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Li J, Wang L, Bible PW, Tu W, Zheng J, Jin P, Liu Y, Du J, Zheng J, Wang YH, Zhan Q. A chromosome-scale genome sequence of sudangrass (Sorghum sudanense) highlights the genome evolution and regulation of dhurrin biosynthesis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:60. [PMID: 36912984 DOI: 10.1007/s00122-023-04262-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
Sudangrass is more similar to US commercial sorghums than to cultivated sorghums from Africa sequence-wise and contain significantly lower dhurrin than sorghums. CYP79A1 is linked to dhurrin content in sorghum. Sudangrass [Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower dhurrin as measured by hydrocyanic acid potential (HCN-p) than cultivated sorghum accessions. Genome-wide association study identified a QTL most tightly associated with HCN-p and the linked SNPs were located in the 3' UTR of Sobic.001G012300 which encodes CYP79A1, the enzyme that catalyzes the first step of dhurrin biosynthesis. As in other grasses such as maize and rice, we also found that copia/gypsy long terminal repeat (LTR) retrotransposons were more abundant in cultivated than in wild sorghums, implying that crop domestication in the grasses was accompanied by increased copia/gypsy LTR retrotransposon insertions in the genomes.
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Affiliation(s)
- Jieqin Li
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Lihua Wang
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Paul W Bible
- College of Arts and Sciences, Department of Mathematics, Marian University, Indianapolis, IN, 46222, USA
| | - Wenmiao Tu
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Jian Zheng
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Peng Jin
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Yanlong Liu
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Junli Du
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Jiacheng Zheng
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China
| | - Yi-Hong Wang
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, 70504, USA.
| | - Qiuwen Zhan
- College of Agriculture, Anhui Science and Technology University, Fengyang, Anhui, China.
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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3
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Arce AL, Mencia R, Cambiagno DA, Lang PL, Liu C, Burbano HA, Weigel D, Manavella PA. Polymorphic inverted repeats near coding genes impact chromatin topology and phenotypic traits in Arabidopsis thaliana. Cell Rep 2023; 42:112029. [PMID: 36689329 DOI: 10.1016/j.celrep.2023.112029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 01/23/2023] Open
Abstract
Transposons are mobile elements that are commonly silenced to protect eukaryotic genome integrity. In plants, transposable element (TE)-derived inverted repeats (IRs) are commonly found near genes, where they affect host gene expression. However, the molecular mechanisms of such regulation are unclear in most cases. Expression of these IRs is associated with production of 24-nt small RNAs, methylation of the IRs, and drastic changes in local 3D chromatin organization. Notably, many of these IRs differ between Arabidopsis thaliana accessions, causing variation in short-range chromatin interactions and gene expression. CRISPR-Cas9-mediated disruption of two IRs leads to a switch in genome topology and gene expression with phenotypic consequences. Our data show that insertion of an IR near a gene provides an anchor point for chromatin interactions that profoundly impact the activity of neighboring loci. This turns IRs into powerful evolutionary agents that can contribute to rapid adaptation.
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Affiliation(s)
- Agustín L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Regina Mencia
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Patricia L Lang
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599 Stuttgart, Germany
| | - Hernán A Burbano
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany; Centre for Life's Origins and Evolution, University College London, London, UK
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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4
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Neyhart JL, Kantar MB, Zalapa J, Vorsa N. Genomic-environmental associations in wild cranberry (Vaccinium macrocarpon Ait.). G3 (BETHESDA, MD.) 2022; 12:jkac203. [PMID: 35944211 PMCID: PMC9526045 DOI: 10.1093/g3journal/jkac203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/01/2022] [Indexed: 06/01/2023]
Abstract
Understanding the genetic basis of local adaptation in natural plant populations, particularly crop wild relatives, may be highly useful for plant breeding. By characterizing genetic variation for adaptation to potentially stressful environmental conditions, breeders can make targeted use of crop wild relatives to develop cultivars for novel or changing environments. This is especially appealing for improving long-lived woody perennial crops such as the American cranberry (Vaccinium macrocarpon Ait.), the cultivation of which is challenged by biotic and abiotic stresses. In this study, we used environmental association analyses in a collection of 111 wild cranberry accessions to identify potentially adaptive genomic regions for a range of bioclimatic and soil conditions. We detected 126 significant associations between SNP marker loci and environmental variables describing temperature, precipitation, and soil attributes. Many of these markers tagged genes with functional annotations strongly suggesting a role in adaptation to biotic or abiotic conditions. Despite relatively low genetic variation in cranberry, our results suggest that local adaptation to divergent environments is indeed present, and the identification of potentially adaptive genetic variation may enable a selective use of this germplasm for breeding more stress-tolerant cultivars.
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Affiliation(s)
- Jeffrey L Neyhart
- USDA, Agricultural Research Service, Genetic Improvement for Fruits & Vegetables Laboratory, Chatsworth, NJ 08019, USA
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA
| | - Juan Zalapa
- USDA, Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Nicholi Vorsa
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
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5
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Tomar S, Subba A, Bala M, Singh AK, Pareek A, Singla-Pareek SL. Genetic Conservation of CBS Domain Containing Protein Family in Oryza Species and Their Association with Abiotic Stress Responses. Int J Mol Sci 2022; 23:ijms23031687. [PMID: 35163610 PMCID: PMC8836131 DOI: 10.3390/ijms23031687] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
Crop Wild Relatives (CWRs) form a comprehensive gene pool that can answer the queries related to plant domestication, speciation, and ecological adaptation. The genus ‘Oryza’ comprises about 27 species, of which two are cultivated, while the remaining are wild. Here, we have attempted to understand the conservation and diversification of the genes encoding Cystathionine β-synthase (CBS) domain-containing proteins (CDCPs) in domesticated and CWRs of rice. Few members of CDCPs were previously identified to be stress-responsive and associated with multiple stress tolerance in rice. Through genome-wide analysis of eleven rice genomes, we identified a total of 36 genes encoding CDCPs in O. longistaminata, 38 in O. glaberrima, 39 each in O. rufipogon, O. glumaepatula, O. brachyantha, O. punctata, and O. sativa subsp. japonica, 40 each in O. barthii and O. meridionalis, 41 in O. nivara, and 42 in O. sativa subsp. indica. Gene duplication analysis as well as non-synonymous and synonymous substitutions in the duplicated gene pairs indicated that this family is shaped majorly by the negative or purifying selection pressure through the long-term evolution process. We identified the presence of two additional hetero-domains, namely TerCH and CoatomerE (specifically in O. sativa subsp. indica), which were not reported previously in plant CDCPs. The in silico expression analysis revealed some of the members to be responsive to various abiotic stresses. Furthermore, the qRT-PCR based analysis identified some members to be highly inducive specifically in salt-tolerant genotype in response to salinity. The cis-regulatory element analysis predicted the presence of numerous stress as well as a few phytohormone-responsive elements in their promoter region. The data presented in this study would be helpful in the characterization of these CDCPs from rice, particularly in relation to abiotic stress tolerance.
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Affiliation(s)
- Surabhi Tomar
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Ashish Subba
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi 834010, India; (M.B.); (A.K.S.)
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India;
- National Agri-Food Biotechnology Institute, Mohali 140306, India
| | - Sneh Lata Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India; (S.T.); (A.S.)
- Correspondence:
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6
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Chang L, Hu M, Ning J, He W, Gao J, Ndjiondjop MN, Fu Y, Liu F, Sun H, Gu P, Sun C, Zhu Z. The genetic control of glabrous glume during African rice domestication. J Genet Genomics 2022; 49:427-436. [DOI: 10.1016/j.jgg.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022]
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7
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Ma T, Wei X, Zhang Y, Li J, Wu F, Yan Q, Yan Z, Zhang Z, Kanzana G, Zhao Y, Yang Y, Zhang J. Development of molecular markers based on LTR retrotransposon in the Cleistogenes songorica genome. J Appl Genet 2021; 63:61-72. [PMID: 34554437 DOI: 10.1007/s13353-021-00658-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 08/09/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) contribute a large fraction of many sequenced plant genomes and play important roles in genomic diversity and phenotypic variations. LTR-RTs are abundantly distributed in plant genomes, facilitating the development of markers based on LTR-RTs for a variety of genotyping purposes. Whole-genome analysis of LTR-RTs was performed in Cleistogenes songorica. A total of 299,079 LTR-RTs were identified and classified as Gypsy type, Copia type, or other type. LTR-RTs were widely distributed in the genome, enriched in the heterochromatic region of the chromosome, and negatively correlated with gene distribution. However, approximately one-fifth of genes were still interrupted by LTR-RTs, and these genes are annotated. Furthermore, four types of primer pairs (PPs) were designed, namely, retrotransposon-based insertion polymorphisms, inter-retrotransposon amplified polymorphisms, insertion site-based polymorphisms, and retrotransposon-microsatellite amplified polymorphisms. A total of 350 PPs were screened in 23 accessions of the genus Cleistogenes, of which 80 PPs showed polymorphism, and 72 PPs showed transferability among Gramineae and non-Gramineae species. In addition, a comparative analysis of homologous LTR-RTs was performed with other related grasses. Taken together, the study will serve as a valuable resource for genotyping applications for C. songorica and related grasses.
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Affiliation(s)
- Tiantian Ma
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Xingyi Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yufei Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jie Li
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Qi Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Gisele Kanzana
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yufeng Zhao
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yingbo Yang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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8
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Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR. Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1195-1214. [PMID: 32920943 DOI: 10.1111/tpj.14988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.
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Affiliation(s)
- Susan M Moenga
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Yunpeng Gai
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Laura M Perilla-Henao
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Douglas R Cook
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
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9
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Fambrini M, Usai G, Vangelisti A, Mascagni F, Pugliesi C. The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 2020; 58:e23399. [DOI: 10.1002/dvg.23399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
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10
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Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020; 11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
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11
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Higo A, Saihara N, Miura F, Higashi Y, Yamada M, Tamaki S, Ito T, Tarutani Y, Sakamoto T, Fujiwara M, Kurata T, Fukao Y, Moritoh S, Terada R, Kinoshita T, Ito T, Kakutani T, Shimamoto K, Tsuji H. DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem. Nat Commun 2020; 11:4079. [PMID: 32796936 PMCID: PMC7429860 DOI: 10.1038/s41467-020-17963-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we show that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also show that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs. The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.
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Affiliation(s)
- Asuka Higo
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Noriko Saihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, Japan
| | - Yoko Higashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Megumi Yamada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Shojiro Tamaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tasuku Ito
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Masayuki Fujiwara
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,YANMAR HOLDINGS Co. Ltd., Chayamachi 1-32, Kita-ku, Osaka, 530-8311, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,EditForce Inc., 4th Fl., Tenjin Fukuoka Seimei Bldg., Tenjin 1-9-17, Fukuoka, 810-0001, Japan
| | - Yoichiro Fukao
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Graduate School of Life Science, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Satoru Moritoh
- National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Rie Terada
- Graduate School of Agriculture, Meijo University, Nagoya, 468-8502, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8602, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Tetsuji Kakutani
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.,Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ko Shimamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan.
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12
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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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13
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Lee H, Chawla HS, Obermeier C, Dreyer F, Abbadi A, Snowdon R. Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:496. [PMID: 32411167 PMCID: PMC7202327 DOI: 10.3389/fpls.2020.00496] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/01/2020] [Indexed: 05/19/2023]
Abstract
Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.
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Affiliation(s)
- HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
- *Correspondence: Rod Snowdon,
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14
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Lee H, Chawla HS, Obermeier C, Dreyer F, Abbadi A, Snowdon R. Chromosome-Scale Assembly of Winter Oilseed Rape Brassica napus. FRONTIERS IN PLANT SCIENCE 2020; 11:496. [PMID: 32411167 DOI: 10.3389/fpls.2020.00496/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/01/2020] [Indexed: 05/21/2023]
Abstract
Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession 'Express 617' using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.
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Affiliation(s)
- HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | | | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
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15
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New clues into the mechanisms of rice domestication. J Biosci 2019. [DOI: 10.1007/s12038-019-9844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Shivaprasad PV. New clues into the mechanisms of rice domestication. J Biosci 2019; 44:28. [PMID: 31180041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Domestication of rice involved incorporation of specific yield-related changes in wild species of rice. This agricultural process has been of significant interest for plant biologists. The recent advance in genomics has provided new tools to investigate the genetic basis and consequences of domestication. Several genes involved in domestication and diversification process have been characterized, and as expected, this list is over-represented by transcription factors and their cofactors. Most often the modification orchestrated expression levels of genes such as those coding for transcription factors. It has been proposed that transcriptional regulators and their regulation is likely a major theme controlling morphological differences between crops and their progenitors. However, recent data indicate that single amino acid changes in genes coding for key proteins as well as epigenetic and small RNA-mediated pathways also contributed towards domesticationassociated phenotypes.
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Affiliation(s)
- Padubidri V Shivaprasad
- National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bengaluru 560 065, India,
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17
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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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18
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Swetha C, Basu D, Pachamuthu K, Tirumalai V, Nair A, Prasad M, Shivaprasad PV. Major Domestication-Related Phenotypes in Indica Rice Are Due to Loss of miRNA-Mediated Laccase Silencing. THE PLANT CELL 2018; 30:2649-2662. [PMID: 30341147 PMCID: PMC6305975 DOI: 10.1105/tpc.18.00472] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/11/2018] [Accepted: 10/15/2018] [Indexed: 05/20/2023]
Abstract
Domestication of rice (Oryza sativa) included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key proteins such as enzymes. Here, we show that multiple yield-related traits associated with indica rice domestication are linked to micro (mi) RNA-mediated regulation. Analysis of small (s) RNA data sets from cultivated indica rice lines, a few landraces, and two wild relatives of rice revealed the presence of abundant 22-nucleotide (nt) reads in wild relatives that mapped to miR397 precursors. miR397 was expressed at very high levels in wild relatives and at negligible levels in high-yielding cultivated lines. In its genera-specific form of 22-nt, miR397 targeted mRNAs encoding laccases that decayed and induced robust secondary cascade silencing in wild species that required RNA-dependent RNA polymerase 6. In wild species of rice, reduced expression of laccases resulted in low lignification. As expected, overexpression of miR397 induced de-domestication phenotypes. At least 26 uncharacterized QTLs previously implicated in rice yield overlapped with laccases and miR397 genes. These results suggest that miRNAs contribute to rice domestication-associated phenotypes.
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Affiliation(s)
- Chenna Swetha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Debjani Basu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Varsha Tirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Ashwin Nair
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
- SASTRA University, Thirumalaisamudram, Thanjavur, 613401, India
| | - Melvin Prasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
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19
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Dubin MJ, Mittelsten Scheid O, Becker C. Transposons: a blessing curse. CURRENT OPINION IN PLANT BIOLOGY 2018; 42:23-29. [PMID: 29453028 DOI: 10.1016/j.pbi.2018.01.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 05/18/2023]
Abstract
The genomes of most plant species are dominated by transposable elements (TEs). Once considered as 'junk DNA', TEs are now known to have a major role in driving genome evolution. Over the last decade, it has become apparent that some stress conditions and other environmental stimuli can drive bursts of activity of certain TE families and consequently new TE insertions. These can give rise to altered gene expression patterns and phenotypes, with new TE insertions sometimes causing flanking genes to become transcriptionally responsive to the same stress conditions that activated the TE in the first place. Such connections between TE-mediated increases in diversity and an accelerated rate of genome evolution provide powerful mechanisms for plants to adapt more rapidly to new environmental conditions. This review will focus on environmentally induced transposition, the mechanisms by which it alters gene expression, and the consequences for plant genome evolution and breeding.
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Affiliation(s)
- Manu J Dubin
- Université de Lille CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France.
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria.
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20
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Haritha G, Malathi S, Divya B, Swamy BPM, Mangrauthia SK, Sarla N. Oryza nivara Sharma et Shastry. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-71997-9_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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