Biology subjects

Sierra, P.

Publications and source records attributed to Sierra, P..

5 recordsLinked to original sources

bioRxiv2024

EMERGENCE OF OXA-48-LIKE CARBAPENEMASES IN CLINICAL ENTEROBACTERALES FROM GUATEMALA

Five isolates (four Klebsiella pneumoniae and one Escherichia coli) displaying resistance to piperacillin/tazobactam and ertapenem and reduced susceptibility to imipenem were found positive for blaOXA-48-like genes (blaOXA-181 and blaOXA-232) carried on plasmids described previously. Although two K. pneumoniae recovered in 2020 were clonally related, the results suggest that blaOXA-48-like genes have been circulating in Guatemala since 2019. This is the first report of this type of carbapenemase in Central America.

microbiology↗

bioRxiv2024

Identification of transposable element families from pangenome polymorphisms

BackgroundTransposable Elements (TEs) are fragments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility. ResultsWe develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies. ConclusionsOur results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.

bioinformatics↗

bioRxiv2024

Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes

East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.

evolutionary biology↗

bioRxiv2023

MCHelper automatically curates transposable element libraries across species

The number of species with high quality genome sequences continues to increase, in part due to scaling up of multiple large scale biodiversity sequencing projects. While the need to annotate genic sequences in these genomes is widely acknowledged, the parallel need to annotate transposable element sequences that have been shown to alter genome architecture, rewire gene regulatory networks, and contribute to the evolution of host traits is becoming ever more evident. However, accurate genome-wide annotation of transposable element sequences is still technically challenging. Several de novo transposable element identification tools are now available, but manual curation of the libraries produced by these tools is needed to generate high quality genome annotations. Manual curation is time-consuming, and thus impractical for large-scale genomic studies, and lacks reproducibility. In this work, we present the Manual Curator Helper tool MCHelper, which automates the TE library curation process. By leveraging MCHelpers fully automated mode with the outputs from three de novo transposable element identification tools, RepeatModeler2, EDTA and REPET, in fruit fly, rice, hooded crow, zebrafish, maize, and human, we show a substantial improvement in the quality of the transposable element libraries and genome annotations. MCHelper libraries are less redundant, with up to 65% reduction in the number of consensus sequences, have up to 11.4% fewer false positive sequences, and up to [~]48% fewer "unclassified/unknown" transposable element consensus sequences. Genome-wide transposable element annotations were also improved, including larger unfragmented insertions. Moreover, MCHelper is an easy to install and easy to use tool.

genomics↗

bioRxiv2022

Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse.

PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded non-coding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyse piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between individuals underlie variation in piRNA expression. We report significant differences in piRNA production at loci with endogenous retrovirus insertions. Strain-specific piRNA-producing loci include protein-coding genes. Our findings provide evidence that transposable elements contribute to inter-individual differences in expression, and potentially to the fast evolution of piRNA-producing loci in mammals.

genomics↗