The Experts below are selected from a list of 978 Experts worldwide ranked by ideXlab platform
Edward S Buckler - One of the best experts on this subject based on the ideXlab platform.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
The Plant Genome, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: (L.) L. and Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for genes resistant to pseudogenization in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their homologs are also resisting gene loss. Protein-encoding maize transcripts and their homologs have higher guanine-cytosine (GC) content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their homologs. These results suggest that similar genes may be decaying into pseudogenes in both genera after a shared ancient polyploidy event. The transcriptome assemblies provide a high-quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
bioRxiv, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize and its sister genus, Tripsacum , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum . Genes with experimental protein evidence in maize were good candidates for genes under purifying selection in both genera because pseudogenes by definition do not produce protein. We tested whether genes with protein evidence are resisting gene loss in maize and whether their homologs are also resisting gene loss in Tripsacum . Protein-encoding maize transcripts and their Tripsacum homologs have higher GC content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that gene loss is occurring in a similar fashion in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high quality genomic resource that can provide insight into the evolution of maize, an highly valuable crop worldwide.
-
the evolution of ribosomal dna divergent paralogues and phylogenetic implications
Genetics, 1997Co-Authors: Edward S Buckler, Anthony Ippolito, Timothy P HoltsfordAbstract:Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.
Christine M Gault - One of the best experts on this subject based on the ideXlab platform.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
The Plant Genome, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: (L.) L. and Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for genes resistant to pseudogenization in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their homologs are also resisting gene loss. Protein-encoding maize transcripts and their homologs have higher guanine-cytosine (GC) content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their homologs. These results suggest that similar genes may be decaying into pseudogenes in both genera after a shared ancient polyploidy event. The transcriptome assemblies provide a high-quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
bioRxiv, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize and its sister genus, Tripsacum , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum . Genes with experimental protein evidence in maize were good candidates for genes under purifying selection in both genera because pseudogenes by definition do not produce protein. We tested whether genes with protein evidence are resisting gene loss in maize and whether their homologs are also resisting gene loss in Tripsacum . Protein-encoding maize transcripts and their Tripsacum homologs have higher GC content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that gene loss is occurring in a similar fashion in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high quality genomic resource that can provide insight into the evolution of maize, an highly valuable crop worldwide.
Karl A Kremling - One of the best experts on this subject based on the ideXlab platform.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
The Plant Genome, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole-genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize ( L.) and its sister genus, , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for exist, it is unknown whether grasses and maize have maintained a similar set of genes that have resisted decay into pseudogenes. Here we present high-quality de novo transcriptome assemblies for two species: (L.) L. and Porter ex Vasey. Genes with experimental protein evidence in maize were good candidates for genes resistant to pseudogenization in both genera because pseudogenes by definition do not produce protein. We tested whether 15,160 maize genes with protein evidence are resisting gene loss and whether their homologs are also resisting gene loss. Protein-encoding maize transcripts and their homologs have higher guanine-cytosine (GC) content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their homologs. These results suggest that similar genes may be decaying into pseudogenes in both genera after a shared ancient polyploidy event. The transcriptome assemblies provide a high-quality genomic resource that can provide insight into the evolution of maize, a highly valuable crop worldwide.
-
Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy
bioRxiv, 2018Co-Authors: Christine M Gault, Karl A Kremling, Edward S BucklerAbstract:Plant genomes reduce in size following a whole genome duplication event, and one gene in a duplicate gene pair can lose function in absence of selective pressure to maintain duplicate gene copies. Maize and its sister genus, Tripsacum , share a genome duplication event that occurred 5 to 26 million years ago. Because few genomic resources for Tripsacum exist, it is unknown whether Tripsacum grasses and maize have maintained a similar set of genes under purifying selection. Here we present high quality de novo transcriptome assemblies for two species: Tripsacum dactyloides and Tripsacum floridanum . Genes with experimental protein evidence in maize were good candidates for genes under purifying selection in both genera because pseudogenes by definition do not produce protein. We tested whether genes with protein evidence are resisting gene loss in maize and whether their homologs are also resisting gene loss in Tripsacum . Protein-encoding maize transcripts and their Tripsacum homologs have higher GC content, higher gene expression levels, and more conserved expression levels than putatively untranslated maize transcripts and their Tripsacum homologs. These results indicate that gene loss is occurring in a similar fashion in both genera after a shared ancient polyploidy event. The Tripsacum transcriptome assemblies provide a high quality genomic resource that can provide insight into the evolution of maize, an highly valuable crop worldwide.
Daniel Grimanelli - One of the best experts on this subject based on the ideXlab platform.
-
Seed development and inheritance studies in apomictic maize-Tripsacum hybrids reveal barriers for the transfer of apomixis into sexual crops.
Int J Dev Biol, 2009Co-Authors: Olivier Leblanc, Daniel Grimanelli, Martha Hernandez-rodriguez, Pablo A Galindo, Ana M Soriano-martinez, Enrico PerottiAbstract:Apomixis in plants covers a variety of cloning systems through seeds of great potential for plant breeding. Among long-standing approaches for crop improvement is the attempt to exploit wild relatives as natural, vast reservoirs for novel genetic variation. With regard to apomixis, maize possesses an apomictic wild relative, Tripsacum, which we used to produce advanced maize-Tripsacum hybrid generations. However, introgression of apomixis in maize has failed so far. In order to understand the hows and whys, we undertook characterization of seed development and inheritance studies in these materials. We show that apomictic seeds suffer from epigenetic loads. Both seed tissues, the endosperm and the embryo, displayed developmental defects resulting from imbalanced parental genomic contributions and aberrant methylation patterns, respectively. Progeny characterization of several maize-Tripsacum hybrid generations allowed significant progress toward the unraveling of the genetics of apomixis. First, chromosome deletion mapping showed that expression of apomixis requires one single Tripsacum chromosome. However, inheritance studies revealed that female gametes inheriting this segment were unequivalent carriers depending on their origin: unreduced gametes transmit a functional segment, whereas progeny derived from reduced ones reproduced sexually. Finally, chromosomal or genomic dosage variation barely affected the apomictic phenotype suggesting no dependency for ploidy in these materials. We conclude that epigenetic information imposes constraints for apomictic seed development and seems pivotal for transgenerational propagation of apomixis. The nature of the triggering mechanisms remains unknown as-yet, but it certainly explains the modest success relative to the development of apomictic maize thus far.
-
Timing of the maternal-to-zygotic transition during early seed development in maize.
The Plant cell, 2005Co-Authors: Daniel Grimanelli, Enrico Perotti, Jorge Ramirez, Olivier LeblancAbstract:In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. Recent data in plants also suggest maternal control over early seed development, but the actual timing of zygotic genome activation is unclear. Here, we analyzed the timing of the maternal-to-zygotic transition during early Zea mays seed development. We show that for 16 genes expressed during early seed development, only maternally inherited alleles are detected during 3 d after fertilization in both the embryo and the endosperm. Microarray analyses of precocious embryonic development in apomictic hybrids between maize and its wild relative, Tripsacum, demonstrate that early embryo development occurs without significant quantitative changes to the transcript population in the ovule before fertilization. Precocious embryo development is also correlated with a higher proportion of polyadenylated mRNA in the ovules. Our data suggest that the maternal-to-zygotic transition occurs several days after fertilization. By contrast, novel transcription accompanies early endosperm development, indicating that different mechanisms are involved in the initiation of endosperm and embryo development.
-
Timing of the maternal-to-zygotic transition during early seed development in maize. The Plant Cell 17
2005Co-Authors: Daniel Grimanelli, Enrico Perotti, Jorge Ramirez, Olivier LeblancaAbstract:In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. Recent data in plants also suggest maternal control over early seed development, but the actual timing of zygotic genome activation is unclear. Here, we analyzed the timing of the maternal-to-zygotic transition during early Zea mays seed de-velopment.We show that for 16genes expressedduring early seeddevelopment, onlymaternally inherited alleles are detected during 3dafter fertilization inboth theembryoand theendosperm.Microarray analyses ofprecocious embryonicdevelopment in apomictic hybrids between maize and its wild relative, Tripsacum, demonstrate that early embryo development occurs without significant quantitative changes to the transcript population in the ovule before fertilization. Precocious embryo development is also correlated with a higher proportion of polyadenylated mRNA in the ovules. Our data suggest that the maternal-to-zygotic transition occurs several days after fertilization. By contrast, novel transcription accompanies early endosperm development, indicating that different mechanisms are involved in the initiation of endosperm and embryo development
-
Timing of the maternal-to-zygotic transition during early seed development in maize. Plant Cell 17
2005Co-Authors: Daniel Grimanelli, Enrico Perotti, Jorge Ramirez, Olivier LeblancaAbstract:In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. Recent data in plants also suggest maternal control over early seed development, but the actual timing of zygotic genome activation is unclear. Here, we analyzed the timing of the maternal-to-zygotic transition during early Zea mays seed de-velopment.We show that for 16genes expressedduring early seeddevelopment, onlymaternally inherited alleles are detected during 3dafter fertilization inboth theembryoand theendosperm.Microarray analyses ofprecocious embryonicdevelopment in apomictic hybrids between maize and its wild relative, Tripsacum, demonstrate that early embryo development occurs without significant quantitative changes to the transcript population in the ovule before fertilization. Precocious embryo development is also correlated with a higher proportion of polyadenylated mRNA in the ovules. Our data suggest that the maternal-to-zygotic transition occurs several days after fertilization. By contrast, novel transcription accompanies early endosperm development, indicating that different mechanisms are involved in the initiation of endosperm and embryo development
-
Novel sources of resistance to Striga hermonthica in Tripsacum dactyloides, a wild relative of maize
New Phytologist, 2003Co-Authors: A. L. Gurney, Fred Kanampiu, Daniel Grimanelli, David Hoisington, Julie D. Scholes, Malcolm C. PressAbstract:Summary • The parasitic weed Striga hermonthica lowers cereal yield in small-holder farms in Africa. Complete resistance in maize to S. hermonthica infection has not been identified. A valuable source of resistance to S. hermonthica may lie in the genetic potential of wild germplasm. • The susceptibility of a wild relative of maize, Tripsacum dactyloides and a Zea mays‐T. dactyloides hybrid to S. hermonthica infection was determined. Striga hermonthica development was arrested after attachment to T. dactyloides . Vascular continuity was established between parasite and host but there was poor primary haustorial tissue differentiation on T. dactyloides compared with Z. mays . Partial resistance was inherited in the hybrid. • Striga hermonthica attached to Z. mays was manipulated such that different secondary haustoria could attach to different hosts. Secondary haustoria formation was inhibited on T. dactyloides , moreover, subsequent haustoria formation on Z. mays was also impaired. • Results suggest that T. dactyloides produces a signal that inhibits haustorial development: this signal may be mobile within the parasite haustorial root system.
Olivier Leblanc - One of the best experts on this subject based on the ideXlab platform.
-
Seed development and inheritance studies in apomictic maize-Tripsacum hybrids reveal barriers for the transfer of apomixis into sexual crops.
Int J Dev Biol, 2009Co-Authors: Olivier Leblanc, Daniel Grimanelli, Martha Hernandez-rodriguez, Pablo A Galindo, Ana M Soriano-martinez, Enrico PerottiAbstract:Apomixis in plants covers a variety of cloning systems through seeds of great potential for plant breeding. Among long-standing approaches for crop improvement is the attempt to exploit wild relatives as natural, vast reservoirs for novel genetic variation. With regard to apomixis, maize possesses an apomictic wild relative, Tripsacum, which we used to produce advanced maize-Tripsacum hybrid generations. However, introgression of apomixis in maize has failed so far. In order to understand the hows and whys, we undertook characterization of seed development and inheritance studies in these materials. We show that apomictic seeds suffer from epigenetic loads. Both seed tissues, the endosperm and the embryo, displayed developmental defects resulting from imbalanced parental genomic contributions and aberrant methylation patterns, respectively. Progeny characterization of several maize-Tripsacum hybrid generations allowed significant progress toward the unraveling of the genetics of apomixis. First, chromosome deletion mapping showed that expression of apomixis requires one single Tripsacum chromosome. However, inheritance studies revealed that female gametes inheriting this segment were unequivalent carriers depending on their origin: unreduced gametes transmit a functional segment, whereas progeny derived from reduced ones reproduced sexually. Finally, chromosomal or genomic dosage variation barely affected the apomictic phenotype suggesting no dependency for ploidy in these materials. We conclude that epigenetic information imposes constraints for apomictic seed development and seems pivotal for transgenerational propagation of apomixis. The nature of the triggering mechanisms remains unknown as-yet, but it certainly explains the modest success relative to the development of apomictic maize thus far.
-
Timing of the maternal-to-zygotic transition during early seed development in maize.
The Plant cell, 2005Co-Authors: Daniel Grimanelli, Enrico Perotti, Jorge Ramirez, Olivier LeblancAbstract:In animals, early embryonic development is largely dependent on maternal transcripts synthesized during gametogenesis. Recent data in plants also suggest maternal control over early seed development, but the actual timing of zygotic genome activation is unclear. Here, we analyzed the timing of the maternal-to-zygotic transition during early Zea mays seed development. We show that for 16 genes expressed during early seed development, only maternally inherited alleles are detected during 3 d after fertilization in both the embryo and the endosperm. Microarray analyses of precocious embryonic development in apomictic hybrids between maize and its wild relative, Tripsacum, demonstrate that early embryo development occurs without significant quantitative changes to the transcript population in the ovule before fertilization. Precocious embryo development is also correlated with a higher proportion of polyadenylated mRNA in the ovules. Our data suggest that the maternal-to-zygotic transition occurs several days after fertilization. By contrast, novel transcription accompanies early endosperm development, indicating that different mechanisms are involved in the initiation of endosperm and embryo development.
-
chromosome doubling in Tripsacum the production of artificial sexual tetraploid plants
Plant Breeding, 1995Co-Authors: Olivier Leblanc, M Duenas, Martha Hernandez, S Bello, V Garcia, J Berthaud, Yves SavidanAbstract:A collection of embryogenic diploid calli of Tripsacum was established and treated with colchicine to induce chromosome doubling. Sections containing duplicated cells in calli were identified using flow cytometry and ploidy level was determined in the regenerated plantlets. Tetraploid plants from several origins were obtained. In contrast to wild polyploid plants, which show apomictic development, the regenerated tetraploid plants reproduced sexually. By hybridizing these plants with wild tetra- ploid apomicts, various populations were established; these will allow a study of the inheritance of apomixis in Tripsacum.
