Antimo Di Donato | Università degli Studi di Napoli "Federico II" (original) (raw)
Uploads
Papers by Antimo Di Donato
Euphytica, 2017
The genetic recombination process mediated by crossing over (CO) events is not random along chrom... more The genetic recombination process mediated by crossing over (CO) events is not random along chromosomes and its occurrence can drive molecular evolution and genome organization. In this study, a position-recoding algorithm was developed to convert cytological CO detected in tomato (Solanum lycopersicum) chromosomes into physical genome coordinates. The meiotic recombination profile displays a punctual distribution of the crossover frequency along the chromosomes, which may be used to conduct further analysis. The recombination profile is not uniform and follows the same distribution profile as the coding sequences. On analyzing the positions of resistance (R) genes we found that most nucleotide-binding domain-leucine-rich repeat (NB-LRR) loci accumulate in hot recombination regions of the distal subtelomeric regions, while few NB-LRR loci tend to reside in proximal cold recombination regions. As the local meiotic crossover frequency is known to make an important contribution to the molecular evolution rate of a genome region, this divergent drift of the resistance loci toward hot and cold recombination areas may reflect different evolution needs for the species with respect to plant-pathogen co-evolution. The generation of novel haplotypes, promoted by recombination reshuffling, is more favorable for R loci that require rapid diversification to overcome the emergence of new pathogen races. Instead, cold areas may be more advantageous for maintaining R genes that confer durable resistance over time. Knowledge of chromosome region recombination rates and R-gene distribution may be useful to steer future disease resistance breeding schemes and select favorable allele combinations.
Frontiers in genetics, 2017
Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the res... more Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post inoculation (DPI) at transcriptomic and genomic levels. Results: A comparative RNA-seq experiment on TF (susceptible to ZYMV) and 381e (tolerant to ZYMV), allowed to evaluate 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus, and key regulators of plant virus intercellular movement. Moreover, the genome mapping of transcripts allowed the identification of two chromosome regions rich in SNPs (Sin...
In order to investigate the diversification of important agronomic traits in plants, a conservati... more In order to investigate the diversification of important agronomic traits in plants, a conservation and evolution study of nucleotide binding genes from bacteria to plant kingdom was performed. The pathogen recognition genes were detected and classified in 102 organisms. In particular, the expansion and/or conservation of R-gene subgroups among organisms was investigated. Several large of NLR groups were found involved in important clustering events. A focus on orthologous pathogen recognition gene-rich regions in solanaceous species regions was also provided. A complete catalogue of eggplant (Solanum melongena) and pepper (Capsicum annuum) nucleotide-binding site (NBS), receptor-like protein (RLP) and receptor-like kinase (RLK) genes was generated and compared with tomato (Solanum lycopersicum) genomic repertoire. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analyzed species. The information obtained...
Genome Biology and Evolution
Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intr... more Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multi-taxa reconstruction of NB-domain associations allowed us to identify the first NB-LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from TIR-NB-LRR (TNL) members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis supports the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell surface LRR receptors.
Frontiers in Plant Science
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). I... more The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
Nucleic acids research, Jan 4, 2018
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user... more The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and alg...
Nucleic acids research, Jan 4, 2018
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user... more The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and alg...
BMC Plant Biology, 2015
Background: ATP-binding cassette proteins have been recognized as playing a crucial role in the r... more Background: ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants.
Euphytica, 2017
The genetic recombination process mediated by crossing over (CO) events is not random along chrom... more The genetic recombination process mediated by crossing over (CO) events is not random along chromosomes and its occurrence can drive molecular evolution and genome organization. In this study, a position-recoding algorithm was developed to convert cytological CO detected in tomato (Solanum lycopersicum) chromosomes into physical genome coordinates. The meiotic recombination profile displays a punctual distribution of the crossover frequency along the chromosomes, which may be used to conduct further analysis. The recombination profile is not uniform and follows the same distribution profile as the coding sequences. On analyzing the positions of resistance (R) genes we found that most nucleotide-binding domain-leucine-rich repeat (NB-LRR) loci accumulate in hot recombination regions of the distal subtelomeric regions, while few NB-LRR loci tend to reside in proximal cold recombination regions. As the local meiotic crossover frequency is known to make an important contribution to the molecular evolution rate of a genome region, this divergent drift of the resistance loci toward hot and cold recombination areas may reflect different evolution needs for the species with respect to plant-pathogen co-evolution. The generation of novel haplotypes, promoted by recombination reshuffling, is more favorable for R loci that require rapid diversification to overcome the emergence of new pathogen races. Instead, cold areas may be more advantageous for maintaining R genes that confer durable resistance over time. Knowledge of chromosome region recombination rates and R-gene distribution may be useful to steer future disease resistance breeding schemes and select favorable allele combinations.
Frontiers in genetics, 2017
Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the res... more Background: Cucurbita pepo is high susceptible to Zucchini yellow mosaic virus (ZYMV) and the resistance found in several wild species does not provide complete or broad-spectrum resistance. In this study, a source of tolerance introgressed in C. pepo (381e) from C. moschata, in True French (TF) background, was investigated 12 days post inoculation (DPI) at transcriptomic and genomic levels. Results: A comparative RNA-seq experiment on TF (susceptible to ZYMV) and 381e (tolerant to ZYMV), allowed to evaluate 33,000 expressed transcripts and to identify 146 differentially expressed genes (DEGs) in 381e, mainly involved in photosynthesis, transcription, cytoskeleton organization and callose synthesis. By contrast, the susceptible line True French triggered oxidative processes related to response to biotic stimulus, and key regulators of plant virus intercellular movement. Moreover, the genome mapping of transcripts allowed the identification of two chromosome regions rich in SNPs (Sin...
In order to investigate the diversification of important agronomic traits in plants, a conservati... more In order to investigate the diversification of important agronomic traits in plants, a conservation and evolution study of nucleotide binding genes from bacteria to plant kingdom was performed. The pathogen recognition genes were detected and classified in 102 organisms. In particular, the expansion and/or conservation of R-gene subgroups among organisms was investigated. Several large of NLR groups were found involved in important clustering events. A focus on orthologous pathogen recognition gene-rich regions in solanaceous species regions was also provided. A complete catalogue of eggplant (Solanum melongena) and pepper (Capsicum annuum) nucleotide-binding site (NBS), receptor-like protein (RLP) and receptor-like kinase (RLK) genes was generated and compared with tomato (Solanum lycopersicum) genomic repertoire. Orthologous relationships among clustering loci were found, and interesting reshuffling within given loci was observed for each analyzed species. The information obtained...
Genome Biology and Evolution
Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intr... more Plant innate immunity mostly relies on nucleotide-binding (NB) and leucine-rich repeat (LRR) intracellular receptors to detect pathogen-derived molecules and to induce defense responses. A multi-taxa reconstruction of NB-domain associations allowed us to identify the first NB-LRR arrangement in the Chlorophyta division of the Viridiplantae. Our analysis points out that the basic NOD-like receptor (NLR) unit emerged in Chlorophytes by horizontal transfer and its diversification started from TIR-NB-LRR (TNL) members. The operon-based genomic structure of Chromochloris zofingiensis NLR copies suggests a functional origin of NLR clusters. Moreover, the transmembrane signatures of NLR proteins in the unicellular alga C. zofingiensis supports the hypothesis that the NLR-based immunity system of plants derives from a cell-surface surveillance system. Taken together, our findings suggest that NLRs originated in unicellular algae and may have a common origin with cell surface LRR receptors.
Frontiers in Plant Science
The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). I... more The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture.
Nucleic acids research, Jan 4, 2018
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user... more The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and alg...
Nucleic acids research, Jan 4, 2018
The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user... more The Plant Resistance Genes database (PRGdb; http://prgdb.org) has been redesigned with a new user interface, new sections, new tools and new data for genetic improvement, allowing easy access not only to the plant science research community but also to breeders who want to improve plant disease resistance. The home page offers an overview of easy-to-read search boxes that streamline data queries and directly show plant species for which data from candidate or cloned genes have been collected. Bulk data files and curated resistance gene annotations are made available for each plant species hosted. The new Gene Model view offers detailed information on each cloned resistance gene structure to highlight shared attributes with other genes. PRGdb 3.0 offers 153 reference resistance genes and 177 072 annotated candidate Pathogen Receptor Genes (PRGs). Compared to the previous release, the number of putative genes has been increased from 106 to 177 K from 76 sequenced Viridiplantae and alg...
BMC Plant Biology, 2015
Background: ATP-binding cassette proteins have been recognized as playing a crucial role in the r... more Background: ATP-binding cassette proteins have been recognized as playing a crucial role in the regulation of growth and resistance processes in all kingdoms of life. They have been deeply studied in vertebrates because of their role in drug resistance, but much less is known about ABC superfamily functions in plants.