Georg Haberer | Helmholtz-Zentrum München (original) (raw)
Papers by Georg Haberer
Background: Receptor-like kinases are a prominent class of surface receptors that regulate many a... more Background: Receptor-like kinases are a prominent class of surface receptors that regulate many aspects of the plant life cycle. Despite recent advances the function of most receptor-like kinases remains elusive. Therefore, it is paramount to investigate these receptors. The task is complicated by the fact that receptor-like kinases belong to a large monophyletic family with many sub-clades. In general, functional analysis of gene family members by reverse genetics is often obscured by several issues, such as redundancy, subtle or difficult to detect phenotypes in mutants, or by decision problems regarding suitable biological and biochemical assays. Therefore, in many cases additional strategies have to be employed to allow inference of hypotheses regarding gene function. Results: We approached the function of genes encoding the nine-member STRUBBELIG-RECEPTOR FAMILY (SRF) class of putative leucine-rich repeat receptor-like kinases. Sequence comparisons show overall conservation but also divergence in predicted functional domains among SRF proteins. Interestingly, SRF1 undergoes differential splicing. As a result, SRF1 is predicted to exist in a standard receptor configuration and in a membrane-anchored receptor-like version that lacks most of the intracellular domain. Furthermore, SRF1 is characterised by a high degree of polymorphism between the Ler and Col accessions. Two independent T-DNA-based srf4 mutants showed smaller leaves while 35S::SRF4 plants displayed enlarged leaves. This is in addition to the strubbelig phenotype which has been described before. Additional single and several key double mutant combinations did not reveal obvious mutant phenotypes. Ectopic expression of several SRF genes, using the 35S promoter, resulted in male sterility. To gain possible insights into SRF gene function we employed a computational analysis of publicly available microarray data. We performed global expression profiling, coexpression analysis, and an analysis of the enrichment of gene ontology terms among coexpressed genes. The bioinformatic analyses raise the possibility that some SRF genes affect different aspects of cell wall biology. The results also indicate that redundancy is a minor aspect of the SRF family. Conclusion: The results provide evidence that SRF4 is a positive regulator of leaf size. In addition, they suggest that the SRF family is characterised by functional diversity and that some SRF genes may function in cell wall biology. They also indicate that complementing reverse genetics with bioinformatical data mining of genome-wide expression data aids in inferring hypotheses on possible functions for members of a gene family.
The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements... more The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition large-scale gene expression data for Arabidopsis thaliana have recently become available. Co-expression and evolutionarily conserved sequences are criteria, widely used to identify shared cis-regulatory elements. In our study we employ an integrated approach to combine two sources of information, co-expression and sequence conservation. Best candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes co-expressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified b...
The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera,
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provid... more In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications, tandem and segmental duplications, in Arabidopsis for correlation, conservation, and differences of expression characteristics by making use of large genome-wide expression data as measured by the massively parallel signature sequencing method. Our analysis indicates that large fractions of duplicated gene pairs still share transcriptional characteristics. However, our results also indicate that expression divergence occurs frequently between duplicated gene pairs, a process which frequently might be employed for the retention of sequence redundant gene pairs. Preserved overall similarity between promoters of duplicated genes as well as preservation of individual cis-elements within the respective promoters indicates that the process of transcriptional neoand subfunctionalization is restri...
ABSTRACT Under a Defra-BBSRC funded LINK project between the Roslin Institute, Aviagen Ltd, Hy-Li... more ABSTRACT Under a Defra-BBSRC funded LINK project between the Roslin Institute, Aviagen Ltd, Hy-Line International, Affymetrix Ltd. and in cooperation with the German Synbreed project funded by BMBF we are developing a high density (600K) chicken SNP genotyping array that will enable highly accurate GWAS, genomic selection, selection signature analysis and fine mapping of QTLs. We have re-sequenced a large number of chickens (n=243) from 24 different lines including commercial broiler and layer lines, and experimental inbred layer lines. By aligning the sequence reads to the new version of chicken reference genome (Gallus_gallus-4.0), we identified a staggering 78M SNPs that are segregating in one or more lines. This large number of SNPs was pruned on several steps to select 1.8M for validation. The key selection criteria included SNP quality scores, uniformity of distribution across the genome, equal representation of broiler and layer SNPs, and their predicted reproducibility in arrays. These SNPs were validated for their true reproducibility, stable Mendelian inheritance and polymorphism by genotyping on 288 individuals comprising of commercial broilers, layers and some outgroup individuals. The final panel of 600K has been selected based on the validation results and with the key criteria of uniform distribution across the genome. Moreover, we have annotated the 1.8M SNPs to predict their genomic distribution and effects on protein coding; this information has also been used in selecting the final panel.
Metrics of the selection screens for 136 temperate inbred lines along the ten maize chromosomes b... more Metrics of the selection screens for 136 temperate inbred lines along the ten maize chromosomes based on genotyping data. (PDF 4242 kb)
Highlights d HKT1-type channels mediate a one-way sodium load into quinoa bladder cells d ClC tra... more Highlights d HKT1-type channels mediate a one-way sodium load into quinoa bladder cells d ClC transporters operate in the Cl À sequestration into vacuoles of bladder cells d The bladder cytoplasm is osmotically balanced by potassium and proline import d On the transcript level, bladders are ''constitutively active'' for salt sequestration
Xiangchao Gan, Angela Hay, Michiel Kwantes, Georg Haberer, Asis Hallab, Raffaele Dello Ioio, Hugo... more Xiangchao Gan, Angela Hay, Michiel Kwantes, Georg Haberer, Asis Hallab, Raffaele Dello Ioio, Hugo Hofhuis, Bjorn Pieper, Maria Cartolano, Ulla Neumann, Lachezar A. Nikolov, Baoxing Song, Mohsen Hajheidari, Roman Briskine, Evangelia Kougioumoutzi, Daniela Vlad, Suvi Broholm, Jotun Hein, Khalid Meksem, David Lightfoot, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Martha Imprialou, David Kudrna, Rod Wing, Shusei Sato, Peter Huijser, Dmitry Filatov, Klaus F. X. Mayer, Richard Mott, and Miltos Tsiantis
C. Boschiero, A.A. Gheyas, A. Kranis, F.S. Turner, K. Watson, L. Yu, S. Smith, R. Talbot, P. Kais... more C. Boschiero, A.A. Gheyas, A. Kranis, F.S. Turner, K. Watson, L. Yu, S. Smith, R. Talbot, P. Kaiser, P.M. Hocking, J.E. Fulton, T.M. Strom, G. Haberer, H.R. Fries, S. Weigend, R. Preisinger, S. Qanbari, H. Simianer, F. Brew, J.A.Woolliams, and D.W. Burt Dept. of Genetics and Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK; Aviagen, Newbridge, Midlothian, EH28 8SZ, Scotland, UK; Hy-Line International, Dallas Center, IA, 50063, USA; Inst. of Human Genetic, Helmholtz Center Munich, 85764 Neuherberg, Germany; Inst. for Bioinformatics and Systems, Helmholtz Center Munich, 85764 Neuherberg, Germany; Chair of Animal Breeding, Technische Universität München, 85354 FreisingWeihenstephan, Germany; Inst. of Farm Animal Genetics, Friedrich Loeffler Institute, 31535 Neustadt-Mariensee; Germany; Lohmann Tierzucht GmbH, 27454 Cuxhaven, Germany; Dept. of Animal Sciences, Georg-August-University, Goettingen, Germany; Affymetrix...
ABSTRACTNucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (... more ABSTRACTNucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species, Solanum chilense.We used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from three S. chilense plants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.Using these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.NLRs under selection between habitats ...
The genomic diversity of maize is reflected by a large number of SNPs and substantial structural ... more The genomic diversity of maize is reflected by a large number of SNPs and substantial structural variation. Here, we report the de novo assembly of two European Flint maize lines to remedy the scarcity of sequence resources for the Flint pool. EP1 and F7 are important founder lines of European hybrid breeding programs. The lines were sequenced on an Illumina platform at 320X and 225X coverage. Using NRGene's DeNovoMAGIC 2.0 technology, pseudochromosomes were assembled encompassing a total of 2,463 Mb for EP1 and 2,405 Mb for F7. Structural and functional annotation of the two genomes is currently in progress. The two high-quality de novo assemblies complement the existing maize pan-genome and will pave the way for future functional and comparative studies. (Note: Sandra Unterseer and Michael A. Seidel contributed equally to this work.)
Communications Biology
Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide... more Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence al...
Plant and Cell Physiology
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly... more Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of ...
Nature
Advances in genomics have expedited the improvement of several agriculturally important crops but... more Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a g...
BMC Plant Biology
Background Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical va... more Background Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species. Results Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a p...
Genes
Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domai... more Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signa...
Background Wild tomato species, like Solanum chilense, are important germplasm resources for enha... more Background Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing very heterozygote species limited in-depth studies on the genes involved in the above-mentioned processes. Findings We generated ~134 Gb of DNA and 157 Gb of RNA sequence data, which yielded a draft genome with an estimated length of 914 Mb in total encoding2 5,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNAseq data derived from leaf tissue samples. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% B...
Science (New York, N.Y.), Aug 17, 2018
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecul... more An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Science (New York, N.Y.), Jul 13, 2018
The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles ... more The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.
Cell research, Jan 10, 2017
Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing ... more Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA r...
Background: Receptor-like kinases are a prominent class of surface receptors that regulate many a... more Background: Receptor-like kinases are a prominent class of surface receptors that regulate many aspects of the plant life cycle. Despite recent advances the function of most receptor-like kinases remains elusive. Therefore, it is paramount to investigate these receptors. The task is complicated by the fact that receptor-like kinases belong to a large monophyletic family with many sub-clades. In general, functional analysis of gene family members by reverse genetics is often obscured by several issues, such as redundancy, subtle or difficult to detect phenotypes in mutants, or by decision problems regarding suitable biological and biochemical assays. Therefore, in many cases additional strategies have to be employed to allow inference of hypotheses regarding gene function. Results: We approached the function of genes encoding the nine-member STRUBBELIG-RECEPTOR FAMILY (SRF) class of putative leucine-rich repeat receptor-like kinases. Sequence comparisons show overall conservation but also divergence in predicted functional domains among SRF proteins. Interestingly, SRF1 undergoes differential splicing. As a result, SRF1 is predicted to exist in a standard receptor configuration and in a membrane-anchored receptor-like version that lacks most of the intracellular domain. Furthermore, SRF1 is characterised by a high degree of polymorphism between the Ler and Col accessions. Two independent T-DNA-based srf4 mutants showed smaller leaves while 35S::SRF4 plants displayed enlarged leaves. This is in addition to the strubbelig phenotype which has been described before. Additional single and several key double mutant combinations did not reveal obvious mutant phenotypes. Ectopic expression of several SRF genes, using the 35S promoter, resulted in male sterility. To gain possible insights into SRF gene function we employed a computational analysis of publicly available microarray data. We performed global expression profiling, coexpression analysis, and an analysis of the enrichment of gene ontology terms among coexpressed genes. The bioinformatic analyses raise the possibility that some SRF genes affect different aspects of cell wall biology. The results also indicate that redundancy is a minor aspect of the SRF family. Conclusion: The results provide evidence that SRF4 is a positive regulator of leaf size. In addition, they suggest that the SRF family is characterised by functional diversity and that some SRF genes may function in cell wall biology. They also indicate that complementing reverse genetics with bioinformatical data mining of genome-wide expression data aids in inferring hypotheses on possible functions for members of a gene family.
The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements... more The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition large-scale gene expression data for Arabidopsis thaliana have recently become available. Co-expression and evolutionarily conserved sequences are criteria, widely used to identify shared cis-regulatory elements. In our study we employ an integrated approach to combine two sources of information, co-expression and sequence conservation. Best candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes co-expressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified b...
The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera,
In plants, duplication of individual genes, long chromosomal regions, and complete genomes provid... more In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications, tandem and segmental duplications, in Arabidopsis for correlation, conservation, and differences of expression characteristics by making use of large genome-wide expression data as measured by the massively parallel signature sequencing method. Our analysis indicates that large fractions of duplicated gene pairs still share transcriptional characteristics. However, our results also indicate that expression divergence occurs frequently between duplicated gene pairs, a process which frequently might be employed for the retention of sequence redundant gene pairs. Preserved overall similarity between promoters of duplicated genes as well as preservation of individual cis-elements within the respective promoters indicates that the process of transcriptional neoand subfunctionalization is restri...
ABSTRACT Under a Defra-BBSRC funded LINK project between the Roslin Institute, Aviagen Ltd, Hy-Li... more ABSTRACT Under a Defra-BBSRC funded LINK project between the Roslin Institute, Aviagen Ltd, Hy-Line International, Affymetrix Ltd. and in cooperation with the German Synbreed project funded by BMBF we are developing a high density (600K) chicken SNP genotyping array that will enable highly accurate GWAS, genomic selection, selection signature analysis and fine mapping of QTLs. We have re-sequenced a large number of chickens (n=243) from 24 different lines including commercial broiler and layer lines, and experimental inbred layer lines. By aligning the sequence reads to the new version of chicken reference genome (Gallus_gallus-4.0), we identified a staggering 78M SNPs that are segregating in one or more lines. This large number of SNPs was pruned on several steps to select 1.8M for validation. The key selection criteria included SNP quality scores, uniformity of distribution across the genome, equal representation of broiler and layer SNPs, and their predicted reproducibility in arrays. These SNPs were validated for their true reproducibility, stable Mendelian inheritance and polymorphism by genotyping on 288 individuals comprising of commercial broilers, layers and some outgroup individuals. The final panel of 600K has been selected based on the validation results and with the key criteria of uniform distribution across the genome. Moreover, we have annotated the 1.8M SNPs to predict their genomic distribution and effects on protein coding; this information has also been used in selecting the final panel.
Metrics of the selection screens for 136 temperate inbred lines along the ten maize chromosomes b... more Metrics of the selection screens for 136 temperate inbred lines along the ten maize chromosomes based on genotyping data. (PDF 4242 kb)
Highlights d HKT1-type channels mediate a one-way sodium load into quinoa bladder cells d ClC tra... more Highlights d HKT1-type channels mediate a one-way sodium load into quinoa bladder cells d ClC transporters operate in the Cl À sequestration into vacuoles of bladder cells d The bladder cytoplasm is osmotically balanced by potassium and proline import d On the transcript level, bladders are ''constitutively active'' for salt sequestration
Xiangchao Gan, Angela Hay, Michiel Kwantes, Georg Haberer, Asis Hallab, Raffaele Dello Ioio, Hugo... more Xiangchao Gan, Angela Hay, Michiel Kwantes, Georg Haberer, Asis Hallab, Raffaele Dello Ioio, Hugo Hofhuis, Bjorn Pieper, Maria Cartolano, Ulla Neumann, Lachezar A. Nikolov, Baoxing Song, Mohsen Hajheidari, Roman Briskine, Evangelia Kougioumoutzi, Daniela Vlad, Suvi Broholm, Jotun Hein, Khalid Meksem, David Lightfoot, Kentaro K. Shimizu, Rie Shimizu-Inatsugi, Martha Imprialou, David Kudrna, Rod Wing, Shusei Sato, Peter Huijser, Dmitry Filatov, Klaus F. X. Mayer, Richard Mott, and Miltos Tsiantis
C. Boschiero, A.A. Gheyas, A. Kranis, F.S. Turner, K. Watson, L. Yu, S. Smith, R. Talbot, P. Kais... more C. Boschiero, A.A. Gheyas, A. Kranis, F.S. Turner, K. Watson, L. Yu, S. Smith, R. Talbot, P. Kaiser, P.M. Hocking, J.E. Fulton, T.M. Strom, G. Haberer, H.R. Fries, S. Weigend, R. Preisinger, S. Qanbari, H. Simianer, F. Brew, J.A.Woolliams, and D.W. Burt Dept. of Genetics and Genomics, The Roslin Institute and R(D)SVS, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK; Aviagen, Newbridge, Midlothian, EH28 8SZ, Scotland, UK; Hy-Line International, Dallas Center, IA, 50063, USA; Inst. of Human Genetic, Helmholtz Center Munich, 85764 Neuherberg, Germany; Inst. for Bioinformatics and Systems, Helmholtz Center Munich, 85764 Neuherberg, Germany; Chair of Animal Breeding, Technische Universität München, 85354 FreisingWeihenstephan, Germany; Inst. of Farm Animal Genetics, Friedrich Loeffler Institute, 31535 Neustadt-Mariensee; Germany; Lohmann Tierzucht GmbH, 27454 Cuxhaven, Germany; Dept. of Animal Sciences, Georg-August-University, Goettingen, Germany; Affymetrix...
ABSTRACTNucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (... more ABSTRACTNucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species, Solanum chilense.We used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from three S. chilense plants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.Using these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.NLRs under selection between habitats ...
The genomic diversity of maize is reflected by a large number of SNPs and substantial structural ... more The genomic diversity of maize is reflected by a large number of SNPs and substantial structural variation. Here, we report the de novo assembly of two European Flint maize lines to remedy the scarcity of sequence resources for the Flint pool. EP1 and F7 are important founder lines of European hybrid breeding programs. The lines were sequenced on an Illumina platform at 320X and 225X coverage. Using NRGene's DeNovoMAGIC 2.0 technology, pseudochromosomes were assembled encompassing a total of 2,463 Mb for EP1 and 2,405 Mb for F7. Structural and functional annotation of the two genomes is currently in progress. The two high-quality de novo assemblies complement the existing maize pan-genome and will pave the way for future functional and comparative studies. (Note: Sandra Unterseer and Michael A. Seidel contributed equally to this work.)
Communications Biology
Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide... more Crop productivity must increase at unprecedented rates to meet the needs of the growing worldwide population. Exploiting natural variation for the genetic improvement of crops plays a central role in increasing productivity. Although current genomic technologies can be used for high-throughput identification of genetic variation, methods for efficiently exploiting this genetic potential in a targeted, systematic manner are lacking. Here, we developed a haplotype-based approach to identify genetic diversity for crop improvement using genome assemblies from 15 bread wheat (Triticum aestivum) cultivars. We used stringent criteria to identify identical-by-state haplotypes and distinguish these from near-identical sequences (~99.95% identity). We showed that each cultivar shares ~59 % of its genome with other sequenced cultivars and we detected the presence of extended haplotype blocks containing hundreds to thousands of genes across all wheat chromosomes. We found that genic sequence al...
Plant and Cell Physiology
Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly... more Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of ...
Nature
Advances in genomics have expedited the improvement of several agriculturally important crops but... more Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a g...
BMC Plant Biology
Background Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical va... more Background Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species. Results Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a p...
Genes
Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domai... more Nucleotide-binding leucine-rich-repeat (LRR) receptors (NLRs) with non-canonical integrated domains (NLR-IDs) are widespread in plant genomes. Zinc-finger BED (named after the Drosophila proteins Boundary Element-Associated Factor and DNA Replication-related Element binding Factor, named BED hereafter) are among the most frequently found IDs. Five BED-NLRs conferring resistance against bacterial and fungal pathogens have been characterized. However, it is unknown whether BED-NLRs function in a manner similar to other NLR-IDs. Here, we used chromosome-level assemblies of wheat to explore the Yr7 and Yr5a genomic regions and show that, unlike known NLR-ID loci, there is no evidence for a NLR-partner in their vicinity. Using neighbor-network analyses, we observed that BED domains from BED-NLRs share more similarities with BED domains from single-BED proteins and from BED-containing proteins harboring domains that are conserved in transposases. We identified a nuclear localization signa...
Background Wild tomato species, like Solanum chilense, are important germplasm resources for enha... more Background Wild tomato species, like Solanum chilense, are important germplasm resources for enhanced stress resistance in tomato breeding. In addition, S. chilense serves as a model system to study adaptation of plants to drought and to investigate the evolution of seed banks. However to date, the absence of a well annotated reference genome in this compulsory outcrossing very heterozygote species limited in-depth studies on the genes involved in the above-mentioned processes. Findings We generated ~134 Gb of DNA and 157 Gb of RNA sequence data, which yielded a draft genome with an estimated length of 914 Mb in total encoding2 5,885 high-confidence (hc) predicted gene models, which show homology to known protein-coding genes of other tomato species. Approximately 71% (18,290) of the hc gene models are additionally supported by RNAseq data derived from leaf tissue samples. A Benchmarking with Universal Single-Copy Orthologs (BUSCO) analysis of predicted gene models retrieved 93.3% B...
Science (New York, N.Y.), Aug 17, 2018
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecul... more An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Science (New York, N.Y.), Jul 13, 2018
The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles ... more The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.
Cell research, Jan 10, 2017
Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing ... more Chenopodium quinoa is a halophytic pseudocereal crop that is being cultivated in an ever-growing number of countries. Because quinoa is highly resistant to multiple abiotic stresses and its seed has a better nutritional value than any other major cereals, it is regarded as a future crop to ensure global food security. We generated a high-quality genome draft using an inbred line of the quinoa cultivar Real. The quinoa genome experienced one recent genome duplication about 4.3 million years ago, likely reflecting the genome fusion of two Chenopodium parents, in addition to the γ paleohexaploidization reported for most eudicots. The genome is highly repetitive (64.5% repeat content) and contains 54 438 protein-coding genes and 192 microRNA genes, with more than 99.3% having orthologous genes from glycophylic species. Stress tolerance in quinoa is associated with the expansion of genes involved in ion and nutrient transport, ABA homeostasis and signaling, and enhanced basal-level ABA r...