Andrea Zuccolo
A5032756420- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic Mapping and Diversity in Plants and Animals
- Genetic diversity and population structure
- Plant Disease Resistance and Genetics
- Rangeland and Wildlife Management
- Smart Agriculture and AI
- Plant Virus Research Studies
- Agricultural Systems and Practices
- Plant Molecular Biology Research
- Rice Cultivation and Yield Improvement
- Plant Reproductive Biology
- Plant and Fungal Interactions Research
- Phytochemistry and biological activities of Ficus species
- CRISPR and Genetic Engineering
- Banana Cultivation and Research
- GABA and Rice Research
- Plant Physiology and Cultivation Studies
- Plant Pathogenic Bacteria Studies
- Plant Genetic and Mutation Studies
- Photosynthetic Processes and Mechanisms
- Legume Nitrogen Fixing Symbiosis
- Advanced biosensing and bioanalysis techniques
- Plant responses to water stress
- Bioenergy crop production and management
King Abdullah University of Science and Technology
2019-2025
Scuola Superiore Sant'Anna
2016-2025
Institute of Crop Science
2024
University of Arizona
2005-2018
Istituto di Genomica Applicata
2008-2017
University of Udine
2004-2009
University of Perugia
2007-2008
University of Pisa
2007-2008
Danieli (Italy)
2008
University of Milan
2005
A-Maize-ing Maize is one of our oldest and most important crops, having been domesticated approximately 9000 years ago in central Mexico. Schnable et al. (p. 1112 ; see the cover) present results sequencing B73 inbred maize line. The findings elucidate how became diploid after an ancestral doubling its chromosomes reveals transposable element movement activity recombination. Vielle-Calzada 1078 ) have sequenced Palomero Toluqueño ( landrace, a highland popcorn from Mexico, which, when...
Recent evidence suggests that the microbial community in human intestine may play an important role pathogenesis of obesity. We examined 184,094 sequences 16S rRNA genes from PCR amplicons by using 454 pyrosequencing technology to compare structures 9 individuals, 3 each categories normal weight, morbidly obese, and post-gastric-bypass surgery. Phylogenetic analysis demonstrated although Bacteria intestinal were highly diverse, they fell mainly into 6 bacterial divisions had distinct...
Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated ordered physical, genetic functional sequence resource that describes barley gene-space in structured whole-genome context. We developed physical map 4.98 Gb, more than 3.90 Gb anchored to high-resolution map. Projecting deep shotgun assembly, complementary DNA RNA data onto this framework supports...
Conifers have dominated forests for more than 200 million years and are of huge ecological economic importance. Here we present the draft assembly 20-gigabase genome Norway spruce (Picea abies), first available any gymnosperm. The number well-supported genes (28,354) is similar to >100 times smaller Arabidopsis thaliana, there no evidence a recent whole-genome duplication in gymnosperm lineage. Instead, large size seems result from slow steady accumulation diverse set long-terminal repeat...
The International Peach Genome Initiative reports the high quality draft genome sequence of peach (Prunus persica). They also resequenced ten additional P. persica accessions, as well those Prunus ferganensis, kansuensis, davidiana and mira. Rosaceae is most important fruit-producing clade, its key commercially relevant genera (Fragaria, Rosa, Rubus Prunus) show broadly diverse growth habits, fruit types compact diploid genomes. Peach, a species, one best genetically characterized deciduous...
Genome sequences of nine species citrus, including oranges, pummelos and mandarins, reveal pathways domestication provide resources for breeding. Cultivated citrus are selections from, or hybrids of, wild progenitor whose identities contributions to remain controversial. Here we sequence compare genomes—a high-quality reference haploid clementine genome mandarin, pummelo, sweet-orange sour-orange genomes—and show that cultivated types derive from two species. Although represent one species,...
The genus Oryza is a model system for the study of molecular evolution over time scales ranging from few thousand to 15 million years. Using 13 reference genomes spanning species tree, we show that despite large-scale chromosomal rearrangements rapid diversification mirrored by lineage-specific emergence and turnover many novel elements, including transposons, potential new coding noncoding genes. Our resolves controversial areas phylogeny, showing complex history introgression among...
The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African is not the same origin as Asian (Oryza sativa L.) but rather an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation O. genome detailed analyses its evolutionary history domestication selection. Population genomics 20 94 barthii accessions support hypothesis that was domesticated single region along Niger river opposed to noncentric events...
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of International Genome Sequencing (IRGSP), manually curated annotation sequence, and other genomics information that could be useful for comprehensive understanding rice biology. Since last publication RAP-DB, IRGSP has been revised reassembled. In addition, a large number rice-expressed tags have released, functional resources produced worldwide. Thus, we thoroughly updated our by manual...
Conifers dominate the world's forest ecosystems and are most widely planted tree species. Their giant complex genomes present great challenges for assembling a complete reference genome evolutionary genomic studies. We 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) revealed that its size is mostly attributable to huge intergenic regions long introns with high transposable element (TE) content. Large genes exhibited higher expressions levels. Despite lack recent...
Understanding and exploiting genetic diversity is a key factor for the productive stable production of rice. Here, we utilize 73 high-quality genomes that encompass subpopulation structure Asian rice (Oryza sativa), plus two wild relatives (O. rufipogon O. punctata), to build pan-genome inversion index 1769 non-redundant inversions span an average ~29% sativa cv. Nipponbare reference genome sequence. Using this index, estimate rate ~700 per million years in rice, which 16 50 times higher...
As the human population grows from 7.8 billion to 10 over next 30 years, breeders must do everything possible create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand thus, knowledge full repertoire genetic diversity exists germplasm banks across globe is required. To meet demand, we describe generation, validation preliminary analyses transposable element long-range...
Significance We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels genetic variation. Our results showed positive negative selection broadly affects patterns genomic variation, but to varying degrees across coding noncoding regions. The strength rates divergence were strongly related differences in gene expression coexpression network connectivity. These highlight the importance both...
Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although rice serves as an essential tool for biological research, little is known about evolution of other types. They contain a historical record genomic changes that led to diversification this genus around world well untapped reservoir agriculturally traits. To investigate collective genome, we sequenced and compared nine orthologous regions encompassing Adh1-Adh2 genes (from six diploid with...
Abstract Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, includes the world's most important food crop – rice ( sativa [AA]). Genome size variation in more than 3-fold ranges from 357 Mbp glaberrima [AA] to 1283 polyploid ridleyi [HHJJ]. Because repetitive elements are known play a significant role variation, we constructed random sheared small insert genomic libraries 12 representative species conducted comprehensive study element composition,...
Summary Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size organization. Although LTR retrotransposon content variation is well documented, the dynamics genomic flux caused by their activity are poorly understood on an evolutionary time scale. This primarily because lack experimental system composed closely related species whose divergence times within limits ability to detect ancestrally...
Comparative evolutionary analysis of whole genomes requires not only accurate annotation gene space, but also proper the repetitive fraction which is often largest component most if all larger than 50 kb in size.
The ripening physiology of detached fruit is altered by low oxygen conditions with profound effects on quality parameters. To study hypoxia-related processes and regulatory mechanisms, apple (Malus domestica, cv Granny Smith) fruit, harvested at commercial ripening, were kept 1°C under normoxic (control) hypoxic (0.4 0.8 kPa oxygen) for up to 60 days. NMR analyses cortex tissue identified eight metabolites showing significantly different accumulations between samples, ethanol alanine...
Due to DNA heterozygosity and repeat content, assembly of non-model plant genomes is challenging. Herein, we report a high-quality genome reference one the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single-molecule, real-time sequencing. The ~333 Mbp in size, which 80% has been anchored 13 chromosomes. Genome-wide analysis N6 -methyladenine N4 -methylcytosine revealed high methylation levels both genes transposable elements, prevalence methylated over...
Abstract Pigmented rice ( Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies 5 varieties evaluated the genetic variation among 51 by resequencing an additional 46 varieties. Phylogenetic analyses divided into four varietal groups: Geng-japonica , Xian-indica circum- Aus Basmati. Metabolomics ionomics profiling revealed that black are in aromatic secondary metabolites. We established...
Abstract DNA (class 2) transposons are mobile genetic elements which move within their ‘host’ genome through excising and re-inserting elsewhere. Although the rice contains tens of thousands such elements, actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms species Oryza sativa glaberrima , we find that repair following excisions associated with an increased number mutations sequences neighbouring transposon. Indeed, 3,000 bp flanking excised can contain 10...