhibit a similar effect on translational repression, thus suggesting that MITEs may exert a general regulatory function at the translational level.
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86
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Han MJ, Zhou QZ, Zhang HH, Tong X, Lu C, Zhang Z, Dai F. iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw148. [PMID: 28025339 PMCID: PMC5199201 DOI: 10.1093/database/baw148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/19/2016] [Accepted: 10/18/2016] [Indexed: 01/23/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs) have attracted much attention due to their widespread occurrence and high copy numbers in eukaryotic genomes. However, the systematic knowledge about MITEs in insects and other animals is still lacking. In this study, we identified 6012 MITE families from 98 insect species genomes. Comparison of these MITEs with known MITEs in the NCBI non-redundant database and Repbase showed that 5701(∼95%) of 6012 MITE families are novel. The abundance of MITEs varies drastically among different insect species, and significantly correlates with genome size. In general, larger genomes contain more MITEs than small genomes. Furthermore, all identified MITEs were included in a newly constructed database (iMITEdb) (http://gene.cqu.edu.cn/iMITEdb/), which has functions such as browse, search, BLAST and download. Overall, our results not only provide insight on insect MITEs but will also improve assembly and annotation of insect genomes. More importantly, the results presented in this study will promote studies of MITEs function, evolution and application in insects. Database URL: http://gene.cqu.edu.cn/iMITEdb/
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Affiliation(s)
- Min-Jin Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Qiu-Zhong Zhou
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang 332000, China
| | - Xiaoling Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
| | - Ze Zhang
- Laboratory of Evolutionary and Functional Genomics, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Fangyin Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing 400715, China
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87
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Jiang SH, Li GY, Xiong XM. Novel miniature inverted-repeat transposable elements derived from novel CACTA transposons were discovered in the genome of the ant Camponotus floridanus. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0464-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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88
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Deng X, Song X, Wei L, Liu C, Cao X. Epigenetic regulation and epigenomic landscape in rice. Natl Sci Rev 2016. [DOI: 10.1093/nsr/nww042] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Abstract
Epigenetic regulation has been implicated in the control of complex agronomic traits in rice (Oryza sativa), a staple food crop and model monocot plant. Recent advances in high-throughput sequencing and the moderately complex genome of rice have made it possible to study epigenetic regulation in rice on a genome-wide scale. This review discusses recent advances in our understanding of epigenetic regulation in rice, with an emphasis on the roles of key epigenetic regulators, the epigenomic landscape, epigenetic variation, transposon repression, and plant development.
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Affiliation(s)
- Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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89
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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90
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Zhou M, Tao G, Pi P, Zhu Y, Bai Y, Meng X. Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla). PLANTA 2016; 244:775-787. [PMID: 27160169 DOI: 10.1007/s00425-016-2544-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/01/2016] [Indexed: 06/05/2023]
Abstract
Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.
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Affiliation(s)
- Mingbing Zhou
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China.
| | - Guiyun Tao
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Peiyao Pi
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Yihang Zhu
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Youhuang Bai
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
| | - Xianwen Meng
- The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, LinAn, 311300, Zhejiang Province, People's Republic of China
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91
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Beta-amylase gene variability in introgressive wheat lines. J Appl Genet 2016; 58:143-149. [PMID: 27562405 DOI: 10.1007/s13353-016-0364-3] [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: 04/25/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 10/21/2022]
Abstract
Variability of the beta-amylase gene in bread wheat, artificial amphidiploids, and derived introgression wheat lines was analyzed. Variation in homeologous beta-amylase sequences caused by the presence of MITE (Miniature Inverted-Repeat Transposable Element) and its footprint has been identified in bread wheat. The previously unknown location of MITE in Triticum urartu and T. aestivum L. beta-amylase gene has been found. These species have a MITE sequence in the third intron of beta-amylase, as opposed to Aegilops comosa and a number of other Triticeae species, which have it in the fourth intron. These two MITEs from Ae. comosa and T. aestivum were shown to have low identity scores. Miosa, an artificial amphidiploid, which has the M genome from Ae. comosa was shown to lose the MITE sequences. This loss might be caused by genomic shock due to allopolyploidization.
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92
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Ishchuk OP, Vojvoda Zeljko T, Schifferdecker AJ, Mebrahtu Wisén S, Hagström ÅK, Rozpędowska E, Rørdam Andersen M, Hellborg L, Ling Z, Sibirny AA, Piškur J. Novel Centromeric Loci of the Wine and Beer Yeast Dekkera bruxellensis CEN1 and CEN2. PLoS One 2016; 11:e0161741. [PMID: 27560164 PMCID: PMC4999066 DOI: 10.1371/journal.pone.0161741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/10/2016] [Indexed: 11/19/2022] Open
Abstract
The wine and beer yeast Dekkera bruxellensis thrives in environments that are harsh and limiting, especially in concentrations with low oxygen and high ethanol. Its different strains’ chromosomes greatly vary in number (karyotype). This study isolates two novel centromeric loci (CEN1 and CEN2), which support both the yeast’s autonomous replication and the stable maintenance of plasmids. In the sequenced genome of the D. bruxellensis strain CBS 2499, CEN1 and CEN2 are each present in one copy. They differ from the known “point” CEN elements, and their biological activity is retained within ~900–1300 bp DNA segments. CEN1 and CEN2 have features of both “point” and “regional” centromeres: They contain conserved DNA elements, ARSs, short repeats, one tRNA gene, and transposon-like elements within less than 1 kb. Our discovery of a miniature inverted-repeat transposable element (MITE) next to CEN2 is the first report of such transposons in yeast. The transformants carrying circular plasmids with cloned CEN1 and CEN2 undergo a phenotypic switch: They form fluffy colonies and produce three times more biofilm. The introduction of extra copies of CEN1 and CEN2 promotes both genome rearrangements and ploidy shifts, with these effects mediated by homologous recombination (between circular plasmid and genome centromere copy) or by chromosome breakage when integrated. Also, the proximity of the MITE-like transposon to CEN2 could translocate CEN2 within the genome or cause chromosomal breaks, so promoting genome dynamics. With extra copies of CEN1 and CEN2, the yeast’s enhanced capacities to rearrange its genome and to change its gene expression could increase its abilities for exploiting new and demanding niches.
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Affiliation(s)
- Olena P. Ishchuk
- Department of Biology, Lund University, Lund, Sweden
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
- * E-mail:
| | - Tanja Vojvoda Zeljko
- Department of Biology, Lund University, Lund, Sweden
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | | | | | | | | | | | - Zhihao Ling
- Department of Biology, Lund University, Lund, Sweden
| | - Andrei A. Sibirny
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology, NAS of Ukraine, Lviv, Ukraine
- Department of Biotechnology and Microbiology, University of Rzeszow, Rzeszow, Poland
| | - Jure Piškur
- Department of Biology, Lund University, Lund, Sweden
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93
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Xi X, Li N, Li S, Chen W, Zhang B, Liu B, Zhang H. The characteristics and functions of a miniature inverted-repeat transposable element TaMITE81 in the 5' UTR of TaCHS7BL from Triticum aestivum. Mol Genet Genomics 2016; 291:1991-8. [PMID: 27481288 DOI: 10.1007/s00438-016-1234-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/25/2016] [Indexed: 12/23/2022]
Abstract
Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in eukaryotic and prokaryotic genomes. In this article, a MITE, TaMITE81, was isolated from the 5' untranslated region (UTR) of TaCHS7BL, chalcone synthase (CHS) catalyzing the first committed step of anthocyanin biosynthesis, in the wheat cultivar 'Opata' with white grain. TaMITE81 was only 81 nucleotides, including a terminal inverted repeat with 39 nucleotides and was flanked by two nucleotides, "TA", target site duplications that were typical features of stowaway-like MITEs. Compared with the wheat cultivar 'Gy115' with purple grain, which is without the insertion, the expression of TaCHS7BL was lower in several organs of 'Opata'. The insertion of TaMITE81 into the 5' UTR of the GUS gene also reduced the transient expression of GUS on the coleoptiles of 'Opata', which means the insertion of TaMITE81 was the reason for the low expression of TaCHS7BL in 'Opata'. But the genotype of TaCHS7BL was not linked to phenotype of grain color in the RILs derived from a cross 'Gy115' and 'Opata'. The TaMITE81 density of the hexaploid variety of T. aestivum was more than 10 times that of diploid relatives, which implies that polyploidization caused the amplification of TaMITE81 homologous sequences. Further research should be conducted on decoding the relationship between TaCHS7BL and other traits relative to anthocyanin biosynthesis in wheat, and discovering the mechanism of TaMITE81 transposon action.
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Affiliation(s)
- Xinyuan Xi
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Na Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiming Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, 810008, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, 810008, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.,Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, 810008, China
| | - Baolong Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China. .,Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, 810008, China.
| | - Huaigang Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota (AEPB), Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China. .,Qinghai Province Key Laboratory of Crop Molecular Breeding, Xining, 810008, China.
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94
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van Dam P, Fokkens L, Schmidt SM, Linmans JHJ, Kistler HC, Ma LJ, Rep M. Effector profiles distinguish formae speciales of Fusarium oxysporum. Environ Microbiol 2016; 18:4087-4102. [PMID: 27387256 DOI: 10.1111/1462-2920.13445] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/30/2016] [Indexed: 01/10/2023]
Abstract
Formae speciales (ff.spp.) of the fungus Fusarium oxysporum are often polyphyletic within the species complex, making it impossible to identify them on the basis of conserved genes. However, sequences that determine host-specific pathogenicity may be expected to be similar between strains within the same forma specialis. Whole genome sequencing was performed on strains from five different ff.spp. (cucumerinum, niveum, melonis, radicis-cucumerinum and lycopersici). In each genome, genes for putative effectors were identified based on small size, secretion signal, and vicinity to a "miniature impala" transposable element. The candidate effector genes of all genomes were collected and the presence/absence patterns in each individual genome were clustered. Members of the same forma specialis turned out to group together, with cucurbit-infecting strains forming a supercluster separate from other ff.spp. Moreover, strains from different clonal lineages within the same forma specialis harbour identical effector gene sequences, supporting horizontal transfer of genetic material. These data offer new insight into the genetic basis of host specificity in the F. oxysporum species complex and show that (putative) effectors can be used to predict host specificity in F. oxysporum.
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Affiliation(s)
- Peter van Dam
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Like Fokkens
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Sarah M Schmidt
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - Jasper H J Linmans
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
| | - H Corby Kistler
- United States Department of Agriculture, ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, USA
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Martijn Rep
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, The Netherlands
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95
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Tan F, Zhou C, Zhou Q, Zhou S, Yang W, Zhao Y, Li G, Zhou DX. Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways. PLANT PHYSIOLOGY 2016; 171:2041-54. [PMID: 27208249 PMCID: PMC4936571 DOI: 10.1104/pp.16.00393] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/11/2016] [Indexed: 05/18/2023]
Abstract
Plant DNA methylation that occurs at CG, CHG, and CHH sites (H = A, C, or T) is a hallmark of the repression of repetitive sequences and transposable elements (TEs). The rice (Oryza sativa) genome contains about 40% repetitive sequence and TEs and displays specific patterns of genome-wide DNA methylation. The mechanism responsible for the specific methylation patterns is unclear. Here, we analyzed the function of OsDDM1 (Deficient in DNA Methylation 1) and OsDRM2 (Deficient in DNA Methylation 1) in genome-wide DNA methylation, TE repression, small RNA accumulation, and gene expression. We show that OsDDM1 is essential for high levels of methylation at CHG and, to a lesser extent, CG sites in heterochromatic regions and also is required for CHH methylation that mainly locates in the genic regions of the genome. In addition to a large member of TEs, loss of OsDDM1 leads to hypomethylation and up-regulation of many protein-coding genes, producing very severe growth phenotypes at the initial generation. Importantly, we show that OsDRM2 mutation results in a nearly complete loss of CHH methylation and derepression of mainly small TE-associated genes and that OsDDM1 is involved in facilitating OsDRM2-mediated CHH methylation. Thus, the function of OsDDM1 and OsDRM2 defines distinct DNA methylation pathways in the bulk of DNA methylation of the genome, which is possibly related to the dispersed heterochromatin across chromosomes in rice and suggests that DNA methylation mechanisms may vary among different plant species.
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Affiliation(s)
- Feng Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Chao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Shaoli Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Wenjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
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96
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Palazzo A, Lovero D, D’Addabbo P, Caizzi R, Marsano RM. Identification of Bari Transposons in 23 Sequenced Drosophila Genomes Reveals Novel Structural Variants, MITEs and Horizontal Transfer. PLoS One 2016; 11:e0156014. [PMID: 27213270 PMCID: PMC4877112 DOI: 10.1371/journal.pone.0156014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/09/2016] [Indexed: 11/18/2022] Open
Abstract
Bari elements are members of the Tc1-mariner superfamily of DNA transposons, originally discovered in Drosophila melanogaster, and subsequently identified in silico in 11 sequenced Drosophila genomes and as experimentally isolated in four non-sequenced Drosophila species. Bari-like elements have been also studied for their mobility both in vivo and in vitro. We analyzed 23 Drosophila genomes and carried out a detailed characterization of the Bari elements identified, including those from the heterochromatic Bari1 cluster in D. melanogaster. We have annotated 401 copies of Bari elements classified either as putatively autonomous or inactive according to the structure of the terminal sequences and the presence of a complete transposase-coding region. Analyses of the integration sites revealed that Bari transposase prefers AT-rich sequences in which the TA target is cleaved and duplicated. Furthermore evaluation of transposon’s co-occurrence near the integration sites of Bari elements showed a non-random distribution of other transposable elements. We also unveil the existence of a putatively autonomous Bari1 variant characterized by two identical long Terminal Inverted Repeats, in D. rhopaloa. In addition, we detected MITEs related to Bari transposons in 9 species. Phylogenetic analyses based on transposase gene and the terminal sequences confirmed that Bari-like elements are distributed into three subfamilies. A few inconsistencies in Bari phylogenetic tree with respect to the Drosophila species tree could be explained by the occurrence of horizontal transfer events as also suggested by the results of dS analyses. This study further clarifies the Bari transposon’s evolutionary dynamics and increases our understanding on the Tc1-mariner elements’ biology.
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Affiliation(s)
- Antonio Palazzo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - Domenica Lovero
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Via Amendola 165/A, 70126, Bari, Italy
| | - Pietro D’Addabbo
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - Ruggiero Caizzi
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
| | - René Massimiliano Marsano
- Dipartimento di Biologia, Università degli Studi di Bari “Aldo Moro” via Orabona 4 70125, Bari, Italy
- * E-mail:
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97
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Wang L, Peng Q, Zhao J, Ren F, Zhou H, Wang W, Liao L, Owiti A, Jiang Q, Han Y. Evolutionary origin of Rosaceae-specific active non-autonomous hAT elements and their contribution to gene regulation and genomic structural variation. PLANT MOLECULAR BIOLOGY 2016; 91:179-91. [PMID: 26941188 DOI: 10.1007/s11103-016-0454-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 02/08/2016] [Indexed: 06/05/2023]
Abstract
Transposable elements account for approximately 30 % of the Prunus genome; however, their evolutionary origin and functionality remain largely unclear. In this study, we identified a hAT transposon family, termed Moshan, in Prunus. The Moshan elements consist of three types, aMoshan, tMoshan, and mMoshan. The aMoshan and tMoshan types contain intact or truncated transposase genes, respectively, while the mMoshan type is miniature inverted-repeat transposable element (MITE). The Moshan transposons are unique to Rosaceae, and the copy numbers of different Moshan types are significantly correlated. Sequence homology analysis reveals that the mMoshan MITEs are direct deletion derivatives of the tMoshan progenitors, and one kind of mMoshan containing a MuDR-derived fragment were amplified predominately in the peach genome. The mMoshan sequences contain cis-regulatory elements that can enhance gene expression up to 100-fold. The mMoshan MITEs can serve as potential sources of micro and long noncoding RNAs. Whole-genome re-sequencing analysis indicates that mMoshan elements are highly active, and an insertion into S-haplotype-specific F-box gene was reported to cause the breakdown of self-incompatibility in sour cherry. Taken together, all these results suggest that the mMoshan elements play important roles in regulating gene expression and driving genomic structural variation in Prunus.
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Affiliation(s)
- Lu Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Qian Peng
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Jianbo Zhao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Fei Ren
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China
| | - Hui Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Wei Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Liao Liao
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
| | - Albert Owiti
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China
- Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People's Republic of China
| | - Quan Jiang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, A12, Ruiwangfen, Beijing, 100093, People's Republic of China.
| | - Yuepeng Han
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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98
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Zhang H, Tao Z, Hong H, Chen Z, Wu C, Li X, Xiao J, Wang S. Transposon-derived small RNA is responsible for modified function of WRKY45 locus. NATURE PLANTS 2016; 2:16016. [PMID: 27249351 DOI: 10.1038/nplants.2016.16] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/15/2016] [Indexed: 05/20/2023]
Abstract
Transposable elements (TEs) are an important source for generating small interfering RNAs (siRNAs) in plants and animals. Although TE-siRNA-induced silencing of TEs by RNA-directed DNA methylation (RdDM) in the maintenance of genome integrity has been intensively studied, it is unknown whether this type of silencing occurs in suppressing endogenous non-TE genes during host-pathogen interactions. Here we show that a TE-siRNA, TE-siR815, causes opposite functions for the two alleles, WRKY45-1 and WRKY45-2, of the WRKY45 transcription factor in rice resistance to Xanthomonas oryzae pv. oryzae, which causes the most devastating bacterial disease in rice worldwide. Expression of WRKY45-1, but not WRKY45-2, generated TE-siR815, which in turn repressed ST1, an important component in WRKY45-mediated resistance, by RdDM. Suppression of ST1 abolished WRKY45-mediated resistance leading to pathogen susceptibility. These results suggest that TE-siR815 contributes to the natural variation of the WRKY45 locus and TE-siR815-induced suppression of ST1 results in the negative role of WRKY45-1 but positive role of WRKY45-2 in regulating disease resistance.
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Affiliation(s)
- Haitao Zhang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zeng Tao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hanming Hong
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhihui Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Shiping Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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99
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Characterization and Expression of the Lucina pectinata Oxygen and Sulfide Binding Hemoglobin Genes. PLoS One 2016; 11:e0147977. [PMID: 26824233 PMCID: PMC4732748 DOI: 10.1371/journal.pone.0147977] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/30/2022] Open
Abstract
The clam Lucina pectinata lives in sulfide-rich muds and houses intracellular symbiotic bacteria that need to be supplied with hydrogen sulfide and oxygen. This clam possesses three hemoglobins: hemoglobin I (HbI), a sulfide-reactive protein, and hemoglobin II (HbII) and III (HbIII), which are oxygen-reactive. We characterized the complete gene sequence and promoter regions for the oxygen reactive hemoglobins and the partial structure and promoters of the HbI gene from Lucina pectinata. We show that HbI has two mRNA variants, where the 5'end had either a sequence of 96 bp (long variant) or 37 bp (short variant). The gene structure of the oxygen reactive Hbs is defined by having 4-exons/3-introns with conservation of intron location at B12.2 and G7.0 and the presence of pre-coding introns, while the partial gene structure of HbI has the same intron conservation but appears to have a 5-exon/ 4-intron structure. A search for putative transcription factor binding sites (TFBSs) was done with the promoters for HbII, HbIII, HbI short and HbI long. The HbII, HbIII and HbI long promoters showed similar predicted TFBSs. We also characterized MITE-like elements in the HbI and HbII gene promoters and intronic regions that are similar to sequences found in other mollusk genomes. The gene expression levels of the clam Hbs, from sulfide-rich and sulfide-poor environments showed a significant decrease of expression in the symbiont-containing tissue for those clams in a sulfide-poor environment, suggesting that the sulfide concentration may be involved in the regulation of these proteins. Gene expression evaluation of the two HbI mRNA variants indicated that the longer variant is expressed at higher levels than the shorter variant in both environments.
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100
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Ye C, Ji G, Liang C. detectMITE: A novel approach to detect miniature inverted repeat transposable elements in genomes. Sci Rep 2016; 6:19688. [PMID: 26795595 PMCID: PMC4726161 DOI: 10.1038/srep19688] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 12/14/2015] [Indexed: 12/27/2022] Open
Abstract
Miniature inverted repeat transposable elements (MITEs) are prevalent in eukaryotic genomes, including plants and animals. Classified as a type of non-autonomous DNA transposable elements, they play important roles in genome organization and evolution. Comprehensive and accurate genome-wide detection of MITEs in various eukaryotic genomes can improve our understanding of their origins, transposition processes, regulatory mechanisms, and biological relevance with regard to gene structures, expression, and regulation. In this paper, we present a new MATLAB-based program called detectMITE that employs a novel numeric calculation algorithm to replace conventional string matching algorithms in MITE detection, adopts the Lempel-Ziv complexity algorithm to filter out MITE candidates with low complexity, and utilizes the powerful clustering program CD-HIT to cluster similar MITEs into MITE families. Using the rice genome as test data, we found that detectMITE can more accurately, comprehensively, and efficiently detect MITEs on a genome-wide scale than other popular MITE detection tools. Through comparison with the potential MITEs annotated in Repbase, the widely used eukaryotic repeat database, detectMITE has been shown to find known and novel MITEs with a complete structure and full-length copies in the genome. detectMITE is an open source tool (https://sourceforge.net/projects/detectmite).
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Affiliation(s)
- Congting Ye
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.,Department of Biology, Miami University, Oxford, Ohio 45056, USA
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian 361005, China.,Innovation Center for Cell Biology, Xiamen University, Xiamen, Fujian 361102, China
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio 45056, USA
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