1
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Mahood EH, Bennett AA, Komatsu K, Kruse LH, Lau V, Rahmati Ishka M, Jiang Y, Bravo A, Louie K, Bowen BP, Harrison MJ, Provart NJ, Vatamaniuk OK, Moghe GD. Information theory and machine learning illuminate large-scale metabolomic responses of Brachypodium distachyon to environmental change. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:463-481. [PMID: 36880270 DOI: 10.1111/tpj.16160] [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: 05/20/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 05/10/2023]
Abstract
Plant responses to environmental change are mediated via changes in cellular metabolomes. However, <5% of signals obtained from liquid chromatography tandem mass spectrometry (LC-MS/MS) can be identified, limiting our understanding of how metabolomes change under biotic/abiotic stress. To address this challenge, we performed untargeted LC-MS/MS of leaves, roots, and other organs of Brachypodium distachyon (Poaceae) under 17 organ-condition combinations, including copper deficiency, heat stress, low phosphate, and arbuscular mycorrhizal symbiosis. We found that both leaf and root metabolomes were significantly affected by the growth medium. Leaf metabolomes were more diverse than root metabolomes, but the latter were more specialized and more responsive to environmental change. We found that 1 week of copper deficiency shielded the root, but not the leaf metabolome, from perturbation due to heat stress. Machine learning (ML)-based analysis annotated approximately 81% of the fragmented peaks versus approximately 6% using spectral matches alone. We performed one of the most extensive validations of ML-based peak annotations in plants using thousands of authentic standards, and analyzed approximately 37% of the annotated peaks based on these assessments. Analyzing responsiveness of each predicted metabolite class to environmental change revealed significant perturbations of glycerophospholipids, sphingolipids, and flavonoids. Co-accumulation analysis further identified condition-specific biomarkers. To make these results accessible, we developed a visualization platform on the Bio-Analytic Resource for Plant Biology website (https://bar.utoronto.ca/efp_brachypodium_metabolites/cgi-bin/efpWeb.cgi), where perturbed metabolite classes can be readily visualized. Overall, our study illustrates how emerging chemoinformatic methods can be applied to reveal novel insights into the dynamic plant metabolome and stress adaptation.
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Affiliation(s)
- Elizabeth H Mahood
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Alexandra A Bennett
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Karyn Komatsu
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Lars H Kruse
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vincent Lau
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Maryam Rahmati Ishka
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Yulin Jiang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | | | - Katherine Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Lawrence Berkeley National Laboratory, Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Nicholas J Provart
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Olena K Vatamaniuk
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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2
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Adamski NM, Simmonds J, Brinton JF, Backhaus AE, Chen Y, Smedley M, Hayta S, Florio T, Crane P, Scott P, Pieri A, Hall O, Barclay JE, Clayton M, Doonan JH, Nibau C, Uauy C. Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. THE PLANT CELL 2021; 33:2296-2319. [PMID: 34009390 PMCID: PMC8364232 DOI: 10.1093/plcell/koab119] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/17/2021] [Indexed: 05/20/2023]
Abstract
Flower development is an important determinant of grain yield in crops. In wheat (Triticum spp.), natural variation for the size of spikelet and floral organs is particularly evident in Triticum turgidum ssp. polonicum (also termed Triticum polonicum), a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), which encodes a MADS-box transcription factor belonging to the SHORT VEGETATIVE PHASE family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence rearrangement in intron-1 that results in ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum subspecies-defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across spikelets and within florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can affect agronomic traits in a dosage-dependent manner in polyploid crops.
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Affiliation(s)
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | | | - Yi Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Mark Smedley
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sadiye Hayta
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Tobin Florio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Pamela Crane
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Peter Scott
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alice Pieri
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Olyvia Hall
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Myles Clayton
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - John H. Doonan
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Candida Nibau
- The National Plant Phenomics Centre, Institute of Biological, Rural and Environmental Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, SY23 3EE, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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3
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Morris CF, Luna J, Caffe-Treml M. The Vromindolines of cv. Hayden oat (Avena sativa L.) – A review of the Poeae and Triticeae indolines and a suggested system for harmonization of nomenclature. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2020.103135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Tu M, Li Y. Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1631. [PMID: 33255282 PMCID: PMC7760206 DOI: 10.3390/plants9121631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/03/2022]
Abstract
Kernel hardness is one of the most important single traits of wheat seed. It classifies wheat cultivars, determines milling quality and affects many end-use qualities. Starch granule surfaces, polar lipids, storage protein matrices and Puroindolines potentially form a four-way interaction that controls wheat kernel hardness. As a genetic factor, Puroindoline polymorphism explains over 60% of the variation in kernel hardness. However, genetic factors other than Puroindolines remain to be exploited. Over the past two decades, efforts using population genetics have been increasing, and numerous kernel hardness-associated quantitative trait loci (QTLs) have been identified on almost every chromosome in wheat. Here, we summarize the state of the art for mapping kernel hardness. We emphasize that these steps in progress have benefitted from (1) the standardized methods for measuring kernel hardness, (2) the use of the appropriate germplasm and mapping population, and (3) the improvements in genotyping methods. Recently, abundant genomic resources have become available in wheat and related Triticeae species, including the high-quality reference genomes and advanced genotyping technologies. Finally, we provide perspectives on future research directions that will enhance our understanding of kernel hardness through the identification of multiple QTLs and will address challenges involved in fine-tuning kernel hardness and, consequently, food properties.
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Affiliation(s)
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA;
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5
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Corona-Gomez JA, Garcia-Lopez IJ, Stadler PF, Fernandez-Valverde SL. Splicing conservation signals in plant long noncoding RNAs. RNA (NEW YORK, N.Y.) 2020; 26:784-793. [PMID: 32241834 PMCID: PMC7297117 DOI: 10.1261/rna.074393.119] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/28/2020] [Indexed: 05/12/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently emerged as prominent regulators of gene expression in eukaryotes. LncRNAs often drive the modification and maintenance of gene activation or gene silencing states via chromatin conformation rearrangements. In plants, lncRNAs have been shown to participate in gene regulation, and are essential to processes such as vernalization and photomorphogenesis. Despite their prominent functions, only over a dozen lncRNAs have been experimentally and functionally characterized. Similar to its animal counterparts, the rates of sequence divergence are much higher in plant lncRNAs than in protein coding mRNAs, making it difficult to identify lncRNA conservation using traditional sequence comparison methods. Beyond this, little is known about the evolutionary patterns of lncRNAs in plants. Here, we characterized the splicing conservation of lncRNAs in Brassicaceae. We generated a whole-genome alignment of 16 Brassica species and used it to identify synthenic lncRNA orthologs. Using a scoring system trained on transcriptomes from A. thaliana and B. oleracea, we identified splice sites across the whole alignment and measured their conservation. Our analysis revealed that 17.9% (112/627) of all intergenic lncRNAs display splicing conservation in at least one exon, an estimate that is substantially higher than previous estimates of lncRNA conservation in this group. Our findings agree with similar studies in vertebrates, demonstrating that splicing conservation can be evidence of stabilizing selection. We provide conclusive evidence for the existence of evolutionary deeply conserved lncRNAs in plants and describe a generally applicable computational workflow to identify functional lncRNAs in plants.
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Affiliation(s)
| | | | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, University Leipzig, D-04107 Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University Leipzig, D-04107 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria
- Facultad de Ciencias, Universidad Nacional de Colombia, 11001 Sede Bogotá, Colombia
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
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6
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Lullien-Pellerin V. Both genetic and environmental conditions affect wheat grain texture: Consequences for grain fractionation and flour properties. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2020.102917] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Li X, Li Y, Yu X, Sun F, Yang G, He G. Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species. Int J Mol Sci 2020; 21:E1304. [PMID: 32075191 PMCID: PMC7072932 DOI: 10.3390/ijms21041304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 01/12/2023] Open
Abstract
Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2's contribution to seed traits in wheat.
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Affiliation(s)
- Xiaoyan Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA;
| | - Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Fusheng Sun
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
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8
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Saccharomyces arboricola and Its Hybrids’ Propensity for Sake Production: Interspecific Hybrids Reveal Increased Fermentation Abilities and a Mosaic Metabolic Profile. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6010014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The use of interspecific hybrids during the industrial fermentation process has been well established, positioning the frontier of advancement in brewing to capitalize on the potential of Saccharomyces hybridization. Interspecific yeast hybrids used in modern monoculture inoculations benefit from a wide range of volatile metabolites that broaden the organoleptic complexity. This is the first report of sake brewing by Saccharomyces arboricola and its hybrids. S. arboricola x S. cerevisiae direct-mating generated cryotolerant interspecific hybrids which increased yields of ethanol and ethyl hexanoate compared to parental strains, important flavor attributes of fine Japanese ginjo sake rice wine. Hierarchical clustering heatmapping with principal component analysis for metabolic profiling was used in finding low levels of endogenous amino/organic acids clustered S. arboricola apart from the S. cerevisiae industrial strains. In sake fermentations, hybrid strains showed a mosaic profile of parental strains, while metabolic analysis suggested S. arboricola had a lower amino acid net uptake than S. cerevisiae. Additionally, this research found an increase in ethanolic fermentation from pyruvate and increased sulfur metabolism. Together, these results suggest S. arboricola is poised for in-depth metabolomic exploration in sake fermentation.
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High Density Single Nucleotide Polymorphism (SNP) Mapping and Quantitative Trait Loci (QTL) Analysis in a Biparental Spring Triticale Population Localized Major and Minor Effect Fusarium Head Blight Resistance and Associated Traits QTL. Genes (Basel) 2018; 9:genes9010019. [PMID: 29304028 PMCID: PMC5793172 DOI: 10.3390/genes9010019] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/19/2017] [Accepted: 12/28/2017] [Indexed: 01/09/2023] Open
Abstract
Triticale (xTriticosecale Wittmack) is an important feed crop which suffers severe yield, grade and end-use quality losses due to Fusarium head blight (FHB). Development of resistant triticale cultivars is hindered by lack of effective genetic resistance sources. To dissect FHB resistance, a doubled haploid spring triticale population produced from the cross TMP16315/AC Ultima using a microspore culture method, was phenotyped for FHB incidence, severity, visual rating index (VRI), deoxynivalenol (DON) and some associated traits (ergot, grain protein content, test weight, yield, plant height and lodging) followed by single nucleotide polymorphism (SNP) genotyping. A high-density map consisting of 5274 SNPs, mapped on all 21 chromosomes with a map density of 0.48 cM/SNP, was constructed. Together, 17 major quantitative trait loci were identified for FHB on chromosomes 1A, 2B, 3A, 4A, 4R, 5A, 5R and 6B; two of incidence loci (on 2B and 5R) also co-located with loci for severity and VRI, and two other loci of VRI (on 1A and 4R) with DON accumulation. Major and minor loci were also identified for all other traits in addition to many epistasis loci. This study provides new insight into the genetic basis of FHB resistance and their association with other traits in triticale.
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Boukid F, Folloni S, Sforza S, Vittadini E, Prandi B. Current Trends in Ancient Grains-Based Foodstuffs: Insights into Nutritional Aspects and Technological Applications. Compr Rev Food Sci Food Saf 2017; 17:123-136. [PMID: 33350067 DOI: 10.1111/1541-4337.12315] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/15/2017] [Accepted: 09/22/2017] [Indexed: 12/18/2022]
Abstract
For centuries, ancient grains fed populations, but due to their low yield, they were abandoned and replaced by high-yielding species. However, currently, there is a renewed interest in ancient wheat and pseudocereal grains from consumers, farmers, and manufacturers. Ancient wheat such as einkorn, emmer, spelt, and Kamut®, are being reintegrated because of their low fertilizer input, high adaptability and important genetic diversity. New trends in pseudocereal products are also emerging, and they are mostly appreciated for their nutritional outcomes, particularly by the gluten-free market. Toward healthier lifestyle, ancient grains-based foodstuffs are a growing business and their industrialization is taking 2 pathways, either as a raw ingredient or a functional ingredient. This paper deals with these grain characteristics by focusing on the compositional profile and the technological potential.
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Affiliation(s)
- Fatma Boukid
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | | | - Stefano Sforza
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Elena Vittadini
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
| | - Barbara Prandi
- Food and Drug Dept., Univ. of Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy
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11
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Kögler A, Schmidt T, Wenke T. Evolutionary modes of emergence of short interspersed nuclear element (SINE) families in grasses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:676-695. [PMID: 28857316 DOI: 10.1111/tpj.13676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Short interspersed nuclear elements (SINEs) are non-autonomous transposable elements which are propagated by retrotransposition and constitute an inherent part of the genome of most eukaryotic species. Knowledge of heterogeneous and highly abundant SINEs is crucial for de novo (or improvement of) annotation of whole genome sequences. We scanned Poaceae genome sequences of six important cereals (Oryza sativa, Triticum aestivum, Hordeum vulgare, Panicum virgatum, Sorghum bicolor, Zea mays) and Brachypodium distachyon to examine the diversity and evolution of SINE populations. We comparatively analyzed the structural features, distribution, evolutionary relation and abundance of 32 SINE families and subfamilies within grasses, comprising 11 052 individual copies. The investigation of activity profiles within the Poaceae provides insights into their species-specific diversification and amplification. We found that Poaceae SINEs (PoaS) fall into two length categories: simple SINEs of up to 180 bp and dimeric SINEs larger than 240 bp. Detailed analysis at the nucleotide level revealed that multimerization of related and unrelated SINE copies is an important evolutionary mechanism of SINE formation. We conclude that PoaS families diversify by massive reshuffling between SINE families, likely caused by insertion of truncated copies, and provide a model for this evolutionary scenario. Twenty-eight of 32 PoaS families and subfamilies show significant conservation, in particular either in the 5' or 3' regions, across Poaceae species and share large sequence stretches with one or more other PoaS families.
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Affiliation(s)
- Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
| | - Torsten Wenke
- Institute of Botany, Technische Universität Dresden, Dresden, 01069, Germany
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12
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Zhang W, Xu J, Bennetzen JL, Messing J. Teff, an Orphan Cereal in the Chloridoideae, Provides Insights into the Evolution of Storage Proteins in Grasses. Genome Biol Evol 2016; 8:1712-21. [PMID: 27190000 PMCID: PMC4943188 DOI: 10.1093/gbe/evw117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Seed storage proteins (SSP) in cereals provide essential nutrition for humans and animals. Genes encoding these proteins have undergone rapid evolution in different grass species. To better understand the degree of divergence, we analyzed this gene family in the subfamily Chloridoideae, where the genome of teff (Eragrostis tef) has been sequenced. We find gene duplications, deletions, and rapid mutations in protein-coding sequences. The main SSPs in teff, like other grasses, are prolamins, here called eragrostins. Teff has γ- and δ-prolamins, but has no β-prolamins. One δ-type prolamin (δ1) in teff has higher methionine (33%) levels than in maize (23–25%). The other δ-type prolamin (δ2) has reduced methionine residues (<10%) and is phylogenetically closer to α prolamins. Prolamin δ2 in teff represents an intermediate between δ and α types that appears to have been lost in maize and other Panicoideae, and was replaced by the expansion of α-prolamins. Teff also has considerably larger numbers of α-prolamin genes, which we further divide into five sub-groups, where α2 and α5 represent the most abundant α-prolamins both in number and in expression. In addition, indolines that determine kernel softness are present in teff and the panicoid cereal called foxtail millet (Setaria italica) but not in sorghum or maize, indicating that these genes were only recently lost in some members of the Panicoideae. Moreover, this study provides not only information on the evolution of SSPs in the grass family but also the importance of α-globulins in protein aggregation and germplasm divergence.
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Affiliation(s)
- Wei Zhang
- Waksman Institute of Microbiology, Rutgers University
| | - Jianhong Xu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, Hangzhou China
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13
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Shaaf S, Sharma R, Baloch FS, Badaeva ED, Knüpffer H, Kilian B, Özkan H. The grain Hardness locus characterized in a diverse wheat panel (Triticum aestivum L.) adapted to the central part of the Fertile Crescent: genetic diversity, haplotype structure, and phylogeny. Mol Genet Genomics 2016; 291:1259-75. [DOI: 10.1007/s00438-016-1180-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 02/03/2016] [Indexed: 12/27/2022]
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Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E. SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. Genome Biol Evol 2015; 7:3286-98. [PMID: 26560340 PMCID: PMC4700967 DOI: 10.1093/gbe/evv219] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The identification of conserved syntenic regions enables discovery of predicted
locations for orthologous and homeologous genes, even when no such gene is present.
This capability means that synteny-based methods are far more effective than sequence
similarity-based methods in identifying true-negatives, a necessity for studying gene
loss and gene transposition. However, the identification of syntenic regions requires
complex analyses which must be repeated for pairwise comparisons between any two
species. Therefore, as the number of published genomes increases, there is a growing
demand for scalable, simple-to-use applications to perform comparative genomic
analyses that cater to both gene family studies and genome-scale studies. We
implemented SynFind, a web-based tool that addresses this need. Given one query
genome, SynFind is capable of identifying conserved syntenic regions in any set of
target genomes. SynFind is capable of reporting per-gene information, useful for
researchers studying specific gene families, as well as genome-wide data sets of
syntenic gene and predicted gene locations, critical for researchers focused on
large-scale genomic analyses. Inference of syntenic homologs provides the basis for
correlation of functional changes around genes of interests between related
organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic
data from over 15,000 organisms from all domains of life as well as supporting
multiple releases of the same organism. SynFind makes use of a powerful job execution
framework that promises scalability and reproducibility. SynFind can be accessed at
http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind
using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
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Affiliation(s)
- Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Matthew D Bomhoff
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Evan Briones
- School of Plant Sciences, iPlant Collaborative, University of Arizona
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln
| | - Eric Lyons
- School of Plant Sciences, iPlant Collaborative, University of Arizona
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Saarela JM, Wysocki WP, Barrett CF, Soreng RJ, Davis JI, Clark LG, Kelchner SA, Pires JC, Edger PP, Mayfield DR, Duvall MR. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes. AOB PLANTS 2015; 7:plv046. [PMID: 25940204 PMCID: PMC4480051 DOI: 10.1093/aobpla/plv046] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/21/2015] [Indexed: 05/08/2023]
Abstract
Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.
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Affiliation(s)
- Jeffery M Saarela
- Botany Section, Research and Collections, Canadian Museum of Nature, PO Box 3443 Stn. D, Ottawa, ON, Canada K1P 3P4
| | - William P Wysocki
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
| | - Craig F Barrett
- Department of Biological Sciences, California State University, 5151 State University Dr., Los Angeles, CA 90032-8201, USA
| | - Robert J Soreng
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012, USA
| | - Jerrold I Davis
- Section of Plant Biology, Cornell University, 412 Mann Library, Ithaca, NY 14853, USA
| | - Lynn G Clark
- Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011-1020, USA
| | - Scot A Kelchner
- Biological Sciences, Idaho State University, 921 S. 8th Ave, Pocatello, ID 83209, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California - Berkeley, Berkeley, CA 94720, USA
| | - Dustin R Mayfield
- Division of Biological Sciences, University of Missouri, 1201 Rollins St, Columbia, MO 65211, USA
| | - Melvin R Duvall
- Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, IL 60115-2861, USA
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16
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Chen G, Zhu J, Zhou J, Subburaj S, Zhang M, Han C, Hao P, Li X, Yan Y. Dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon: comparison with common wheat and Aegilops peregrina. BMC PLANT BIOLOGY 2014; 14:198. [PMID: 25095703 PMCID: PMC4256708 DOI: 10.1186/s12870-014-0198-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/15/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND Thorough understanding of seed starch biosynthesis and accumulation mechanisms is of great importance for agriculture and crop improvement strategies. We conducted the first comprehensive study of the dynamic development of starch granules and the regulation of starch biosynthesis in Brachypodium distachyon and compared the findings with those reported for common wheat (Chinese Spring, CS) and Aegilops peregrina. RESULTS Only B-granules were identified in Brachypodium Bd21, and the shape variation and development of starch granules were similar in the B-granules of CS and Bd21. Phylogenetic analysis showed that most of the Bd21 starch synthesis-related genes were more similar to those in wheat than in rice. Early expression of key genes in Bd21 starch biosynthesis mediate starch synthesis in the pericarp; intermediate-stage expression increases the number and size of starch granules. In contrast, these enzymes in CS and Ae. peregrina were mostly expressed at intermediate stages, driving production of new B-granules and increasing the granule size, respectively. Immunogold labeling showed that granule-bound starch synthase (GBSSI; related to amylose synthesis) was mainly present in starch granules: at lower levels in the B-granules of Bd21 than in CS. Furthermore, GBSSI was phosphorylated at threonine 183 and tyrosine 185 in the starch synthase catalytic domain in CS and Ae. peregrina, but neither site was phosphorylated in Bd21, suggesting GBSSI phosphorylation could improve amylose biosynthesis. CONCLUSIONS Bd21 contains only B-granules, and the expression of key genes in the three studied genera is consistent with the dynamic development of starch granules. GBSSI is present in greater amounts in the B-granules of CS than in Bd21; two phosphorylation sites (Thr183 and Tyr185) were found in Triticum and Aegilops; these sites were not phosphorylated in Bd21. GBSSI phosphorylation may reflect its importance in amylose synthesis.
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Affiliation(s)
- Guanxing Chen
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Jiantang Zhu
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Jianwen Zhou
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | | | - Ming Zhang
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Caixia Han
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Pengchao Hao
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Xiaohui Li
- College of Life Science, Capital Normal University, 100048 Beijing, China
| | - Yueming Yan
- College of Life Science, Capital Normal University, 100048 Beijing, China
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17
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Morris CF, Geng H, Beecher BS, Ma D. A review of the occurrence of Grain softness protein-1 genes in wheat (Triticum aestivum L.). PLANT MOLECULAR BIOLOGY 2013; 83:507-21. [PMID: 23904183 DOI: 10.1007/s11103-013-0110-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 07/15/2013] [Indexed: 05/02/2023]
Abstract
Grain softness protein-1 (Gsp-1) is a small, 495-bp intronless gene found throughout the Triticeae tribe at the distal end of group 5 chromosomes. With the Puroindolines, it constitutes a key component of the Hardness locus. Gsp-1 likely plays little role in grain hardness, but has direct interest due to its utility in phylogeny and its role in arabinogalactan peptides. Further role(s) remain to be identified. In the polyploid wheats, Triticum aestivum and T. turgidum, the gene is present in a homoeologous series. Since its discovery, there have been conflicting reports and data as to the number of Gsp-1 genes and the level of sequence polymorphism. Little is known about allelic variation within a species. In the simplest model, a single Gsp-1 gene is present in each wheat and Aegilops tauschii genome. The present review critically re-examines the published and some unpublished data (sequence available in the NCBI nucleotide and MIPS Wheat Genome Databases). A number of testable hypotheses are identified, and include the level of polymorphism that may represent (and define) different Gsp-1 alleles, the existence of a fourth Gsp-1 gene, and the apparent, at times, high level of naturally-occurring or artifactual gene chimeras. In summary, the present data provide firm evidence for at most, three Gsp-1 genes in wheat, although there are numerous data that suggest a more complex model.
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Affiliation(s)
- Craig F Morris
- USDA-ARS Western Wheat Quality Laboratory, E-202 Food Quality Bldg., Washington State University, P.O. Box 646394, Pullman, WA, 99164-6394, USA,
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18
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Morris CF, Fuerst EP, Beecher BS, McLean DJ, James CP, Geng HW. Did the house mouse (Mus musculus L.) shape the evolutionary trajectory of wheat (Triticum aestivum L.)? Ecol Evol 2013; 3:3447-54. [PMID: 24223281 PMCID: PMC3797490 DOI: 10.1002/ece3.724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/09/2013] [Accepted: 07/10/2013] [Indexed: 11/09/2022] Open
Abstract
Wheat (Triticum aestivum L.) is one of the most successful domesticated plant species in the world. The majority of wheat carries mutations in the Puroindoline genes that result in a hard kernel phenotype. An evolutionary explanation, or selective advantage, for the spread and persistence of these hard kernel mutations has yet to be established. Here, we demonstrate that the house mouse (Mus musculus L.) exerts a pronounced feeding preference for soft over hard kernels. When allele frequencies ranged from 0.5 to 0.009, mouse predation increased the hard allele frequency as much as 10-fold. Studies involving a single hard kernel mixed with ∼1000 soft kernels failed to recover the mutant kernel. Nevertheless, the study clearly demonstrates that the house mouse could have played a role in the evolution of wheat, and therefore the cultural trajectory of humankind.
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Affiliation(s)
- C F Morris
- USDA-ARS Western Wheat Quality Laboratory Pullman, Washington
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19
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Identification and distribution of Puroindoline b-2 variant gene homologs in Hordeum. Genetica 2013; 141:359-68. [PMID: 24043611 DOI: 10.1007/s10709-013-9735-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 09/03/2013] [Indexed: 10/26/2022]
Abstract
The barley hordoindoline genes (Hina and Hinb) are homologous to the wheat puroindoline genes (Pina and Pinb). These genes are involved in grain hardness, which is an important quality for barley processing. We identified novel variants of Hina and Hinb in 10 wild Hordeum species (H. bogdanii, H. brachyantherum, H. bulbosum, H. chilense, H. comosum, H. marinum, H. murinum, H. patagonicum, H. pusillum, and H. roshevitzii) covering all Hordeum genomes and preliminarily named them Hinc. These nucleotide sequences were highly similar to those of Puroindoline b-2 variant genes (Pinb-2v) and were located on chromosome 7I in H. chilense. The Hinc genes in H. bogdanii, H. bulbosum, H. patagonicum, and H. roshevitzii were pseudogenes possessing in-frame stop codons. We also found a partial Hinc sequence in H. murinum. This gene was not found in cultivated barley and H. vulgare subsp. spontaneum. The phylogenetic tree of Gsp-1, Hin, and Pin genes demonstrates that Hinc and Pinb-2v genes formed one cluster. Therefore, we considered that Hinc and Pinb-2v genes shared a common ancestral gene and were homologous to each other. We also studied the evolutional process of Gsp-1, Hin, and Pin genes. Our results suggested that Gsp-1 might be the most closely related to a putative ancestral gene on Ha locus.
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21
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012. [PMID: 23161406 DOI: 10.1007/s10142‐012‐0300‐5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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22
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Feuillet C, Stein N, Rossini L, Praud S, Mayer K, Schulman A, Eversole K, Appels R. Integrating cereal genomics to support innovation in the Triticeae. Funct Integr Genomics 2012; 12:573-83. [PMID: 23161406 PMCID: PMC3508266 DOI: 10.1007/s10142-012-0300-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 10/31/2012] [Indexed: 11/26/2022]
Abstract
The genomic resources of small grain cereals that include some of the most important crop species such as wheat, barley, and rye are attaining a level of completion that now is contributing to new structural and functional studies as well as refining molecular marker development and mapping strategies for increasing the efficiency of breeding processes. The integration of new efforts to obtain reference sequences in bread wheat and barley, in particular, is accelerating the acquisition and interpretation of genome-level analyses in both of these major crops.
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Affiliation(s)
- C Feuillet
- INRA-UBP UMR 1095 Genetics and Diversity of Cereals, Clermont-Ferrand, France.
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23
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Judelson HS, Shrivastava J, Manson J. Decay of genes encoding the oomycete flagellar proteome in the downy mildew Hyaloperonospora arabidopsidis. PLoS One 2012; 7:e47624. [PMID: 23077652 PMCID: PMC3471859 DOI: 10.1371/journal.pone.0047624] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 09/19/2012] [Indexed: 11/19/2022] Open
Abstract
Zoospores are central to the life cycles of most of the eukaryotic microbes known as oomycetes, but some genera have lost the ability to form these flagellated cells. In the plant pathogen Phytophthora infestans, genes encoding 257 proteins associated with flagella were identified by comparative genomics. These included the main structural components of the axoneme and basal body, proteins involved in intraflagellar transport, regulatory proteins, enzymes for maintaining ATP levels, and others. Transcripts for over three-quarters of the genes were up-regulated during sporulation, and persisted to varying degrees in the pre-zoospore stage (sporangia) and motile zoospores. Nearly all of these genes had orthologs in other eukaryotes that form flagella or cilia, but not species that lack the organelle. Orthologs of 211 of the genes were also absent from a sister taxon to P. infestans that lost the ability to form flagella, the downy mildew Hyaloperonospora arabidopsidis. Many of the genes retained in H. arabidopsidis were also present in other non-flagellates, suggesting that they play roles both in flagella and other cellular processes. Remnants of the missing genes were often detected in the H. arabidopsidis genome. Degradation of the genes was associated with local compaction of the chromosome and a heightened propensity towards genome rearrangements, as such regions were less likely to share synteny with P. infestans.
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Affiliation(s)
- Howard S Judelson
- Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California, United States of America.
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Fursova O, Pogorelko G, Zabotina OA. An efficient method for transient gene expression in monocots applied to modify the Brachypodium distachyon cell wall. ANNALS OF BOTANY 2012; 110:47-56. [PMID: 22589326 PMCID: PMC3380599 DOI: 10.1093/aob/mcs103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 03/26/2012] [Indexed: 05/28/2023]
Abstract
BACKGROUND Agrobacterium-mediated transformation is widely used to produce insertions into plant genomes. There are a number of well-developed Agrobacterium-mediated transformation methods for dicotyledonous plants, but there are few for monocotyledonous plants. METHODS Three hydrolase genes were transiently expressed in Brachypodium distachyon plants using specially designed vectors that express the gene product of interest and target it to the plant cell wall. Expression of functional hydrolases in genotyped plants was confirmed using western blotting, activity assays, cell wall compositional analysis and digestibility tests. KEY RESULTS An efficient, new, Agrobacterium-mediated approach was developed for transient gene expression in the grass B. distachyon, using co-cultivation of mature seeds with bacterial cells. This method allows transformed tissues to be obtained rapidly, within 3-4 weeks after co-cultivation. Also, the plants carried transgenic tissue and maintained transgenic protein expression throughout plant maturation. The efficiency of transformation was estimated at around 5 % of initially co-cultivated seeds. Application of this approach to express three Aspergillus nidulans hydrolases in the Brachypodium cell wall successfully confirmed its utility and resulted in the expected expression of active microbial proteins and alterations of cell wall composition. Cell wall modifications caused by expression of A. nidulans α-arabinofuranosidase and α-galactosidase increased the biodegradability of plant biomass. CONCLUSIONS This newly developed approach is a quick and efficient technique for expressing genes of interest in Brachypodium plants, which express the gene product throughout development. In the future, this could be used for broad functional genomics studies of monocots and for biotechnological applications, such as plant biomass modification for biofuel production.
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Gao D, Chen J, Chen M, Meyers BC, Jackson S. A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One 2012; 7:e32010. [PMID: 22359654 PMCID: PMC3281118 DOI: 10.1371/journal.pone.0032010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 01/18/2012] [Indexed: 12/31/2022] Open
Abstract
LTR retrotransposons are often the most abundant components of plant genomes and can impact gene and genome evolution. Most reported LTR retrotransposons are large elements (>4 kb) and are most often found in heterochromatic (gene poor) regions. We report the smallest LTR retrotransposon found to date, only 292 bp. The element is found in rice, maize, sorghum and other grass genomes, which indicates that it was present in the ancestor of grass species, at least 50-80 MYA. Estimated insertion times, comparisons between sequenced rice lines, and mRNA data indicate that this element may still be active in some genomes. Unlike other LTR retrotransposons, the small LTR retrotransposons (SMARTs) are distributed throughout the genomes and are often located within or near genes with insertion patterns similar to MITEs (miniature inverted repeat transposable elements). Our data suggests that insertions of SMARTs into or near genes can, in a few instances, alter both gene structures and gene expression. Further evidence for a role in regulating gene expression, SMART-specific small RNAs (sRNAs) were identified that may be involved in gene regulation. Thus, SMARTs may have played an important role in genome evolution and genic innovation and may provide a valuable tool for gene tagging systems in grass.
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Affiliation(s)
- Dongying Gao
- Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Blake C. Meyers
- Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware, United States of America
| | - Scott Jackson
- Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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26
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Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X, Lee TH, Jin H, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 2012; 40:e49. [PMID: 22217600 PMCID: PMC3326336 DOI: 10.1093/nar/gkr1293] [Citation(s) in RCA: 3435] [Impact Index Per Article: 286.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.
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Affiliation(s)
- Yupeng Wang
- Plant Genome Mapping Laboratory, Institute of Bioinformatics, Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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28
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Compact genomes and complex evolution in the genus Brachypodium. Chromosoma 2010; 120:199-212. [DOI: 10.1007/s00412-010-0303-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 12/01/2010] [Accepted: 12/03/2010] [Indexed: 12/31/2022]
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Narsai R, Castleden I, Whelan J. Common and distinct organ and stress responsive transcriptomic patterns in Oryza sativa and Arabidopsis thaliana. BMC PLANT BIOLOGY 2010; 10:262. [PMID: 21106056 PMCID: PMC3095337 DOI: 10.1186/1471-2229-10-262] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 11/24/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND Arabidopsis thaliana is clearly established as the model plant species. Given the ever-growing demand for food, there is a need to translate the knowledge learned in Arabidopsis to agronomically important species, such as rice (Oryza sativa). To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation. RESULTS Organ specific transcripts in rice and Arabidopsis display less overlap in terms of gene orthology compared to the orthology observed between both genomes. Although greater overlap in terms of functional classification was observed between root specific transcripts in rice and Arabidopsis, this did not extend to flower, leaf or seed specific transcripts. In contrast, the overall abiotic stress response transcriptome displayed a significantly greater overlap in terms of gene orthology compared to the orthology observed between both genomes. However, ~50% or less of these orthologues responded in a similar manner in both species. In fact, under cold and heat treatments as many or more orthologous genes responded in an opposite manner or were unchanged in one species compared to the other. Examples of transcripts that responded oppositely include several genes encoding proteins involved in stress and redox responses and non-symbiotic hemoglobins that play central roles in stress signalling pathways. The differences observed in the abiotic transcriptomes were mirrored in the presence of cis-acting regulatory elements in the promoter regions of stress responsive genes and the transcription factors that potentially bind these regulatory elements. Thus, both the abiotic transcriptome and its regulation differ between rice and Arabidopsis. CONCLUSIONS These results reveal significant divergence between Arabidopsis and rice, in terms of the abiotic stress response and its regulation. Both plants are shown to employ unique combinations of genes to achieve growth and stress responses. Comparison of these networks provides a more rational approach to translational studies that is based on the response observed in these two diverse plant models.
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316 University of Western Australia
- Centre for Computational Systems Biology, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - Ian Castleden
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316 University of Western Australia
- Centre for Computational Systems Biology, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, MCS Building M316 University of Western Australia
- Centre for Computational Systems Biology, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
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Besnard G, Christin PA. Evolutionary genomics of C4 photosynthesis in grasses requires a large species sampling. C R Biol 2010; 333:577-81. [PMID: 20688277 DOI: 10.1016/j.crvi.2010.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2009] [Revised: 02/12/2010] [Accepted: 03/29/2010] [Indexed: 01/18/2023]
Abstract
Recent advances in genomics open promising opportunities to investigate adaptive trait evolution at the molecular level. However, the accuracy of comparative genomic studies strongly relies on the taxonomic coverage, which can be insufficient when based solely on a few completely sequenced genomes. In particular, when distantly-related genomes are compared, orthology of some genes can be misidentified and long branches of the phylogenetic reconstructions make inappropriate positive selection tests, as recently exemplified with investigations on the evolution of the C(4) photosynthetic pathway in grasses. Complementary studies addressing the diversification of multigene families in a broad taxonomic sample can help circumvent these issues.
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Affiliation(s)
- Guillaume Besnard
- Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire SL5 7PY, UK.
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Bevan MW, Garvin DF, Vogel JP. Brachypodium distachyon genomics for sustainable food and fuel production. Curr Opin Biotechnol 2010; 21:211-7. [PMID: 20362425 DOI: 10.1016/j.copbio.2010.03.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 03/09/2010] [Accepted: 03/09/2010] [Indexed: 01/10/2023]
Abstract
Grass crops are the most important sources of human nutrition, and their improvement is centrally important for meeting the challenges of sustainable agriculture, for feeding the world's population and for developing renewable supplies of fuel and industrial products. We describe the complete sequence of the compact genome of Brachypodium distachyon (Brachypodium) the first pooid grass to be sequenced. We demonstrate the many favorable characteristics of Brachypodium as an experimental system and show how it can be used to navigate the large and complex genomes of closely related grasses. The functional genomics and other experimental resources that are being developed will provide a key resource for improving food and forage crops, in particular wheat, barley and forage grasses, and for establishing new grass crops for sustainable energy production.
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Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010; 463:763-8. [PMID: 20148030 DOI: 10.1038/nature08747] [Citation(s) in RCA: 1210] [Impact Index Per Article: 86.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2009] [Accepted: 12/09/2009] [Indexed: 11/09/2022]
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