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Hu J, Wang J, Muhammad T, Tuerdiyusufu D, Yang T, Li N, Yang H, Wang B, Yu Q. Functional analysis of fasciclin-like arabinogalactan in carotenoid synthesis during tomato fruit ripening. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108589. [PMID: 38593485 DOI: 10.1016/j.plaphy.2024.108589] [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: 01/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024]
Abstract
Carotenoids are important pigmented nutrients synthesized by tomato fruits during ripening. To reveal the molecular mechanism underlying carotenoid synthesis during tomato fruit ripening, we analyzed carotenoid metabolites and transcriptomes in six development stages of tomato fruits. A total of thirty different carotenoids were detected and quantified in tomato fruits from 10 to 60 DPA. Based on differential gene expression profiles and WGCNA, we explored several genes that were highly significant and negatively correlated with lycopene, all of which encode fasciclin-like arabinogalactan proteins (FLAs). The FLAs are involved in plant signal transduction, however the functional role of these proteins has not been studied in tomato. Genome-wide analysis revealed that cultivated and wild tomato species contained 18 to 22 FLA family members, clustered into four groups, and mainly evolved by means of segmental duplication. The functional characterization of FLAs showed that silencing of SlFLA1, 5, and 13 were found to contribute to the early coloration of tomato fruits, and the expression of carotenoid synthesis-related genes was up-regulated in fruits that changed phenotypically, especially in SlFLA13-silenced plants. Furthermore, the content of multiple carotenoids (including (E/Z)-phytoene, lycopene, γ-carotene, and α-carotene) was significantly increased in SlFLA13-silenced fruits, suggesting that SlFLA13 has a potential inhibitory function in regulating carotenoid synthesis in tomato fruits. The results of the present study broaden the idea of analyzing the biological functions of tomato FLAs and preliminary evidence for the inhibitory role of SlFLA13 in carotenoid synthesis in fruit, providing the theoretical basis and a candidate for improving tomato fruit quality.
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Affiliation(s)
- Jiahui Hu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Juan Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Tayeb Muhammad
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Diliaremu Tuerdiyusufu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Computer and Information Engineering, Xinjiang Agricultural University, Urumqi, China
| | - Tao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Ning Li
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Haitao Yang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China
| | - Baike Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China.
| | - Qinghui Yu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences (Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables), Urumqi, China; College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
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Nkurikiyimfura O, Waheed A, Fang H, Yuan X, Chen L, Wang YP, Lu G, Zhan J, Yang L. Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene. BMC Ecol Evol 2024; 24:36. [PMID: 38494489 PMCID: PMC10946160 DOI: 10.1186/s12862-024-02223-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. RESULTS We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. CONCLUSION Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.
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Affiliation(s)
- Oswald Nkurikiyimfura
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Abdul Waheed
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hanmei Fang
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoxian Yuan
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixia Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, 611130, China
| | - Guodong Lu
- Department of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
| | - Lina Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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Cheng H, Zhang H, Song J, Jiang J, Chen S, Chen F, Wang L. GERDH: an interactive multi-omics database for cross-species data mining in horticultural crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1018-1029. [PMID: 37310261 DOI: 10.1111/tpj.16350] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/07/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023]
Abstract
Horticultural plants contribute immensely to the quality of human's life. The rapid development of omics studies on horticultural plants has resulted in large volumes of valuable growth- and development-related data. Genes that are essential for growth and development are highly conserved in evolution. Cross-species data mining reduces the impact of species heterogeneity and has been extensively used for conserved gene identification. Owing to the lack of a comprehensive database for cross-species data mining using multi-omics data from all horticultural plant species, the current resources in this field are far from satisfactory. Here, we introduce GERDH (https://dphdatabase.com), a database platform for cross-species data mining among horticultural plants, based on 12 961 uniformly processed publicly available omics libraries from more than 150 horticultural plant accessions, including fruits, vegetables and ornamental plants. Important and conserved genes that are essential for a specific biological process can be obtained by cross-species analysis module with interactive web-based data analysis and visualization. Moreover, GERDH is equipped with seven online analysis tools, including gene expression, in-species analysis, epigenetic regulation, gene co-expression, enrichment/pathway and phylogenetic analysis. By interactive cross-species analysis, we identified key genes contributing to postharvest storage. By gene expression analysis, we explored new functions of CmEIN3 in flower development, which was validated by transgenic chrysanthemum analysis. We believe that GERDH will be a useful resource for key gene identification and will allow for omics big data to be more available and accessible to horticultural plant community members.
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Affiliation(s)
- Hua Cheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hua Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jing Song
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Likai Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Flower Biology and Germplasm Innovation, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, Nanjing Agricultural University, Nanjing, 210095, China
- Zhongshan Biological Breeding Laboratory, No.50 Zhongling Street, Nanjing, 210014, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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Vuruputoor VS, Monyak D, Fetter KC, Webster C, Bhattarai A, Shrestha B, Zaman S, Bennett J, McEvoy SL, Caballero M, Wegrzyn JL. Welcome to the big leaves: Best practices for improving genome annotation in non-model plant genomes. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11533. [PMID: 37601314 PMCID: PMC10439824 DOI: 10.1002/aps3.11533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 08/22/2023]
Abstract
Premise Robust standards to evaluate quality and completeness are lacking in eukaryotic structural genome annotation, as genome annotation software is developed using model organisms and typically lacks benchmarking to comprehensively evaluate the quality and accuracy of the final predictions. The annotation of plant genomes is particularly challenging due to their large sizes, abundant transposable elements, and variable ploidies. This study investigates the impact of genome quality, complexity, sequence read input, and method on protein-coding gene predictions. Methods The impact of repeat masking, long-read and short-read inputs, and de novo and genome-guided protein evidence was examined in the context of the popular BRAKER and MAKER workflows for five plant genomes. The annotations were benchmarked for structural traits and sequence similarity. Results Benchmarks that reflect gene structures, reciprocal similarity search alignments, and mono-exonic/multi-exonic gene counts provide a more complete view of annotation accuracy. Transcripts derived from RNA-read alignments alone are not sufficient for genome annotation. Gene prediction workflows that combine evidence-based and ab initio approaches are recommended, and a combination of short and long reads can improve genome annotation. Adding protein evidence from de novo assemblies, genome-guided transcriptome assemblies, or full-length proteins from OrthoDB generates more putative false positives as implemented in the current workflows. Post-processing with functional and structural filters is highly recommended. Discussion While the annotation of non-model plant genomes remains complex, this study provides recommendations for inputs and methodological approaches. We discuss a set of best practices to generate an optimal plant genome annotation and present a more robust set of metrics to evaluate the resulting predictions.
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Affiliation(s)
- Vidya S. Vuruputoor
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Daniel Monyak
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Karl C. Fetter
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Cynthia Webster
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Bikash Shrestha
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Jeremy Bennett
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Susan L. McEvoy
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Madison Caballero
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
| | - Jill L. Wegrzyn
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269USA
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5
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Koh SWH, Diaz-Ardila HN, Bascom CS, Berenguer E, Ingram G, Estelle M, Hardtke CS. Heterologous expression of a lycophyte protein enhances angiosperm seedling vigor. Development 2022; 149:dev200917. [PMID: 36196593 PMCID: PMC10655917 DOI: 10.1242/dev.200917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/26/2022] [Indexed: 03/15/2023]
Abstract
Seedling vigor is a key agronomic trait that determines juvenile plant performance. Angiosperm seeds develop inside fruits and are connected to the mother plant through vascular tissues. Their formation requires plant-specific genes, such as BREVIS RADIX (BRX) in Arabidopsis thaliana roots. BRX family proteins are found throughout the euphyllophytes but also occur in non-vascular bryophytes and non-seed lycophytes. They consist of four conserved domains, including the tandem BRX domains. We found that bryophyte or lycophyte BRX homologs can only partially substitute for Arabidopsis BRX (AtBRX) because they miss key features in the linker between the BRX domains. Intriguingly, however, expression of a BRX homolog from the lycophyte Selaginella moellendorffii (SmBRX) in an A. thaliana wild-type background confers robustly enhanced root growth vigor that persists throughout the life cycle. This effect can be traced to a substantial increase in seed and embryo size, is associated with enhanced vascular tissue proliferation, and can be reproduced with a modified, SmBRX-like variant of AtBRX. Our results thus suggest that BRX variants can boost seedling vigor and shed light on the activity of ancient, non-angiosperm BRX family proteins.
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Affiliation(s)
- Samuel W. H. Koh
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Carlisle S. Bascom
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Eduardo Berenguer
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, 69364 Lyon, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, 69364 Lyon, France
| | - Mark Estelle
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Christian S. Hardtke
- Department of Plant Molecular Biology, University of Lausanne, CH-1015 Lausanne, Switzerland
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6
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Rinkert A, Misiewicz TM, Carter BE, Salmaan A, Whittall JB. Bird nests as botanical time capsules: DNA barcoding identifies the contents of contemporary and historical nests. PLoS One 2021; 16:e0257624. [PMID: 34614003 PMCID: PMC8494352 DOI: 10.1371/journal.pone.0257624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/06/2021] [Indexed: 11/18/2022] Open
Abstract
Bird nests in natural history collections are an abundant yet vastly underutilized source of genetic information. We sequenced the nuclear ribosomal internal transcribed spacer to identify plant species used as nest material in two contemporary (2003 and 2018) and two historical (both 1915) nest specimens constructed by Song Sparrows (Melospiza melodia) and Savannah Sparrows (Passerculus sandwichensis). A total of 13 (22%) samples yielded single, strong bands that could be identified using GenBank resources: six plants (Angiospermae), six green algae (Chlorophyta), and one ciliate (Ciliophora). Two native plant species identified in the nests included Festuca microstachys, which was introduced to the nest collection site by restoration practitioners, and Rosa californica, identified in a nest collected from a lost habitat that existed about 100 years ago. Successful sequencing was correlated with higher sample mass and DNA quality, suggesting future studies should select larger pieces of contiguous material from nests and materials that appear to have been fresh when incorporated into the nest. This molecular approach was used to distinguish plant species that were not visually identifiable, and did not require disassembling the nest specimens as is a traditional practice with nest material studies. The many thousands of nest specimens in natural history collections hold great promise as sources of genetic information to address myriad ecological questions.
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Affiliation(s)
- Alex Rinkert
- Department of Biological Sciences, San José State University, San José, CA, United States of America
- * E-mail:
| | - Tracy M. Misiewicz
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States of America
| | - Benjamin E. Carter
- Department of Biological Sciences, San José State University, San José, CA, United States of America
| | - Aleezah Salmaan
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
| | - Justen B. Whittall
- Department of Biology, Santa Clara University, Santa Clara, CA, United States of America
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Stuttmann J, Barthel K, Martin P, Ordon J, Erickson JL, Herr R, Ferik F, Kretschmer C, Berner T, Keilwagen J, Marillonnet S, Bonas U. Highly efficient multiplex editing: one-shot generation of 8× Nicotiana benthamiana and 12× Arabidopsis mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:8-22. [PMID: 33577114 DOI: 10.1111/tpj.15197] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Genome editing by RNA-guided nucleases, such as SpCas9, has been used in numerous different plant species. However, to what extent multiple independent loci can be targeted simultaneously by multiplexing has not been well documented. Here, we developed a toolkit, based on a highly intron-optimized zCas9i gene, which allows assembly of nuclease constructs expressing up to 32 single guide RNAs (sgRNAs). We used this toolkit to explore the limits of multiplexing in two major model species, and report on the isolation of transgene-free octuple (8×) Nicotiana benthamiana and duodecuple (12×) Arabidopsis thaliana mutant lines in a single generation (T1 and T2 , respectively). We developed novel counter-selection markers for N. benthamiana, most importantly Sl-FAST2, comparable to the well-established Arabidopsis seed fluorescence marker, and FCY-UPP, based on the production of toxic 5-fluorouracil in the presence of a precursor. Targeting eight genes with an array of nine different sgRNAs and relying on FCY-UPP for selection of non-transgenic T1 , we identified N. benthamiana mutant lines with astonishingly high efficiencies: All analyzed plants carried mutations in all genes (approximately 112/116 target sites edited). Furthermore, we targeted 12 genes by an array of 24 sgRNAs in A. thaliana. Efficiency was significantly lower in A. thaliana, and our results indicate Cas9 availability is the limiting factor in such higher-order multiplexing applications. We identified a duodecuple mutant line by a combination of phenotypic screening and amplicon sequencing. The resources and results presented provide new perspectives for how multiplexing can be used to generate complex genotypes or to functionally interrogate groups of candidate genes.
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Affiliation(s)
- Johannes Stuttmann
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Karen Barthel
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Patrick Martin
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jana Ordon
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Jessica L Erickson
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Rosalie Herr
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Filiz Ferik
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Carola Kretschmer
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
| | - Thomas Berner
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), 06120, Germany
| | - Ulla Bonas
- Department of Plant Genetics, Institute for Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, Halle (Saale), 06120, Germany
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Ruduś I, Cembrowska-Lech D, Jaworska A, Kępczyński J. Involvement of ethylene biosynthesis and perception during germination of dormant Avena fatua L. caryopses induced by KAR 1 or GA 3. PLANTA 2019; 249:719-738. [PMID: 30370496 DOI: 10.1007/s00425-018-3032-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/19/2018] [Indexed: 05/07/2023]
Abstract
Germination of primary dormant wild oat caused by KAR1 or GA3 is associated with ACC accumulation and increased ethylene production shortly before radicle protrusion as a result of the non-transcriptional and transcriptional activation of ACS and ACO enzymes, respectively. Response to both compounds involves the modulation of ethylene sensitivity through ethylene receptor genes. Harvested Avena fatua caryopses are primary dormant and, therefore, germinated poorly at 20 °C. Karrikin 1 (KAR1), which action probably requires endogenous gibberellins (GAs), and gibberellin A3 (GA3) was found to induce dormant caryopses to germinate. The stimulatory effects were accompanied by the activation of the ethylene biosynthesis pathway and depended on undisturbed ethylene perception. KAR1 and GA3 promoted 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation during coleorhizae emergence and ethylene production shortly prior to the radicle protrusion, which resulted from the enhanced activity of two ethylene biosynthesis enzymes, ACC synthase (ACS) and ACC oxidase (ACO). The inhibitor of ACS adversely affected beneficial impacts of both KAR1 and GA3 on A. fatua caryopses germination, while the inhibitor of ACO more efficiently impeded the GA3 effect. The inhibitors of ethylene action markedly lowered germination in response to KAR1 and GA3. Gene expression studies preceded by the identification of several genes related to ethylene biosynthesis (AfACS6, AfACO1, and AfACO5) and perception (AfERS1b, AfERS1c, AfERS2, AfETR2, AfETR3, and AfETR4) provided further evidence for the engagement of ethylene in KAR1 and GA3 induced germination of A. fatua caryopses. Both AfACO1 and AfACO5 were upregulated, whereas AfACS6 remained unaffected by the treatment. This suggests the existence of different regulatory mechanisms of enzymatic activity, transcriptional for ACO and non-transcriptional for ACS. During imbibition in water, AfERS1b was stronger expressed than other receptor genes. In the presence of KAR1 or GA3, the expression of AfETR3 was substantially induced. Differential expression of ethylene receptor genes implies the modulation of caryopses sensitivity adjusted to ethylene availability and suggests the functional diversification of individual receptors.
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Affiliation(s)
- Izabela Ruduś
- Department of Plant Physiology and Genetic Engineering, Faculty of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Department of Plant Physiology and Genetic Engineering, Faculty of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Anna Jaworska
- Department of Plant Physiology and Genetic Engineering, Faculty of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Jan Kępczyński
- Department of Plant Physiology and Genetic Engineering, Faculty of Biology, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
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Pal T, Padhan JK, Kumar P, Sood H, Chauhan RS. Comparative transcriptomics uncovers differences in photoautotrophic versus photoheterotrophic modes of nutrition in relation to secondary metabolites biosynthesis in Swertia chirayita. Mol Biol Rep 2018; 45:77-98. [PMID: 29349608 DOI: 10.1007/s11033-017-4135-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/12/2017] [Indexed: 12/13/2022]
Abstract
Swertia chirayita is a high-value medicinal herb exhibiting antidiabetic, hepatoprotective, anticancer, antiediematogenic and antipyretic properties. Scarcity of its plant material has necessitated in vitro production of therapeutic metabolites; however, their yields were low compared to field grown plants. Possible reasons for this could be differences in physiological and biochemical processes between plants grown in photoautotrophic versus photoheterotrophic modes of nutrition. Comparative transcriptomes of S. chirayita were generated to decipher the crucial molecular components associated with the secondary metabolites biosynthesis. Illumina HiSeq sequencing yielded 57,460 and 43,702 transcripts for green house grown (SCFG) and tissue cultured (SCTC) plants, respectively. Biological role analysis (GO and COG assignments) revealed major differences in SCFG and SCTC transcriptomes. KEGG orthology mapped 351 and 341 transcripts onto secondary metabolites biosynthesis pathways for SCFG and SCTC transcriptomes, respectively. Nineteen out of 30 genes from primary metabolism showed higher in silico expression (FPKM) in SCFG versus SCTC, possibly indicating their involvement in regulating the central carbon pool. In silico data were validated by RT-qPCR using a set of 16 genes, wherein 10 genes showed similar expression pattern across both the methods. Comparative transcriptomes identified differentially expressed transcription factors and ABC-type transporters putatively associated with secondary metabolism in S. chirayita. Additionally, functional classification was performed using NCBI Biosystems database. This study identified the molecular components implicated in differential modes of nutrition (photoautotrophic vs. photoheterotrophic) in relation to secondary metabolites production in S. chirayita.
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Affiliation(s)
- Tarun Pal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Jibesh Kumar Padhan
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Pawan Kumar
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Hemant Sood
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, 173234, India
| | - Rajinder S Chauhan
- Department of Biotechnology, Bennett University, a Times Group Initiative, Plot No 8-11, TechZone II, Greater Noida, Uttar Pradesh, 201310, India.
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Maphosa MN, Steenkamp ET, Wingfield BD. Genome-Based Selection and Characterization of Fusarium circinatum-Specific Sequences. G3 (BETHESDA, MD.) 2016; 6:631-9. [PMID: 26888868 PMCID: PMC4777126 DOI: 10.1534/g3.115.025817] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 01/01/2016] [Indexed: 12/20/2022]
Abstract
Fusarium circinatum is an important pathogen of pine trees and its management in the commercial forestry environment relies largely on early detection, particularly in seedling nurseries. The fact that the entire genome of this pathogen is available opens new avenues for the development of diagnostic tools for this fungus. In this study we identified open reading frames (ORFs) unique to F. circinatum and determined that they were specific to the pathogen. The ORF identification process involved bioinformatics-based screening of all the putative F. circinatum ORFs against public databases. This was followed by functional characterization of ORFs found to be unique to F. circinatum. We used PCR- and hybridization-based approaches to confirm the presence of selected unique genes in different strains of F. circinatum and their absence from other Fusarium species for which genome sequence data are not yet available. These included species that are closely related to F. circinatum as well as those that are commonly encountered in the forestry environment. Thirty-six ORFs were identified as potentially unique to F. circinatum. Nineteen of these encode proteins with known domains while the other 17 encode proteins of unknown function. The results of our PCR analyses and hybridization assays showed that three of the selected genes were present in all of the strains of F. circinatum tested and absent from the other Fusarium species screened. These data thus indicate that the selected genes are common and unique to F. circinatum. These genes thus could be good candidates for use in rapid, in-the-field diagnostic assays specific to F. circinatum. Our study further demonstrates how genome sequence information can be mined for the identification of new diagnostic markers for the detection of plant pathogens.
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Affiliation(s)
- Mkhululi N Maphosa
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, 0028 South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, 0028 South Africa
| | - Brenda D Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, 0028 South Africa
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Li Z, Defoort J, Tasdighian S, Maere S, Van de Peer Y, De Smet R. Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. THE PLANT CELL 2016; 28:326-44. [PMID: 26744215 PMCID: PMC4790876 DOI: 10.1105/tpc.15.00877] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/04/2016] [Indexed: 05/02/2023]
Abstract
Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes.
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Affiliation(s)
- Zhen Li
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Jonas Defoort
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Setareh Tasdighian
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Steven Maere
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Riet De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, B-9052 Ghent, Belgium
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Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Sci Rep 2015; 5:11600. [PMID: 26111882 PMCID: PMC4481378 DOI: 10.1038/srep11600] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/26/2015] [Indexed: 11/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.
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Li Q, Yu H, Cao PB, Fawal N, Mathé C, Azar S, Cassan-Wang H, Myburg AA, Grima-Pettenati J, Marque C, Teulières C, Dunand C. Explosive tandem and segmental duplications of multigenic families in Eucalyptus grandis. Genome Biol Evol 2015; 7:1068-81. [PMID: 25769696 PMCID: PMC4419795 DOI: 10.1093/gbe/evv048] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Plant organisms contain a large number of genes belonging to numerous multigenic families whose evolution size reflects some functional constraints. Sequences from eight multigenic families, involved in biotic and abiotic responses, have been analyzed in Eucalyptus grandis and compared with Arabidopsis thaliana. Two transcription factor families APETALA 2 (AP2)/ethylene responsive factor and GRAS, two auxin transporter families PIN-FORMED and AUX/LAX, two oxidoreductase families (ascorbate peroxidases [APx] and Class III peroxidases [CIII Prx]), and two families of protective molecules late embryogenesis abundant (LEA) and DNAj were annotated in expert and exhaustive manner. Many recent tandem duplications leading to the emergence of species-specific gene clusters and the explosion of the gene numbers have been observed for the AP2, GRAS, LEA, PIN, and CIII Prx in E. grandis, while the APx, the AUX/LAX and DNAj are conserved between species. Although no direct evidence has yet demonstrated the roles of these recent duplicated genes observed in E. grandis, this could indicate their putative implications in the morphological and physiological characteristics of E. grandis, and be the key factor for the survival of this nondormant species. Global analysis of key families would be a good criterion to evaluate the capabilities of some organisms to adapt to environmental variations.
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Affiliation(s)
- Qiang Li
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Hong Yu
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Phi Bang Cao
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Nizar Fawal
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Catherine Mathé
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Sahar Azar
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa Genomics Research Institute (GRI), University of Pretoria, South Africa
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Christiane Marque
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Chantal Teulières
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, UPS, UMR 5546, Université de Toulouse, Castanet-Tolosan, France CNRS, UMR 5546, Castanet-Tolosan, France
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De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol 2015; 7:1002-15. [PMID: 25747252 PMCID: PMC4419791 DOI: 10.1093/gbe/evv044] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
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Affiliation(s)
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Genomics Research Institute, University of Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Sweden Umeå Plant Science Centre, Umeå, Sweden
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15
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Gene expression profiling for seed protein and oil synthesis during early seed development in soybean. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0269-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Rühle T, Leister D. Photosystem II Assembly from Scratch. FRONTIERS IN PLANT SCIENCE 2015; 6:1234. [PMID: 26793213 PMCID: PMC4709462 DOI: 10.3389/fpls.2015.01234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/19/2015] [Indexed: 05/06/2023]
Affiliation(s)
- Thilo Rühle
- Plant Molecular Biology, Department of Biology, Ludwig-Maximilians-University MunichMunich, Germany
| | - Dario Leister
- Plant Molecular Biology, Department of Biology, Ludwig-Maximilians-University MunichMunich, Germany
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of CopenhagenCopenhagen, Denmark
- *Correspondence: Dario Leister
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18
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Huep G, Kleinboelting N, Weisshaar B. An easy-to-use primer design tool to address paralogous loci and T-DNA insertion sites in the genome of Arabidopsis thaliana. PLANT METHODS 2014; 10:28. [PMID: 25324895 PMCID: PMC4169229 DOI: 10.1186/1746-4811-10-28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 09/09/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND More than 90% of the Arabidopsis thaliana genes are members of multigene families. DNA sequence similarities present in such related genes can cause trouble, e.g. when molecularly analysing mutant alleles of these genes. Also, flanking-sequence-tag (FST) based predictions of T-DNA insertion positions are often located within paralogous regions of the genome. In such cases, the prediction of the correct insertion site must include careful sequence analyses on the one hand and a paralog specific primer design for experimental confirmation of the prediction on the other hand. RESULTS GABI-Kat is a large A. thaliana insertion line resource, which uses in-house confirmation to provide highly reliable access to T-DNA insertion alleles. To offer trustworthy mutant alleles of paralogous loci, we considered multiple insertion site predictions for single FSTs and implemented this 1-to-N relation in our database. The resulting paralogous predictions were addressed experimentally and the correct insertion locus was identified in most cases, including cases in which there were multiple predictions with identical prediction scores. A newly developed primer design tool that takes paralogous regions into account was developed to streamline the confirmation process for paralogs. The tool is suitable for all parts of the genome and is freely available at the GABI-Kat website. Although the tool was initially designed for the analysis of T-DNA insertion mutants, it can be used for any experiment that requires locus-specific primers for the A. thaliana genome. It is easy to use and also able to design amplimers with two genome-specific primers as required for genotyping segregating families of insertion mutants when looking for homozygous offspring. CONCLUSIONS The paralog-aware confirmation process significantly improved the reliability of the insertion site assignment when paralogous regions of the genome were affected. An automatic online primer design tool that incorporates experience from the in-house confirmation of T-DNA insertion lines has been made available. It provides easy access to primers for the analysis of T-DNA insertion alleles, but it is also beneficial for other applications as well.
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Affiliation(s)
- Gunnar Huep
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Nils Kleinboelting
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
| | - Bernd Weisshaar
- Center for Biotechnology & Department of Biology, Bielefeld University, Universitaetsstrasse 25, D-33615 Bielefeld, Germany
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Busi MV, Gomez-Casati DF, Martín M, Barchiesi J, Grisolía MJ, Hedín N, Carrillo JB. Starch Metabolism in Green Plants. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_78-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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20
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Cupp JD, Nielsen BL. Arabidopsis thaliana organellar DNA polymerase IB mutants exhibit reduced mtDNA levels with a decrease in mitochondrial area density. PHYSIOLOGIA PLANTARUM 2013; 149:91-103. [PMID: 23167278 DOI: 10.1111/ppl.12009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 05/04/2023]
Abstract
Plant organelle genomes are complex and the mechanisms for their replication and maintenance remain unclear. Arabidopsis thaliana has two DNA polymerase genes, DNA polymerase IA (polIA) and polIB, that are dual targeted to mitochondria and chloroplasts and are differentially expressed in primary plant tissues. PolIB gene expression occurs at higher levels in tissues not primary for photosynthesis. Arabidopsis T-DNA polIB mutants have a 30% reduction in relative mitochondrial DNA (mtDNA) levels, but also exhibit a 70% increase in polIA gene expression. The polIB mutant shows an increase in mitochondrial numbers but a significant decrease in mitochondrial area density within the hypocotyl epidermis, shoot apex and root tips. Chloroplast numbers are not significantly different in mesophyll protoplasts. These mutants do not have a significant difference in total dark mitorespiration levels but exhibit a difference in light respiration levels and photosynthesis capacity. Organelle-encoded genes for components of respiration and photosynthesis are upregulated in polIB mutants. The mutants exhibited slow growth in conjunction with a decreased rate of cell expansion and other secondary phenotypic effects. Evidence suggests that early plastid development and DNA levels are directly affected by a polIB mutation but are resolved to wild-type levels over time. However, mitochondria numbers and DNA levels never reach wild-type levels in the polIB mutant. We propose that both polIA and polIB are required for mtDNA replication. The results suggest that polIB mutants undergo an adjustment in cell homeostasis, enabling them to maintain functional mitochondria at the cost of normal cell expansion and plant growth.
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Affiliation(s)
- John D Cupp
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
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Bolle C, Huep G, Kleinbölting N, Haberer G, Mayer K, Leister D, Weisshaar B. GABI-DUPLO: a collection of double mutants to overcome genetic redundancy in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:157-171. [PMID: 23573814 DOI: 10.1111/tpj.12197] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 03/28/2013] [Accepted: 04/04/2013] [Indexed: 05/08/2023]
Abstract
Owing to duplication events in its progenitor, more than 90% of the genes in the Arabidopsis thaliana genome are members of multigene families. A set of 2108 gene families, each consisting of precisely two unlinked paralogous genes, was identified in the nuclear genome of A. thaliana on the basis of sequence similarity. A systematic method for the creation of double knock-out lines for such gene pairs, designated as DUPLO lines, was established and 200 lines are now publicly available. Their initial phenotypic characterisation led to the identification of seven lines with defects that emerge only in the adult stage. A further six lines display seedling lethality and 23 lines were lethal before germination. Another 14 lines are known to show phenotypes under non-standard conditions or at the molecular level. Knock-out of gene pairs with very similar coding sequences or expression profiles is more likely to produce a mutant phenotype than inactivation of gene pairs with dissimilar profiles or sequences. High coding sequence similarity and highly similar expression profiles are only weakly correlated, implying that promoter and coding regions of these gene pairs display different degrees of diversification.
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Affiliation(s)
- Cordelia Bolle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Gunnar Huep
- Genome Research, Department of Biology, Bielefeld University, 33594, Bielefeld, Germany
| | - Nils Kleinbölting
- Genome Research, Department of Biology, Bielefeld University, 33594, Bielefeld, Germany
| | - Georg Haberer
- MIPS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Klaus Mayer
- MIPS, Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Dario Leister
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152, Planegg-Martinsried, Germany
| | - Bernd Weisshaar
- Genome Research, Department of Biology, Bielefeld University, 33594, Bielefeld, Germany
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22
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Affiliation(s)
- María V. Busi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
- IIB - Universidad Nacional de General San Martín (UNSAM); San Martín Buenos Aires Argentina
| | - Julieta Barchiesi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
| | - Mariana Martín
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
| | - Diego F. Gomez-Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI-CONICET); Universidad Nacional de Rosario; Suipacha Rosario Argentina
- IIB - Universidad Nacional de General San Martín (UNSAM); San Martín Buenos Aires Argentina
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23
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Grau J, Wolf A, Reschke M, Bonas U, Posch S, Boch J. Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol 2013; 9:e1002962. [PMID: 23526890 PMCID: PMC3597551 DOI: 10.1371/journal.pcbi.1002962] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 01/14/2013] [Indexed: 11/19/2022] Open
Abstract
Transcription activator-like (TAL) effectors are injected into host plant cells by Xanthomonas bacteria to function as transcriptional activators for the benefit of the pathogen. The DNA binding domain of TAL effectors is composed of conserved amino acid repeat structures containing repeat-variable diresidues (RVDs) that determine DNA binding specificity. In this paper, we present TALgetter, a new approach for predicting TAL effector target sites based on a statistical model. In contrast to previous approaches, the parameters of TALgetter are estimated from training data computationally. We demonstrate that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite. We study the binding specificities estimated by TALgetter and approve that different RVDs are differently important for transcriptional activation. In subsequent studies, the predictions of TALgetter indicate a previously unreported positional preference of TAL effector target sites relative to the transcription start site. In addition, several TAL effectors are predicted to bind to the TATA-box, which might constitute one general mode of transcriptional activation by TAL effectors. Scrutinizing the predicted target sites of TALgetter, we propose several novel TAL effector virulence targets in rice and sweet orange. TAL-mediated induction of the candidates is supported by gene expression microarrays. Validity of these targets is also supported by functional analogy to known TAL effector targets, by an over-representation of TAL effector targets with similar function, or by a biological function related to pathogen infection. Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors. TALgetter is implemented as part of the open-source Java library Jstacs, and is freely available as a web-application and a command line program.
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Affiliation(s)
- Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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24
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Convergent gene loss following gene and genome duplications creates single-copy families in flowering plants. Proc Natl Acad Sci U S A 2013; 110:2898-903. [PMID: 23382190 DOI: 10.1073/pnas.1300127110] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The importance of gene gain through duplication has long been appreciated. In contrast, the importance of gene loss has only recently attracted attention. Indeed, studies in organisms ranging from plants to worms and humans suggest that duplication of some genes might be better tolerated than that of others. Here we have undertaken a large-scale study to investigate the existence of duplication-resistant genes in the sequenced genomes of 20 flowering plants. We demonstrate that there is a large set of genes that is convergently restored to single-copy status following multiple genome-wide and smaller scale duplication events. We rule out the possibility that such a pattern could be explained by random gene loss only and therefore propose that there is selection pressure to preserve such genes as singletons. This is further substantiated by the observation that angiosperm single-copy genes do not comprise a random fraction of the genome, but instead are often involved in essential housekeeping functions that are highly conserved across all eukaryotes. Furthermore, single-copy genes are generally expressed more highly and in more tissues than non-single-copy genes, and they exhibit higher sequence conservation. Finally, we propose different hypotheses to explain their resistance against duplication.
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25
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Dunand C, Mathé C, Lazzarotto F, Margis R, Margis-Pinheiro M. Ascorbate peroxidase-related (APx-R) is not a duplicable gene. PLANT SIGNALING & BEHAVIOR 2011; 6:1908-13. [PMID: 22231200 PMCID: PMC3337176 DOI: 10.4161/psb.6.12.18098] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Phylogenetic, genomic and functional analyses have allowed the identification of a new class of putative heme peroxidases, so called APx-R (APx-Related). These new class, mainly present in the green lineage (including green algae and land plants), can also be detected in other unicellular chloroplastic organisms. Except for recent polyploid organisms, only single-copy of APx-R gene was detected in each genome, suggesting that the majority of the APx-R extra-copies were lost after chromosomal or segmental duplications. In a similar way, most APx-R co-expressed genes in Arabidopsis genome do not have conserved extra-copies after chromosomal duplications and are predicted to be localized in organelles, as are the APx-R. The member of this gene network can be considered as unique gene, well conserved through the evolution due to a strong negative selection pressure and a low evolution rate.
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Affiliation(s)
- Christophe Dunand
- Université de Toulouse, UPS; UMR 5546, Laboratoire de Recherche en Sciences Végétales, Castanet-Tolosan, France.
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26
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Yue JX, Li J, Wang D, Araki H, Tian D, Yang S. Genome-wide investigation reveals high evolutionary rates in annual model plants. BMC PLANT BIOLOGY 2010; 10:242. [PMID: 21062446 PMCID: PMC3095324 DOI: 10.1186/1471-2229-10-242] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 11/09/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials. RESULTS According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level. CONCLUSIONS The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the mechanism determining the molecular evolutionary rate at the genomic level.
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Affiliation(s)
- Jia-Xing Yue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
- Department of Ecology and Evolutionary Biology, Rice University, Houston, TX 77005, USA
| | - Jinpeng Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
| | - Dan Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
| | - Hitoshi Araki
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, 210093, Nanjing, PR China
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27
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Natural diversity in flowering responses of Arabidopsis thaliana caused by variation in a tandem gene array. Genetics 2010; 186:263-76. [PMID: 20551443 DOI: 10.1534/genetics.110.116392] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tandemly arrayed genes that belong to gene families characterize genomes of many organisms. Gene duplication and subsequent relaxation of selection can lead to the establishment of paralogous cluster members that may evolve along different trajectories. Here, we report on the structural variation in MADS AFFECTING FLOWERING 2 (MAF2) gene, one member of the tandemly duplicated cluster of MADS-box-containing transcription factors in Arabidopsis thaliana. The altered gene structure at the MAF2 locus is present as a moderate-frequency polymorphism in Arabidopsis and leads to the extensive diversity in transcript patterns due to alternative splicing. Rearrangements at the MAF2 locus are associated with an early flowering phenotype in BC(5) lines. The lack of suppression of flowering time in a MAF2-insertion line expressing the MAF2-specific artificial miRNA suggests that these MAF2 variants are behaving as loss-of-function alleles. The variation in gene architecture is also associated with segregation distortion, which may have facilitated the spread and the establishment of the corresponding alleles throughout the Eurasian range of the A. thaliana population.
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28
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Bernard V, Brunaud V, Lecharny A. TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. BMC Genomics 2010; 11:166. [PMID: 20222994 PMCID: PMC2842252 DOI: 10.1186/1471-2164-11-166] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 03/12/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model organisms studied so far have been found to contain either one of these elements. Indeed different core-promoter elements are involved in the recruitment of the TATA-box-binding protein. Here we assessed the possibility of identifying novel functional motifs in plant genes, sharing the TATA-box topological constraints. RESULTS We developed an ab-initio approach considering the preferential location of motifs relative to the TSS. We identified motifs observed at the TATA-box expected location and conserved in both Arabidopsis thaliana and Oryza sativa promoters. We identified TC-elements within non-TA-rich promoters 30 bases upstream of the TSS. As with the TATA-box and TATA-variant sequences, it was possible to construct a unique distance graph with the TC-element sequences. The structural and functional features of TC-element-containing genes were distinct from those of TATA-box- or TATA-variant-containing genes. Arabidopsis thaliana transcriptome analysis revealed that TATA-box-containing genes were generally those showing relatively high levels of expression and that TC-element-containing genes were generally those expressed in specific conditions. CONCLUSIONS Our observations suggest that the TC-elements might constitute a class of novel regulatory elements participating towards the complex modulation of gene expression in plants.
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Affiliation(s)
- Virginie Bernard
- Unité de Recherche en Génomique Végétale (URGV), UMR INRA 1165-CNRS 8114-UEVE, 2 Rue Gaston Crémieux, 91057 Evry Cedex, France
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29
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FIDEL-a retrovirus-like retrotransposon and its distinct evolutionary histories in the A- and B-genome components of cultivated peanut. Chromosome Res 2010; 18:227-46. [PMID: 20127167 PMCID: PMC2844528 DOI: 10.1007/s10577-009-9109-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 12/16/2009] [Indexed: 12/26/2022]
Abstract
In this paper, we describe a Ty3-gypsy retrotransposon from allotetraploid peanut (Arachis hypogaea) and its putative diploid ancestors Arachis duranensis (A-genome) and Arachis ipaënsis (B-genome). The consensus sequence is 11,223 bp. The element, named FIDEL (Fairly long Inter-Dispersed Euchromatic LTR retrotransposon), is more frequent in the A- than in the B-genome, with copy numbers of about 3,000 (±950, A. duranensis), 820 (±480, A. ipaënsis), and 3,900 (±1,500, A. hypogaea) per haploid genome. Phylogenetic analysis of reverse transcriptase sequences showed distinct evolution of FIDEL in the ancestor species. Fluorescent in situ hybridization revealed disperse distribution in euchromatin and absence from centromeres, telomeric regions, and the nucleolar organizer region. Using paired sequences from bacterial artificial chromosomes, we showed that elements appear less likely to insert near conserved ancestral genes than near the fast evolving disease resistance gene homologs. Within the Ty3-gypsy elements, FIDEL is most closely related with the Athila/Calypso group of retrovirus-like retrotransposons. Putative transmembrane domains were identified, supporting the presence of a vestigial envelope gene. The results emphasize the importance of FIDEL in the evolution and divergence of different Arachis genomes and also may serve as an example of the role of retrotransposons in the evolution of legume genomes in general.
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