Biology subjects

Di Palma, F.

Publications and source records attributed to Di Palma, F..

3 recordsLinked to original sources

bioRxiv2018

The evolutionary dynamics of microRNAs in domestic mammals

MicroRNAs are crucial regulators of gene expression found across both the plant and animal kingdoms. While the numberof annotated microRNAs deposited in miRBase has greatly increased in recent years, few studies provided comparative analyses across sets of related species, or investigated the role of microRNAs in the evolution of gene regulation.\n\nWe generated small RNA libraries across 5 mammalian species (cow, dog, horse, pig and rabbit) from 4 different tissues (brain, heart, kidney and testis). We identified 1675 miRBase and 413 novel microRNAs by manually curating the set of computational predictions obtained from miRCat and miRDeep2.\n\nOur dataset spanning five species has enabled us to investigate the molecular mechanisms and selective pressures driving the evolution of microRNAs in mammals. We highlight the important contributions of intronic sequences (366 orthogroups), duplication events (135 orthogroups) and repetitive elements (37 orthogroups) in the emergence of new microRNA loci.\n\nWe use this framework to estimate the patterns of gains and losses across the phylogeny, and observe high levels of microRNA turnover. Additionally, the identification of lineage-specific losses enables the characterisation of the selective constraints acting on the associated target sites.\n\nCompared to the miRBase subset, novel microRNAs tend to be more tissue specific. 20 percent of novel orthogroups are restricted to the brain, and their target repertoires appear to be enriched for neuron activity and differentiation processes. These findings may reflect an important role for young microRNAs in the evolution of brain expression plasticity.\n\nMany seed sequences appear to be specific to either the cow or the dog. Analyses on the associated targets highlightthe presence of several genes under artificial positive selection, suggesting an involvement of these microRNAs in the domestication process.\n\nAltogether, we provide an overview on the evolutionary mechanisms responsible for microRNA turnover in 5 domestic species, and their possible contribution to the evolution of gene regulation.

evolutionary biology↗

bioRxiv2017

W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data

Producing high-quality whole-genome shotgun de novo assemblies from plant and animal species with large and complex genomes using low-cost short read sequencing technologies remains a challenge. But when the right sequencing data, with appropriate quality control, is assembled using approaches focused on robustness of the process rather than maximization of a single metric such as the usual contiguity estimators, good quality assemblies with informative value for comparative analyses can be produced. Here we present a complete method described from data generation and qc all the way up to scaffold of complex genomes using Illumina short reads and its application to data from plants and human datasets. We show how to use the w2rap pipeline following a metric-guided approach to produce cost-effective assemblies. The assemblies are highly accurate, provide good coverage of the genome and show good short range contiguity. Our pipeline has already enabled the rapid, cost-effective generation of de novo genome assemblies from large, polyploid crop species with a focus on comparative genomics.\n\nAvailabilityw2rap is available under MIT license, with some subcomponents under GPL-licenses. A ready-to-run docker with all software pre-requisites and example data is also available.\n\nhttp://github.com/bioinfologics/w2rap\n\nhttp://github.com/bioinfologics/w2rap-contigger

bioinformatics↗

bioRxiv2016

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]

genomics↗