Biology subjects

Sanderson, H.

Publications and source records attributed to Sanderson, H..

4 recordsLinked to original sources

bioRxiv2025

The genome sequence of the hemlock woolly adelgid, Adelges tsugae Annand 1924

The genome of the hemlock woolly adelgid (Adelges tsugae) is presented in 10 chromosomal pseudomolecules along with 132 unplaced scaffolds for a combined length of 216.56 Mb. The genome is highly contiguous, with a benchmarking universal single-copy orthologs (BUSCO) completion score of 98.25%, an N50 of 20.54 Mb, and the longest scaffold 37.41 Mb in length. On the basis of chromosomal synteny with other aphid genomes, the hemlock woolly adelgids genome is composed of 8 autosomes and two sex (X) chromosomes. Annotation of the assembly identified 11,800 coding genes, 1,930 non-coding genes, and 20,403 mRNA transcripts. The mitogenome is also presented in a single, annotated, circular contig 25,980 bases in length. Species taxonomyEukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Paraneoptera; Hemiptera; Sternorrhyncha; Aphidomorpha; Adelgoidea; Adelgidae; Adelges; Annandina; Adelges (Annandina) tsugae Annand, 1924 (NCBI:txid357502)

genomics↗

bioRxiv2024

PlasEval: a framework for comparing and evaluating plasmid detection tools

Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem and a very active research area. Plasmid binning aims at detecting, in a draft genome assembly, groups (bins) of contigs likely to originate from the same plasmid. Several methods for plasmid binning have been developed recently, such as PlasBin-flow, HyAsP, gplas, MOB-suite, and plasmidSPAdes. This motivates the problem of evaluating the performances of plasmid binning methods, either against a given ground truth or between them. We describe PlasEval, a novel method aimed at comparing the results of plasmid binning tools. PlasEval computes a dissimilarity measure between two sets of plasmid bins, that can originate either from two plasmid binning tools, or from a plasmid binning tool and a ground truth set of plasmid bins. The PlasEval dissimilarity accounts for the contig content of plasmid bins, the length of contigs and is repeat-aware. Moreover, the dissimilarity score computed by PlasEval is broken down into several parts, that allows to understand qualitative differences between the compared sets of plasmid bins. We illustrate the use of PlasEval by benchmarking four recently developed plasmid binning tools - PlasBin-flow, HyAsP, gplas, and MOB-recon - on a data set of 54 E. coli bacterial genomes. PlasEval is freely available at https://github.com/acme92/PlasEval

bioinformatics↗

bioRxiv2022

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Enterococcus faecium is a ubiquitous opportunistic pathogen that is exhibiting increasing levels of antimicrobial resistance (AMR). Many of the genes that confer resistance and pathogenic functions are localized on mobile genetic elements (MGEs), which facilitate their transfer between lineages. Here, features including resistance determinants, virulence factors, and MGEs were profiled in a set of 1273 E. faecium genomes from two disparate geographic locations (in the UK and Canada) from a range of agricultural, clinical, and associated habitats. Neither lineages of E. faecium nor MGEs are constrained by geographic proximity, but our results show evidence of a strong association of many profiled genes and MGEs with habitat. Many features were associated with a group of clinical and municipal wastewater genomes that are likely forming a new human-associated ecotype. The evolutionary dynamics of E. faecium make it a highly versatile emerging pathogen, and its ability to acquire, transmit, and lose features presents a high risk for the emergence of new pathogenic variants and novel resistance combinations. This study provides a workflow for MGE-centric surveillance of AMR in Enterococcus that can be adapted to other pathogens.

genomics↗

bioRxiv2020

Evolution of mouse circadian enhancers from transposable elements

BackgroundTransposable elements are increasingly recognized as a source of cis-regulatory variation. Previous studies have revealed that transposons are often bound by transcription factors and some have been co-opted into functional enhancers regulating host gene expression. However, the process by which transposons mature into complex regulatory elements, like enhancers, remains poorly understood. To investigate this process, we examined the contribution of transposons to the cis-regulatory network controlling circadian gene expression in the mouse liver, a well-characterized network serving an important physiological function. ResultsChIP-seq analyses revealed that transposons and other repeats contribute ~14% of the binding sites for core circadian regulators (CRs) including BMAL1, CLOCK, PER1/2, and CRY1/2, in the mouse liver. RSINE1, an abundant murine-specific SINE, was the only transposon family enriched for CR binding sites across all datasets. Sequence analyses and reporter assays revealed that the circadian regulatory activity of RSINE1 stems from the presence of imperfect CR binding motifs in the ancestral RSINE1 sequence. These motifs matured into canonical motifs through point mutations after transposition. Furthermore, maturation occurred preferentially within elements inserted in proximity of ancestral CR binding sites. RSINE1 also acquired motifs that recruit nuclear receptors known to cooperate with CR to regulate circadian gene expression specifically in the liver. ConclusionsOur results suggest that the birth of enhancers from transposons is predicated both by the sequence of the transposon and by the cis-regulatory landscape surrounding their genomic integration site. This model illuminates how transposition fuels the emergence and turnover of enhancers during mammalian evolution.

genomics↗