Federica Cattonaro
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View article: Assembly and Annotation of Red Spruce (Picea rubens) Chloroplast Genome, Identification of Simple Sequence Repeats, and Phylogenetic Analysis in Picea
Assembly and Annotation of Red Spruce (Picea rubens) Chloroplast Genome, Identification of Simple Sequence Repeats, and Phylogenetic Analysis in Picea Open
We have sequenced the chloroplast genome of red spruce (Picea rubens) for the first time using the single-end, short-reads (44 bp) Illumina sequences, assembled and functionally annotated it, and identified simple sequence repeats (SSRs). …
View article: A new Genomic resource for Populus nigra and its deployment for genetic studies
A new Genomic resource for Populus nigra and its deployment for genetic studies Open
Black poplar (Populus nigra L., Salicaceae) is an Eurasian native species distributed within fluvial corridors. As a pioneer species, P. nigra plays an important role in the establishment of riparian ecosystems. The species has important a…
View article: Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats
Structural Variations Affecting Genes and Transposable Elements of Chromosome 3B in Wheats Open
Structural variations (SVs) such as copy number and presence-absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference…
View article: Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies
Do you cov me? Effect of coverage reduction on metagenome shotgun sequencing studies Open
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructin…
View article: Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing Open
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructin…
View article: A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in <i>Taxus baccata</i> L
A multiscale approach to detect selection in nonmodel tree species: Widespread adaptation despite population decline in <i>Taxus baccata</i> L Open
Detecting the molecular basis of local adaptation and identifying selective drivers is still challenging in nonmodel species. The use of purely population genetic approaches is limited by some characteristics of genetic systems, such as pl…
View article: Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Our study updates and expands the de novo transcriptome reference assembly available for durum wheat. Out of 180,108 assembled transcripts, 13,636 were specific to the Svevo cultivar as compared to the only other reference transcriptome av…
View article: Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize
Single primer enrichment technology as a tool for massive genotyping: a benchmark on black poplar and maize Open
Background and Aims The advent of molecular breeding is advocated to improve the productivity and sustainability of second-generation bioenergy crops. Advanced molecular breeding in bioenergy crops relies on the ability to massively sample…
View article: Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing Open
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructin…
View article: Additional file 7: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 7: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S4. List of the 58 wheat genes from chromosome 3 with the relative accession numbers. (XLSX 12 kb)
View article: Additional file 14: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 14: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S10. Unique proteins matching with T. durum transcripts. Unique proteins matching with T. durum transcripts divided by plant species. (XLSX 10 kb)
View article: Additional file 13: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 13: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S9. Annotation Statistics. Annotation statistics for the Svevo RNA-seq transcriptome assembly divided into high and low confidence annotation. Annotations with either BioMart or BAR+. Gene Ontology (GO) computed with Blast2GO (B2GO).…
View article: Additional file 2: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 2: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S2. Summary of RNA sequencing for durum wheat cv. Svevo cDNA libraries. Two libraries, named “a” and “b”, were constructed for each tissue. They differ on fragment size recovered by gel-electrophoresis. For each library, tissue, frag…
View article: Additional file 17 of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 17 of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S11 Significant differential expression between homoeolog genes. Under the GLM fit analysis, lines in green/brown represent genes with concordant/discordant homoeolog expression in phased blocks within the same gene. (XLSX 1605 kb)
View article: Additional file 8: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 8: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S5. BLASTn results between the homoeolog genes of T. aestivum chromosome 3. (XLSX 16 kb)
View article: Additional file 3: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 3: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S3. Detailed report of the de novo assemblies. (XLSX 15 kb)
View article: Detection of natural and induced mutations from next generation sequencing data in sweet orange bud sports
Detection of natural and induced mutations from next generation sequencing data in sweet orange bud sports Open
Somatic mutations are a cause of intraspecific diversity in many fruit crops, including citrus.In the case of sweet orange [Citrus sinensis (L.) Osbeck], intraspecific variability is determined only by somatic mutations.Tools for clonal fi…
View article: Additional file 9: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 9: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S6. Homoeologs reconstruction. Number of copies reconstructed among the 58 genes (Additional file 6: Table S4) of â Supplementary File 2â in the de novo assembly. (XLSX 9 kb)
View article: Additional file 1: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 1: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S1. Durum wheat accessions description and RNA-Seq data. Accession name, pedigree, accession feature and the constitutor for the 13 varieties used for RNA sequencing and SNP discovery are reported along with the associated sequencing…
View article: Additional file 18: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 18: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S12. Validation set. Primer pair for eight validation transcripts aligned with original homeolog-specific RNA-Seq data. (XLSX 12 kb)
View article: Additional file 10: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 10: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S7. List of Svevo private contigs with GO annotation derived from BLASTn comparison between Svevo and Kronos contigs. (XLSX 338 kb)
View article: Additional file 11: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Additional file 11: of Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm Open
Table S8. Transcriptomes of the plant species used for BLASTx. Plant species from Ensembl Plants used for BLASTx alignment of transcripts, to infer functional annotation. (XLSX 9 kb)
View article: Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing
Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing Open
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms in a single experiment, with the possibility of de novo reconstruction of…
The microbiota of hematophagous ectoparasites collected from migratory birds Open
Arthropod vectors are responsible for the transmission of human pathogens worldwide. Several arthropod species are bird ectoparasites, however, no study to date has characterized their microbiota as a whole. We sampled hematophagous ectopa…
View article: Physical Map of the Short Arm of Bread Wheat Chromosome 3D
Physical Map of the Short Arm of Bread Wheat Chromosome 3D Open
Bread wheat ( Triticum aestivum L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics‐assisted breeding and gene cloning, its gener…
View article: Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra†
Genes and gene clusters related to genotype and drought-induced variation in saccharification potential, lignin content and wood anatomical traits in Populus nigra† Open
Wood is a renewable resource that can be employed for the production of second generation biofuels by enzymatic saccharification and subsequent fermentation. Knowledge on how the saccharification potential is affected by genotype-related v…
View article: MOESM7 of De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock
MOESM7 of De novo assembly, functional annotation, and analysis of the giant reed (Arundo donax L.) leaf transcriptome provide tools for the development of a biofuel feedstock Open
Additional file 7: Table S5. Description of the identified simple sequence repeat (SSR) types for the A. donax leaf transcriptome. Table S6. SSR repeat motifs in A. donax unitranscripts.