Biology subjects

Porceddu, A.

Publications and source records attributed to Porceddu, A..

6 recordsLinked to original sources

bioRxiv2025

The reference-free pangenome of Arabidopsis thaliana

For several decades, scientists relied on unique reference genomes as the basis for various genomic studies. This methodology presents multiple drawbacks, particularly for variation studies, often yielding unrepresentative and incomplete observations regarding the diversity of the species or group under study. Pangenomes are collections of genomic sequences from several individuals of a species or population, which allow to overcome the limitations of studies based on a single reference genome. In this study, we produced a 93-assembly pangenome of the model plant Arabidopsis thaliana using the reference-free method PanGenome Graph Builder (PGGB). The aim was to investigate the diversity within this species using this novel methodology, encompassing genomic sequences, genes, and pseudogenes. The pangenome exhibited a total length of 488.78 Mb, consisting of 30,391,243 nodes and 7,189,634 edges. We mapped a total of 2,325,577 genes and 23,894 pseudogenes across 93 assemblies, of which 36% and 0.9%, respectively, were classified as core. The observed variation in terms of genes and especially pseudogenes related to the geographical distance between sampling sites. Since the simulated pangenome growth curve based on gene did not reach a plateau, new accessions could potentially expand the represented diversity. This study enriches our understanding of intra-specific variation in A. thaliana and provides a new viewpoint on the potential applications of pangenomes in diversity research.

genomics↗

bioRxiv2024

Identification and structural characterization of pseudogenes in Fusarium graminearum.

Pseudogenes provide valuable insight into the evolutionary history of genomes which can be challenging to ascertain through the examination of functional loci alone. This study presents the findings of a comprehensive, two-step genome-wide survey for the identification and characterization of pseudogenes in Fusarium graminearum, the primary causal agent of wheat head blight. By analysing the sequence homology between non-coding regions of the genome and predicted protein sequences, we identified regions with homology to putative paralogous functional sequences. These regions were characterised in terms of their matching sequence structure and position. Most identified pseudogenes were mapped within the fast-evolving genomic compartment and were derived from transposition events. The number of processed and putatively retroposed pseudogenes was found to be comparable. The number of identified pseudogenes was low, which is consistent with the low number of gene duplicates in F. graminearum. No compelling evidence was found to suggest that pseudogene formation can be explained by evolutionary accidents during gene family expansion or as caused by RIP-associated mutagenic events. Notably, about one-third (144/436) of the pseudogenes were found to overlap with untranslated or intron sequences of functional loci, indicating the potential to be transcribed. Using Fusarium comparative genomics, we identified genomic regions with homology to genes lacking functional orthologs in F. graminearum. These were investigated as putative unitary pseudogenes and, in some cases, their original functions were completely lost after the radiation of F. graminearum. Interestingly, the paters of 18 loss-of-function pseudogenes showed homology to domains previously identified in proteins involved in pathogenesis.

genomics↗

bioRxiv2024

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly

BackgroundDe novo assembly creates reference genomes that underpin many modern biodiversity and conservation studies. Large numbers of new genomes are being assembled by labs around the world. To avoid duplication of efforts and variable data quality, we desire a best-practice assembly process, implemented as an automated portable workflow. ResultsHere we present Colora, a Snakemake workflow that produces chromosome-scale de novo primary or phased genome assemblies complete with organelles using PacBio HiFi, Hi-C, and optionally ONT reads as input. The source code of Colora is available on GitHub: https://github.com/LiaOb21/colora. Colora is also available at the Snakemake Workflow Catalog (https://snakemake.github.io/snakemake-workflow-catalog/?usage=LiaOb21%2Fcolora). ConclusionColora is a user-friendly, versatile, and reproducible pipeline that is ready to use by researchers looking for an automated way to obtain high-quality de novo genome assemblies.

genomics↗

bioRxiv2024

Comparative analysis of the genomic architecture of six Fusarium species

Comparative analyses of several plant pathogens have revealed that genome plasticity could be associated with different genomic architectures. In certain species, genomic compartments are characterised by highly conserved regions that contain mainly housekeeping genes and rearranged regions that are enriched for genes related to virulence and adaptation. The compositional and structural characteristics of genomic regions have been significantly associated with compartment membership in single species, but little information is available on the covariation of these features between species. Here, the results of a comparative analysis of the genomic architectures of six agriculturally relevant Fusarium species, which differ for several biological and pathogenic characteristics, are presented. These include F. culmorum, F. fujikoroi, F. graminearum, F. oxysporum, F. solani, and F. verticillioides. The genome sequences of these species were partitioned into adjacent windows, with the average level of gene collinearity with the other species used as an index of compartment membership. High collinearity is typical of conserved regions, while low collinearity is typical of rearranged regions. Several genic and genomic variables were found to be consistently associated with compartment definition among all the Fusarium species that were investigated. The compartment that was characterised by lower collinearity (i.e., high genomic rearrangements) contained more relocated genes, species-specific genes and secreted protein-encoding genes than regions with low collinearity. Furthermore, several molecular evidence indicates that low-collinearity regions are more likely to be subjected to selective pressure than high-collinearity regions. Indeed, genes residing in the former regions exhibited higher rates of sequence evolution than in the latter, as indicated by the high non-synonymous-to-synonymous substitution rates. However, they exhibited signatures of selection to minimise the costs of transcription, as indicated by their high coding density. Our data suggests that although variable genomic compartments evolved mostly after species radiation, they share similar genomic features across related species and perhaps evolve with similar mechanisms.

evolutionary biology↗

bioRxiv2023

Benchmarking of Hi-C tools for scaffolding de novo genome assemblies

The implementation of Hi-C reads in the de novo genome assembly allows to order large regions of the genome in scaffolds, obtaining chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and all have pros and cons which need to be carefully evaluated before adoption. We developed assemblyQC, a bash pipeline that combines QUAST, BUSCO, Merqury and, optionally, Liftoff, plus a gene positioning validation script to evaluate and benchmark the performance of three scaffolders, 3d-dna, SALSA2, and YaHS, on two de novo assembly of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data. In our analysis, YaHS proved to be the best-performing bioinformatic tool for scaffolding of de novo genome assembly.

genomics↗

bioRxiv2019

Methylation content sensitive enzyme ddRAD (MCSeEd): a reference-free, whole genome profiling system to address cytosine/ adenine methylation changes

Methods for investigating DNA methylation nowadays either require a reference genome and high coverage, or investigate only CG methylation. Moreover, no large-scale analysis can be performed for N6-methyladenosine (6mA). Here we describe the methylation content sensitive enzyme double-digest restriction-site-associated DNA (ddRAD) technique (MCSeEd), a reduced-representation, reference-free, cost-effective approach for characterizing whole genome methylation patterns across different methylation contexts (e.g., CG, CHG, CHH, 6mA). MCSeEd can also detect genetic variations among hundreds of samples. MCSeEd is based on parallel restrictions carried out by combinations of methylation insensitive and sensitive endonucleases, followed by next-generation sequencing. Moreover, we present a robust bioinformatic pipeline (available at https://bitbucket.org/capemaster/mcseed/src/master/) for differential methylation analysis combined with single nucleotide polymorphism calling without or with a reference genome.

genomics↗