1
|
Lebherz MK, Fouks B, Schmidt J, Bornberg-Bauer E, Grandchamp A. DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs. Genome Biol Evol 2024; 16:evae134. [PMID: 38934893 PMCID: PMC11264136 DOI: 10.1093/gbe/evae134] [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: 01/17/2024] [Revised: 06/11/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024] Open
Abstract
De novo genes emerge from noncoding regions of genomes via succession of mutations. Among others, such mutations activate transcription and create a new open reading frame (ORF). Although the mechanisms underlying ORF emergence are well documented, relatively little is known about the mechanisms enabling new transcription events. Yet, in many species a continuum between absent and very prominent transcription has been reported for essentially all regions of the genome. In this study, we searched for de novo transcripts by using newly assembled genomes and transcriptomes of seven inbred lines of Drosophila melanogaster, originating from six European and one African population. This setup allowed us to detect sample specific de novo transcripts, and compare them to their homologous nontranscribed regions in other samples, as well as genic and intergenic control sequences. We studied the association with transposable elements (TEs) and the enrichment of transcription factor motifs upstream of de novo emerged transcripts and compared them with regulatory elements. We found that de novo transcripts overlap with TEs more often than expected by chance. The emergence of new transcripts correlates with regions of high guanine-cytosine content and TE expression. Moreover, upstream regions of de novo transcripts are highly enriched with regulatory motifs. Such motifs are more enriched in new transcripts overlapping with TEs, particularly DNA TEs, and are more conserved upstream de novo transcripts than upstream their 'nontranscribed homologs'. Overall, our study demonstrates that TE insertion is important for transcript emergence, partly by introducing new regulatory motifs from DNA TE families.
Collapse
Affiliation(s)
| | - Bertrand Fouks
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
| | - Julian Schmidt
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| |
Collapse
|
2
|
Bengtsson JD, Wallis JG, Browse J. Expression of Physaria longchain acyl-CoA synthetases and hydroxy fatty acid accumulation in transgenic Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 274:153717. [PMID: 35584570 PMCID: PMC9494924 DOI: 10.1016/j.jplph.2022.153717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Hydroxy fatty acids (HFA) are industrially useful chemical feedstocks that accumulate in seed-storage triacylglycerols (TAG) of several plant species, including castor (Ricinus communis) and Physaria (Physaria fendleri). For researchers, HFA also offer a unique opportunity to trace fatty acid metabolism and modification. Past work producing HFA in Arabidopsis (Arabidopsis thaliana) has demonstrated the importance of isozymes of TAG synthesis from plants that evolved to store HFA and as a result have a high degree of specificity towards HFA substrates. Castor phospholipase A2α (RcPLA2) has specificity for HFA-containing phosphatidylcholine. However, expression of RcPLA2 in HFA-accumulating Arabidopsis line CL37-PLA2 reduced HFA content of TAG. This loss was interpreted as being due to poor ability of Arabidopsis longchain acyl-CoA synthetases (LACSs) to utilize HFAs substrates. LACS enzymes are essential to activate HFA to HFA-CoA for TAG synthesis. Physaria is a close relative of Arabidopsis in the Brassicaceae family. To test the hypothesis that this close relatedness would allow Physaria LACSs to interface successfully with Arabidopsis enzymes of seed lipid metabolism and thereby restore HFA accumulation, we transformed PfLACS4 and PfLACS8 constructs into the CL37-PLA2 line. However, HFA content was not recovered, and biochemical characterization of recombinant PfLACS4 and PfLACS8 indicated that these isozymes have substrate specificities and selectivities that are similar to their Arabidopsis orthologues. These and other results pose an important question about how HFA synthesized on phosphatidylcholine can be transferred into the acyl-CoA pool for TAG synthesis.
Collapse
Affiliation(s)
- Jesse D Bengtsson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - James G Wallis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
| |
Collapse
|
3
|
Rahmani RS, Decap D, Fostier J, Marchal K. BLSSpeller to discover novel regulatory motifs in maize. DNA Res 2022; 29:6651838. [PMID: 35904558 PMCID: PMC9358016 DOI: 10.1093/dnares/dsac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with larger sequence datasets. BLSSpeller was used to identify novel motifs in Zea mays in a comparative genomics setting with 16 monocot lineages. We discovered 61 motifs of which 20 matched previously described motif models in Arabidopsis. In addition, novel, yet uncharacterized motifs were detected, several of which are supported by available sequence-based and/or functional data. Instances of the predicted motifs were enriched around transcription start sites and contained signatures of selection. Moreover, the enrichment of the predicted motif instances in open chromatin and TF binding sites indicates their functionality, supported by the fact that genes carrying instances of these motifs were often found to be co-expressed and/or enriched in similar GO functions. Overall, our study unveiled several novel candidate motifs that might help our understanding of the genotype to phenotype association in crops.
Collapse
Affiliation(s)
- Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University , Gent, Belgium
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Dries Decap
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Jan Fostier
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University , Gent, Belgium
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria, South Africa
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C. The modular nature of protein evolution: domain rearrangement rates across eukaryotic life. BMC Evol Biol 2020; 20:30. [PMID: 32059645 PMCID: PMC7023805 DOI: 10.1186/s12862-020-1591-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/31/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Modularity is important for evolutionary innovation. The recombination of existing units to form larger complexes with new functionalities spares the need to create novel elements from scratch. In proteins, this principle can be observed at the level of protein domains, functional subunits which are regularly rearranged to acquire new functions. RESULTS In this study we analyse the mechanisms leading to new domain arrangements in five major eukaryotic clades (vertebrates, insects, fungi, monocots and eudicots) at unprecedented depth and breadth. This allows, for the first time, to directly compare rates of rearrangements between different clades and identify both lineage specific and general patterns of evolution in the context of domain rearrangements. We analyse arrangement changes along phylogenetic trees by reconstructing ancestral domain content in combination with feasible single step events, such as fusion or fission. Using this approach we explain up to 70% of all rearrangements by tracing them back to their precursors. We find that rates in general and the ratio between these rates for a given clade in particular, are highly consistent across all clades. In agreement with previous studies, fusions are the most frequent event leading to new domain arrangements. A lineage specific pattern in fungi reveals exceptionally high loss rates compared to other clades, supporting recent studies highlighting the importance of loss for evolutionary innovation. Furthermore, our methodology allows us to link domain emergences at specific nodes in the phylogenetic tree to important functional developments, such as the origin of hair in mammals. CONCLUSIONS Our results demonstrate that domain rearrangements are based on a canonical set of mutational events with rates which lie within a relatively narrow and consistent range. In addition, gained knowledge about these rates provides a basis for advanced domain-based methodologies for phylogenetics and homology analysis which complement current sequence-based methods.
Collapse
Affiliation(s)
- Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany.,Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen, 45665, Germany
| | - Steffen Klasberg
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany
| | - Sören Perrey
- Institute for Bioinformatics and Chemoinformatics, Westphalian University of Applied Sciences, August-Schmidt-Ring 10, Recklinghausen, 45665, Germany
| | - Carsten Kemena
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstrasse 1, Münster, 48149, Germany.
| |
Collapse
|
6
|
Assis R. Lineage-Specific Expression Divergence in Grasses Is Associated with Male Reproduction, Host-Pathogen Defense, and Domestication. Genome Biol Evol 2019; 11:207-219. [PMID: 30398650 PMCID: PMC6331041 DOI: 10.1093/gbe/evy245] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2018] [Indexed: 02/02/2023] Open
Abstract
Poaceae (grasses) is an agriculturally important and widely distributed family of plants with extraordinary phenotypic diversity, much of which was generated under recent lineage-specific evolution. Yet, little is known about the genes and functional modules involved in the lineage-specific divergence of grasses. Here, I address this question on a genome-wide scale by applying a novel branch-based statistic of lineage-specific expression divergence, LED, to RNA-seq data from nine tissues of the wild grass Brachypodium distachyon and its domesticated relatives Oryza sativa japonica (rice) and Sorghum bicolor (sorghum). I find that LED is generally smallest in B. distachyon and largest in O. sativa japonica, which underwent domestication earlier than S. bicolor, supporting the hypothesis that domestication may increase the rate of lineage-specific expression divergence in grasses. Moreover, in all three species, LED is positively correlated with protein-coding sequence divergence and tissue specificity, and negatively correlated with network connectivity. Further analysis reveals that genes with large LED are often primarily expressed in anther, implicating lineage-specific expression divergence in the evolution of male reproductive phenotypes. Gene ontology enrichment analysis also identifies an overrepresentation of terms related to male reproduction in the two domesticated grasses, as well as to those involved in host-pathogen defense in all three species. Last, examinations of genes with the largest LED reveal that their lineage-specific expression divergence may have contributed to antimicrobial functions in B. distachyon, to enhanced adaptation and yield during domestication in O. sativa japonica, and to defense against a widespread and devastating fungal pathogen in S. bicolor. Together, these findings suggest that lineage-specific expression divergence in grasses may increase under domestication and preferentially target rapidly evolving genes involved in male reproduction, host-pathogen defense, and the origin of domesticated phenotypes.
Collapse
Affiliation(s)
- Raquel Assis
- Department of Biology, Pennsylvania State University, University Park
| |
Collapse
|
7
|
Liang P, Saqib HSA, Zhang X, Zhang L, Tang H. Single-Base Resolution Map of Evolutionary Constraints and Annotation of Conserved Elements across Major Grass Genomes. Genome Biol Evol 2018; 10:473-488. [PMID: 29378032 PMCID: PMC5798027 DOI: 10.1093/gbe/evy006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2018] [Indexed: 12/20/2022] Open
Abstract
Conserved noncoding sequences (CNSs) are evolutionarily conserved DNA sequences that do not encode proteins but may have potential regulatory roles in gene expression. CNS in crop genomes could be linked to many important agronomic traits and ecological adaptations. Compared with the relatively mature exon annotation protocols, efficient methods are lacking to predict the location of noncoding sequences in the plant genomes. We implemented a computational pipeline that is tailored to the comparisons of plant genomes, yielding a large number of conserved sequences using rice genome as the reference. In this study, we used 17 published grass genomes, along with five monocot genomes as well as the basal angiosperm genome of Amborella trichopoda. Genome alignments among these genomes suggest that at least 12.05% of the rice genome appears to be evolving under constraints in the Poaceae lineage, with close to half of the evolutionarily constrained sequences located outside protein-coding regions. We found evidence for purifying selection acting on the conserved sequences by analyzing segregating SNPs within the rice population. Furthermore, we found that known functional motifs were significantly enriched within CNS, with many motifs associated with the preferred binding of ubiquitous transcription factors. The conserved elements that we have curated are accessible through our public database and the JBrowse server. In-depth functional annotations and evolutionary dynamics of the identified conserved sequences provide a solid foundation for studying gene regulation, genome evolution, as well as to inform gene isolation for cereal biologists.
Collapse
Affiliation(s)
- Pingping Liang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, China
| | - Hafiz Sohaib Ahmed Saqib
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingtan Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangsheng Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Center for Genomics and Biotechnology, Ministry of Education; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
8
|
Dufayard JF, Bettembourg M, Fischer I, Droc G, Guiderdoni E, Périn C, Chantret N, Diévart A. New Insights on Leucine-Rich Repeats Receptor-Like Kinase Orthologous Relationships in Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:381. [PMID: 28424707 PMCID: PMC5380761 DOI: 10.3389/fpls.2017.00381] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 05/18/2023]
Abstract
Leucine-Rich Repeats Receptor-Like Kinase (LRR-RLK) genes represent a large and complex gene family in plants, mainly involved in development and stress responses. These receptors are composed of an LRR-containing extracellular domain (ECD), a transmembrane domain (TM) and an intracellular kinase domain (KD). To provide new perspectives on functional analyses of these genes in model and non-model plant species, we performed a phylogenetic analysis on 8,360 LRR-RLK receptors in 31 angiosperm genomes (8 monocots and 23 dicots). We identified 101 orthologous groups (OGs) of genes being conserved among almost all monocot and dicot species analyzed. We observed that more than 10% of these OGs are absent in the Brassicaceae species studied. We show that the ECD structural features are not always conserved among orthologs, suggesting that functions may have diverged in some OG sets. Moreover, we looked at targets of positive selection footprints in 12 pairs of OGs and noticed that depending on the subgroups, positive selection occurred more frequently either in the ECDs or in the KDs.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Nathalie Chantret
- INRA, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
| | - Anne Diévart
- CIRAD, UMR AGAPMontpellier, France
- *Correspondence: Anne Diévart, Nathalie Chantret,
| |
Collapse
|
9
|
AVCI MK, AYVAZ M, UYSAL H, SEVİNDİK E, ÖRENAY BOYACIOĞLU S, YAMANER Ç. Order-wide in silico comparative analysis and identification ofgrowth-regulating factor proteins in Malpighiales. Turk J Biol 2016. [DOI: 10.3906/biy-1502-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
10
|
CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea. J Biosci 2015; 40:579-92. [PMID: 26333404 DOI: 10.1007/s12038-015-9545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
Collapse
|
11
|
De Witte D, Van de Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J. BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. Bioinformatics 2015; 31:3758-66. [PMID: 26254488 PMCID: PMC4653392 DOI: 10.1093/bioinformatics/btv466] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 08/03/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. RESULTS We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. AVAILABILITY AND IMPLEMENTATION BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller CONTACT Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Dieter De Witte
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| | - Jan Van de Velde
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Dries Decap
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Pieter Audenaert
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| | - Piet Demeester
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| | - Bart Dhoedt
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jan Fostier
- Department of Information Technology (INTEC), Ghent University-iMinds, Ghent, Belgium
| |
Collapse
|
12
|
Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1271-90. [PMID: 25504138 PMCID: PMC4339591 DOI: 10.1093/jxb/eru478] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
Collapse
Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
13
|
Hutin M, Pérez-Quintero AL, Lopez C, Szurek B. MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility. FRONTIERS IN PLANT SCIENCE 2015. [PMID: 26236326 DOI: 10.3389/fpls.2015.0053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.
Collapse
Affiliation(s)
- Mathilde Hutin
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
| | - Alvaro L Pérez-Quintero
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
| | - Camilo Lopez
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France ; Biology Department, Universidad Nacional de Colombia Bogota, Colombia
| | - Boris Szurek
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2 Montpellier, France
| |
Collapse
|
14
|
Hutin M, Pérez-Quintero AL, Lopez C, Szurek B. MorTAL Kombat: the story of defense against TAL effectors through loss-of-susceptibility. FRONTIERS IN PLANT SCIENCE 2015; 6:535. [PMID: 26236326 PMCID: PMC4500901 DOI: 10.3389/fpls.2015.00535] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/30/2015] [Indexed: 05/21/2023]
Abstract
Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.
Collapse
Affiliation(s)
- Mathilde Hutin
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
| | - Alvaro L. Pérez-Quintero
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
| | - Camilo Lopez
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
- Biology Department, Universidad Nacional de ColombiaBogota, Colombia
| | - Boris Szurek
- UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2Montpellier, France
- *Correspondence: Boris Szurek, UMR IPME, Institut de Recherche Pour le Développement, IRD-CIRAD-Université Montpellier 2, 911 Avenue Agropolis BP 64501, 34394 Montpellier Cedex 5, France,
| |
Collapse
|
15
|
Filiz E, Tombuloğlu H. In Silico Analysis of DREB Transcription Factor Genes and Proteins in Grasses. Appl Biochem Biotechnol 2014; 174:1272-1285. [DOI: 10.1007/s12010-014-1093-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/21/2014] [Indexed: 10/24/2022]
|
16
|
Van de Velde J, Heyndrickx KS, Vandepoele K. Inference of transcriptional networks in Arabidopsis through conserved noncoding sequence analysis. THE PLANT CELL 2014; 26:2729-45. [PMID: 24989046 PMCID: PMC4145110 DOI: 10.1105/tpc.114.127001] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a)biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.
Collapse
Affiliation(s)
- Jan Van de Velde
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Ken S Heyndrickx
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| |
Collapse
|
17
|
Burgess D, Freeling M. The most deeply conserved noncoding sequences in plants serve similar functions to those in vertebrates despite large differences in evolutionary rates. THE PLANT CELL 2014; 26:946-61. [PMID: 24681619 PMCID: PMC4001403 DOI: 10.1105/tpc.113.121905] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing-associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates.
Collapse
|
18
|
Subramaniam S, Wang X, Freeling M, Pires JC. The fate of Arabidopsis thaliana homeologous CNSs and their motifs in the Paleohexaploid Brassica rapa. Genome Biol Evol 2013; 5:646-60. [PMID: 23493633 PMCID: PMC3641636 DOI: 10.1093/gbe/evt035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Following polyploidy, duplicate genes are often deleted, and if they are not, then duplicate regulatory regions are sometimes lost. By what mechanism is this loss and what is the chance that such a loss removes function? To explore these questions, we followed individual Arabidopsis thaliana–A. thaliana conserved noncoding sequences (CNSs) into the Brassica ancestor, through a paleohexaploidy and into Brassica rapa. Thus, a single Brassicaceae CNS has six potential orthologous positions in B. rapa; a single Arabidopsis CNS has three potential homeologous positions. We reasoned that a CNS, if present on a singlet Brassica gene, would be unlikely to lose function compared with a more redundant CNS, and this is the case. Redundant CNSs go nondetectable often. Using this logic, each mechanism of CNS loss was assigned a metric of functionality. By definition, proved deletions do not function as sequence. Our results indicated that CNSs that go nondetectable by base substitution or large insertion are almost certainly still functional (redundancy does not matter much to their detectability frequency), whereas those lost by inferred deletion or indels are approximately 75% likely to be nonfunctional. Overall, an average nondetectable, once-redundant CNS more than 30 bp in length has a 72% chance of being nonfunctional, and that makes sense because 97% of them sort to a molecular mechanism with “deletion” in its description, but base substitutions do cause loss. Similarly, proved-functional G-boxes go undetectable by deletion 82% of the time. Fractionation mutagenesis is a procedure that uses polyploidy as a mutagenic agent to genetically alter RNA expression profiles, and then to construct testable hypotheses as to the function of the lost regulatory site. We show fractionation mutagenesis to be a “deletion machine” in the Brassica lineage.
Collapse
|
19
|
Haudry A, Platts AE, Vello E, Hoen DR, Leclercq M, Williamson RJ, Forczek E, Joly-Lopez Z, Steffen JG, Hazzouri KM, Dewar K, Stinchcombe JR, Schoen DJ, Wang X, Schmutz J, Town CD, Edger PP, Pires JC, Schumaker KS, Jarvis DE, Mandáková T, Lysak MA, van den Bergh E, Schranz ME, Harrison PM, Moses AM, Bureau TE, Wright SI, Blanchette M. An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet 2013; 45:891-8. [PMID: 23817568 DOI: 10.1038/ng.2684] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Accepted: 06/04/2013] [Indexed: 12/17/2022]
Abstract
Despite the central importance of noncoding DNA to gene regulation and evolution, understanding of the extent of selection on plant noncoding DNA remains limited compared to that of other organisms. Here we report sequencing of genomes from three Brassicaceae species (Leavenworthia alabamica, Sisymbrium irio and Aethionema arabicum) and their joint analysis with six previously sequenced crucifer genomes. Conservation across orthologous bases suggests that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions. Much of this sequence can be localized to approximately 90,000 conserved noncoding sequences (CNSs) that show evidence of transcriptional and post-transcriptional regulation. Population genomics analyses of two crucifer species, A. thaliana and Capsella grandiflora, confirm that most of the identified CNSs are evolving under medium to strong purifying selection. Overall, these CNSs highlight both similarities and several key differences between the regulatory DNA of plants and other species.
Collapse
Affiliation(s)
- Annabelle Haudry
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Towards a transferable and cost-effective plant AFLP protocol. PLoS One 2013; 8:e61704. [PMID: 23613908 PMCID: PMC3628351 DOI: 10.1371/journal.pone.0061704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 03/15/2013] [Indexed: 11/30/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae), Pennisetum setaceum and Poa annua (Poaceae), Lantana camara (Verbenaceae), Bassia diffusa (Chenopodiaceae), Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae)). Highly polymorphic and reproducible genotypic fingerprints (between 37–144 polymorphic loci per species tested) were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.
Collapse
|
21
|
Turco G, Schnable JC, Pedersen B, Freeling M. Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses. FRONTIERS IN PLANT SCIENCE 2013; 4:170. [PMID: 23874343 PMCID: PMC3708275 DOI: 10.3389/fpls.2013.00170] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 05/13/2013] [Indexed: 05/07/2023]
Abstract
Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs with additional functions, and identify previously undetected genes encoding RNA and protein in the genomes of five grass species. We provide a list of 15,363 orthologous CNSs conserved across all grasses tested. We were also able to identify regulatory sequences present in the common ancestor of grasses that have been lost in one or more extant grass lineages. Lists of orthologous gene pairs and associated CNSs are provided for reference inbred lines of arabidopsis, Japonica rice, foxtail millet, sorghum, brachypodium, and maize.
Collapse
Affiliation(s)
| | - James C. Schnable
- *Correspondence: James C. Schnable and Michael Freeling, Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA e-mail: ;
| | | | - Michael Freeling
- *Correspondence: James C. Schnable and Michael Freeling, Department of Plant and Microbial Biology, University of California, 111 Koshland Hall, Berkeley, CA 94720, USA e-mail: ;
| |
Collapse
|
22
|
Baxter L, Jironkin A, Hickman R, Moore J, Barrington C, Krusche P, Dyer NP, Buchanan-Wollaston V, Tiskin A, Beynon J, Denby K, Ott S. Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. THE PLANT CELL 2012; 24:3949-65. [PMID: 23110901 PMCID: PMC3517229 DOI: 10.1105/tpc.112.103010] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Conserved noncoding sequences (CNSs) in DNA are reliable pointers to regulatory elements controlling gene expression. Using a comparative genomics approach with four dicotyledonous plant species (Arabidopsis thaliana, papaya [Carica papaya], poplar [Populus trichocarpa], and grape [Vitis vinifera]), we detected hundreds of CNSs upstream of Arabidopsis genes. Distinct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs play a functional role in transcriptional regulation. The enrichment of transcription factors within the set of genes associated with CNS is consistent with the hypothesis that together they form part of a conserved transcriptional network whose function is to regulate other transcription factors and control development. We identified a set of promoters where regulatory mechanisms are likely to be shared between the model organism Arabidopsis and other dicots, providing areas of focus for further research.
Collapse
Affiliation(s)
- Laura Baxter
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Aleksey Jironkin
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Richard Hickman
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jay Moore
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Peter Krusche
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nigel P. Dyer
- Molecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Vicky Buchanan-Wollaston
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Alexander Tiskin
- Department of Computer Science, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jim Beynon
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Katherine Denby
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Sascha Ott
- Warwick Systems Biology Centre, University of Warwick, Coventry CV4 7AL, United Kingdom
- Address correspondence to
| |
Collapse
|
23
|
Ma X, Sela H, Jiao G, Li C, Wang A, Pourkheirandish M, Weiner D, Sakuma S, Krugman T, Nevo E, Komatsuda T, Korol A, Chen G. Population-genetic analysis of HvABCG31 promoter sequence in wild barley (Hordeum vulgare ssp. spontaneum). BMC Evol Biol 2012; 12:188. [PMID: 23006777 PMCID: PMC3544613 DOI: 10.1186/1471-2148-12-188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 09/18/2012] [Indexed: 01/31/2023] Open
Abstract
Background The cuticle is an important adaptive structure whose origin played a crucial role in the transition of plants from aqueous to terrestrial conditions. HvABCG31/Eibi1 is an ABCG transporter gene, involved in cuticle formation that was recently identified in wild barley (Hordeum vulgare ssp. spontaneum). To study the genetic variation of HvABCG31 in different habitats, its 2 kb promoter region was sequenced from 112 wild barley accessions collected from five natural populations from southern and northern Israel. The sites included three mesic and two xeric habitats, and differed in annual rainfall, soil type, and soil water capacity. Results Phylogenetic analysis of the aligned HvABCG31 promoter sequences clustered the majority of accessions (69 out of 71) from the three northern mesic populations into one cluster, while all 21 accessions from the Dead Sea area, a xeric southern population, and two isolated accessions (one from a xeric population at Mitzpe Ramon and one from the xeric ‘African Slope’ of “Evolution Canyon”) formed the second cluster. The southern arid populations included six haplotypes, but they differed from the consensus sequence at a large number of positions, while the northern mesic populations included 15 haplotypes that were, on average, more similar to the consensus sequence. Most of the haplotypes (20 of 22) were unique to a population. Interestingly, higher genetic variation occurred within populations (54.2%) than among populations (45.8%). Analysis of the promoter region detected a large number of transcription factor binding sites: 121–128 and 121–134 sites in the two southern arid populations, and 123–128,125–128, and 123–125 sites in the three northern mesic populations. Three types of TFBSs were significantly enriched: those related to GA (gibberellin), Dof (DNA binding with one finger), and light. Conclusions Drought stress and adaptive natural selection may have been important determinants in the observed sequence variation of HvABCG31 promoter. Abiotic stresses may be involved in the HvABCG31 gene transcription regulations, generating more protective cuticles in plants under stresses.
Collapse
Affiliation(s)
- Xiaoying Ma
- Extreme Stress Resistance and Biotechnology Laboratory, Cold and Arid Regions Environmental and Engineering Institute, Chinese Academy of Sciences, Lanzhou 730000, China
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Murat F, de Peer YV, Salse J. Decoding plant and animal genome plasticity from differential paleo-evolutionary patterns and processes. Genome Biol Evol 2012; 4:917-28. [PMID: 22833223 PMCID: PMC3516226 DOI: 10.1093/gbe/evs066] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Continuing advances in genome sequencing technologies and computational methods for comparative genomics currently allow inferring the evolutionary history of entire plant and animal genomes. Based on the comparison of the plant and animal genome paleohistory, major differences are unveiled in 1) evolutionary mechanisms (i.e., polyploidization versus diploidization processes), 2) genome conservation (i.e., coding versus noncoding sequence maintenance), and 3) modern genome architecture (i.e., genome organization including repeats expansion versus contraction phenomena). This article discusses how extant animal and plant genomes are the result of inherently different rates and modes of genome evolution resulting in relatively stable animal and much more dynamic and plastic plant genomes.
Collapse
Affiliation(s)
- Florent Murat
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jérôme Salse
- INRA/UBP UMR 1095 GDEC ‘Génétique, Diversité et Ecophysiologie des Céréales’, Clermont Ferrand, France
- *Corresponding author: E-mail:
| |
Collapse
|
25
|
Kersting AR, Bornberg-Bauer E, Moore AD, Grath S. Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution. Genome Biol Evol 2012; 4:316-29. [PMID: 22250127 PMCID: PMC3318442 DOI: 10.1093/gbe/evs004] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plant genomes are generally very large, mostly paleopolyploid, and have numerous gene duplicates and complex genomic features such as repeats and transposable elements. Many of these features have been hypothesized to enable plants, which cannot easily escape environmental challenges, to rapidly adapt. Another mechanism, which has recently been well described as a major facilitator of rapid adaptation in bacteria, animals, and fungi but not yet for plants, is modular rearrangement of protein-coding genes. Due to the high precision of profile-based methods, rearrangements can be well captured at the protein level by characterizing the emergence, loss, and rearrangements of protein domains, their structural, functional, and evolutionary building blocks. Here, we study the dynamics of domain rearrangements and explore their adaptive benefit in 27 plant and 3 algal genomes. We use a phylogenomic approach by which we can explain the formation of 88% of all arrangements by single-step events, such as fusion, fission, and terminal loss of domains. We find many domains are lost along every lineage, but at least 500 domains are novel, that is, they are unique to green plants and emerged more or less recently. These novel domains duplicate and rearrange more readily within their genomes than ancient domains and are overproportionally involved in stress response and developmental innovations. Novel domains more often affect regulatory proteins and show a higher degree of structural disorder than ancient domains. Whereas a relatively large and well-conserved core set of single-domain proteins exists, long multi-domain arrangements tend to be species-specific. We find that duplicated genes are more often involved in rearrangements. Although fission events typically impact metabolic proteins, fusion events often create new signaling proteins essential for environmental sensing. Taken together, the high volatility of single domains and complex arrangements in plant genomes demonstrate the importance of modularity for environmental adaptability of plants.
Collapse
Affiliation(s)
- Anna R Kersting
- Evolutionary Bioinformatics Group, Institute for Evolution and Biodiversity, University of Muenster (WWU), Germany
| | | | | | | |
Collapse
|
26
|
Walcher CL, Nemhauser JL. Bipartite promoter element required for auxin response. PLANT PHYSIOLOGY 2012; 158:273-82. [PMID: 22100645 PMCID: PMC3252081 DOI: 10.1104/pp.111.187559] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 11/16/2011] [Indexed: 05/19/2023]
Abstract
Multiple mechanisms have been described for coordination of responses to the plant hormones auxin and brassinosteroids (Zhang et al., 2009). One unexplained phenomenon is the reliance of the auxin transcriptional response on a functional brassinosteroid pathway. In this study, we used luciferase reporters to interrogate the promoter of SMALL AUXIN-UP RNA15 (SAUR15), a well-characterized auxin and brassinosteroid early response gene in Arabidopsis (Arabidopsis thaliana). After identifying a minimal region sufficient for auxin response, we targeted predicted cis-regulatory elements contained within this sequence and found a critical subset required for hormone response. Specifically, reporter sensitivity to auxin treatment required two elements: a Hormone Up at Dawn (HUD)-type E-box and an AuxRE-related TGTCT element. Reporter response to brassinosteroid treatment relied on the same two elements. Consistent with these findings, the transcription factors BRASSINOSTEROID INSENSITIVE1-EMS SUPPESSOR1 and MONOPTEROS (MP)/ AUXIN RESPONSE FACTOR5 (ARF5) showed enhanced binding to the critical promoter region containing these elements. Treatment with auxin or brassinosteroids could enhance binding of either transcription factor, and brassinosteroid enhancement of MP/ARF5 binding required an intact HUD element. Conservation of clustered HUD elements and AuxRE-related sequences in promoters of putative SAUR15 orthologs in a number of flowering plant species, in combination with evidence for statistically significant clustering of these elements across all Arabidopsis promoters, provided further evidence of the functional importance of coordinated transcription factor binding.
Collapse
|