Andrea Zuccolo
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View article: Reference-grade genomes as a tool for conserving Kazakhstan’s national pride species: the cases of the Caspian seal and Greig’s tulip
Reference-grade genomes as a tool for conserving Kazakhstan’s national pride species: the cases of the Caspian seal and Greig’s tulip Open
This article presents the potential of third-generation sequencing (TGS) technologies to support biodiversity conservation efforts in Kazakhstan. We focus on two emblematic species - Pusa caspica (Caspian seal) and Tulipa greigii - that ar…
View article: Transposable elements drive evolution and perturb gene expression in <i>Brassica rapa</i> and <i>B. oleracea</i>
Transposable elements drive evolution and perturb gene expression in <i>Brassica rapa</i> and <i>B. oleracea</i> Open
SUMMARY Transposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea , with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, …
View article: High-Quality PacBio Genome Assembly of <i>Populus alba</i> L. “Villafranca”
High-Quality PacBio Genome Assembly of <i>Populus alba</i> L. “Villafranca” Open
This study presents the high-quality genome assemblies for Populus alba L. “Villafranca” using PacBio HiFi sequencing. The assembly span 498.95 Mb, an N50 of 18.18 Mb and largest contig of 52.03 Mb. BUSCO analysis revealed genome completen…
View article: PacBio genome assembly of Olea europaea L. subsp. europaea cultivars Frantoio and Leccino
PacBio genome assembly of Olea europaea L. subsp. europaea cultivars Frantoio and Leccino Open
We present two high-quality genome assemblies for Olea europaea L. cultivars 'Frantoio' and 'Leccino,' leveraging PacBio HiFi sequencing to achieve approximately 30 × genome coverage for each cultivar. The assemblies span 1.18 Gbp and 1.43…
View article: 1000 conifer genomes: Genome innovation, organisation and diversity
1000 conifer genomes: Genome innovation, organisation and diversity Open
Norway spruce (Picea abies L. Karst) and Scots pine (Pinus sylvestris L.) are the dominant tree species in northern Eurasia with global importance for carbon sequestration and that are increasingly at risk from climate change. Here, we pre…
View article: Oryza genome evolution through a tetraploid lens
Oryza genome evolution through a tetraploid lens Open
Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present…
View article: Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing
Nutritional quality and genetic differences of five amaranth cultivars revealed by metabolome profiling and whole-genome sequencing Open
Background: Amaranth (Amaranthus spp.) has high nutritional quality, with edible grain and leaves, and many agronomic advantages, making it a promising part of the solution for global food insecurity. However, we lack comprehensive metabol…
View article: Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility
Chromosome-scale pearl millet genomes reveal CLAMT1b as key determinant of strigolactone pattern and Striga susceptibility Open
View article: Oryza genome evolution through a tetraploid lens
Oryza genome evolution through a tetraploid lens Open
Oryza is remarkable genus - with two domesticated (i.e. Asian and African rice) and 25 diploid and tetraploid wild species, 11 extant genome types, and a ~3.4-fold genome size variation - that possesses a virtually untapped reservoir of ge…
View article: Chromosome-scale pearl millet genomes reveal a<i>CARLACTONOIC ACID METHYL TRANSFERASE</i>as key determinant of strigolactone pattern and Striga susceptibility
Chromosome-scale pearl millet genomes reveal a<i>CARLACTONOIC ACID METHYL TRANSFERASE</i>as key determinant of strigolactone pattern and Striga susceptibility Open
The yield of pearl millet, a resilient cereal crop crucial for African food security, is severely impacted by the root parasitic weed Striga hermonthica, which requires host-released strigolactones (SLs) for seed germination. Herein, we id…
View article: Multitrait engineering of Hassawi red rice for sustainable cultivation
Multitrait engineering of Hassawi red rice for sustainable cultivation Open
View article: A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset
A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset Open
View article: Multitrait engineering of Hassawi red rice for sustainable cultivation
Multitrait engineering of Hassawi red rice for sustainable cultivation Open
Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the re…
View article: HPC-based genome variant calling workflow (HPC-GVCW)
HPC-based genome variant calling workflow (HPC-GVCW) Open
A high-performance computing genome variant calling workflow was designed to run GATK on HPC platforms. This workflow efficiently called an average of 27.3 M, 32.6 M, 168.9 M, and 16.2 M SNPs for rice, sorghum, maize, and soybean, respecti…
View article: Multi-omics resources for targeted agronomic improvement of pigmented rice
Multi-omics resources for targeted agronomic improvement of pigmented rice Open
View article: Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice Open
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice ( Oryza sativa ), plus the g…
View article: The gyrfalcon (<i>Falco rusticolus</i>) genome
The gyrfalcon (<i>Falco rusticolus</i>) genome Open
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and popula…
View article: Genome‐wide identification and characterization of exapted transposable elements in the large genome of sunflower (<i>Helianthus annuus</i>L.)
Genome‐wide identification and characterization of exapted transposable elements in the large genome of sunflower (<i>Helianthus annuus</i>L.) Open
SUMMARY Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well‐known phenomena, TEs may undergo the exaptation process and generate the so‐called e…
View article: The International<i>Oryza</i>Map Alignment Project (I<i>O</i>MAP): the Americas—past achievements and future directions
The International<i>Oryza</i>Map Alignment Project (I<i>O</i>MAP): the Americas—past achievements and future directions Open
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources …
View article: Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (<i>Oryza sativa</i>)
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (<i>Oryza sativa</i>) Open
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice ( O. sativa ), plus the genomes of …
View article: The Chinese pine genome and methylome unveil key features of conifer evolution
The Chinese pine genome and methylome unveil key features of conifer evolution Open
View article: DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows
DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows Open
Genome sizes of eukaryotic organisms vary substantially, with whole-genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and Umbra…
View article: DNA transposon expansion is associated with genome size increase in mudminnows
DNA transposon expansion is associated with genome size increase in mudminnows Open
Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi …
View article: Two gap-free reference genomes and a global view of the centromere architecture in rice
Two gap-free reference genomes and a global view of the centromere architecture in rice Open
View article: DNA transposon expansion is associated with genome size increase in mudminnows
DNA transposon expansion is associated with genome size increase in mudminnows Open
Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. py…
View article: A route to de novo domestication of wild allotetraploid rice
A route to de novo domestication of wild allotetraploid rice Open
View article: The Chromosome-Scale Genome and Methylome of Pinus Tabuliformis and the Evolution of Conifers
The Chromosome-Scale Genome and Methylome of Pinus Tabuliformis and the Evolution of Conifers Open
View article: Assembly and Validation of Two Gap-free Reference Genomes for<i>Xian/indica</i>Rice Reveals Insights into Plant Centromere Architecture
Assembly and Validation of Two Gap-free Reference Genomes for<i>Xian/indica</i>Rice Reveals Insights into Plant Centromere Architecture Open
Rice ( Oryza sativa ), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome completed almost two decades ago. However, all sequenced genomes to date contain gaps and missing sequ…
View article: Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice
Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice Open
As the world's population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to co…
View article: A draft genome of sweet cherry (<i>Prunus avium</i> L.) reveals genome‐wide and local effects of domestication
A draft genome of sweet cherry (<i>Prunus avium</i> L.) reveals genome‐wide and local effects of domestication Open
Summary Sweet cherry ( Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geog…