Biology subjects

Letcher, B.

Publications and source records attributed to Letcher, B..

7 recordsLinked to original sources

bioRxiv2025

Interplay between petal identity and cell layer identity in petunia flowers

In flowering plants, floral organ identity is specified by the combinatorial action of homeotic genes. While the role of these genes in the early specification of organ identity is well established, their late function throughout floral organ development and in specific cell types is much less characterized. In particular, since plant organs are structured in clonally-independent cell layers, whether and how homeotic identity interacts with cell layer identity is unknown. We have previously identified cell layer-specific mutants for the petal identity gene PhDEF in petunia flowers, resulting in drastically different petal phenotypes whether PhDEF is expressed in the petal epidermis or in the mesophyll. In this study, using a combination of single-cell RNA-Seq and chromatin immunoprecipitation on phdef cell layer-specific mutants, we find that PhDEF regulates a different set of target genes in the petal epidermis and mesophyll, with a major regulatory action in the epidermis. We uncover a high diversity of binding profiles in PhDEF target genes, with a complex combination of layer-specific or non-specific binding sites, and a much more prominent binding of PhDEF in the epidermis than in the mesophyll. Our study highlights that floral homeotic genes like PhDEF can have different regulatory actions in different cell contexts, here different cell layers, demonstrating that cell layer identity indeed influences the regulatory processes underlying homeotic identity.

developmental biology↗

bioRxiv2025

Somatic Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes

All cells of a multicellular organism usually share an identical genome, faithfully transmitted through successive divisions. Yet, a number of animal species deviate from this dogma, as parts of their DNA are systematically eliminated in all their somatic nuclei, in a process called Programmed DNA Elimination (PDE). PDE leads to the unexpected reorganisation of the genome at every generation in all somatic cells but its molecular mechanism, evolutionary origins, and functional significance remain unknown. This lack of understanding partially stems from limitations in genetically tractable model species. PDE can target an entire chromosome, or involve chromosome fragmentation followed by selective fragment retention and elimination, raising further questions on genome stability, genome integrity and mechanisms of DNA repair. PDE by chromosome fragmentation has been described in parasitic nematodes in the family Ascarididae, copepods in the genus Cyclops and unicellular ciliates. More recently, PDE has been discovered in three non-parasitic, lab-tractable nematode species from the Rhabditidae family, opening new perspectives. In this study, we used cytological approaches to screen 25 new Rhabditidae species for PDE. We found evidence of PDE in 17 species. Our work reveals that PDE is present in 12 out of 17 tested genera, demonstrating its widespread presence in Rhabditidae nematodes, with the notable exception of C. elegans. Genetic tools have already been established for some species. This work provides a collection of lab-tractable species that can be used to test many aspects of somatic Programmed DNA Elimination by chromosome fragmentation in animals.

evolutionary biology↗

bioRxiv2025

Emergence and stabilisation of a neo-Y chromosome in nematode species with rare males

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction - for example, parthenogens with rare sex, or species where the paternal genome is set aside - have been found to carry either no sex chromosomes, or sex chromosomes but no male-specific sex chromosome (i. e., no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome emerged once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare ([~]10%) males that are needed for fertilisation, but that do not contribute to the female genome. Analysing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: i) they accumulated male-beneficial genes, and ii) they display a strong fertilisation drive, in that mainly Y-bearing sperm fertilise female oocytes. Both features are likely evolutionarily favourable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly genetically useless, males.

evolutionary biology↗

bioRxiv2023

Gene conversion drives allelic dimorphism in two paralogous surface antigens of the malaria parasite P. falciparum

While the malaria parasite P. falciparum has low average genome-wide diversity levels, likely due to its recent introduction from a gorilla-infecting ancestor ([~]10,000-50,000 years ago), some genes display extremely high diversity levels. In particular, certain proteins expressed on the surface of human red-blood-cell-infecting merozoites (merozoite surface proteins, MSPs) possess exactly two deeply-diverged allelic forms that have not recombined. This phenomenon, called allelic dimorphism, is of considerable interest, but its origin and maintenance remains unknown. In this study, we analysed the dimorphism in two highly-variable and paralogous MSPs, DBLMSP and DBLMSP2. Despite thousands of available Illumina WGS datasets from malaria-endemic countries, diversity in these genes has been hard to fully characterise as reads containing highly-diverged alleles fail to align to the reference genome. To solve this, we developed a pipeline leveraging genome graphs, enabling us to genotype them at high accuracy and completeness in comparison to a state-of-the-art GATK-based pipeline. Using our newly-resolved sequences we found both genes are dimorphic in a specific protein domain (DBL), and that one of the two forms is shared across the genes. We identified clear evidence of non-allelic gene conversion between the two genes as the likely mechanism behind sharing, leading us to propose a new model for allelic dimorphism through gene conversion between diverged paralogs. This model is consistent with high diversity levels in these two genes despite the strong historical P. falciparum transmission bottleneck.

genomics↗

bioRxiv2021

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Short-read variant calling for bacterial genomics is a mature field, and there are many widely-used software tools. Different underlying approaches (eg pileup, local or global assembly, paired-read use, haplotype use) lend each tool different strengths, especially when considering non-SNP (single nucleotide polymorphism) variation or potentially distant reference genomes. It would therefore be valuable to be able to integrate the results from multiple variant callers, using a robust statistical approach to "adjudicate" at loci where there is disagreement between callers. To this end, we present a tool, Minos, for variant adjudication by mapping reads to a genome graph of variant calls. Minos allows users to combine output from multiple variant callers without loss of precision. Minos also addresses a second problem of joint genotyping SNPs and indels in bacterial cohorts, which can also be framed as an adjudication problem. We benchmark on 62 samples from 3 species (Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae) and an outbreak of 385 M. tuberculosis samples. Finally, we joint genotype a large M. tuberculosis cohort (N{approx}15k) for which the rifampicin phenotype is known. We build a map of non-synonymous variants in the RRDR (rifampicin resistance determining region) of the rpoB gene and extend current knowledge relating RRDR SNPs to heterogeneity in rifampicin resistance levels. We replicate this finding in a second M. tuberculosis cohort (N{approx}13k). Minos is released under the MIT license, available at https://github.com/iqbal-lab-org/minos.

bioinformatics↗

bioRxiv2021

Enabling multiscale variation analysis with genome graphs

BackgroundStandard approaches to characterising genetic variation revolve around mapping reads to a reference genome and describing variants in terms of differences from the reference; this is based on the assumption that these differences will be small and provides a simple coordinate system. However this fails, and the coordinates break down, when there are diverged haplotypes at a locus (e.g. one haplotype contains a multi-kilobase deletion, a second contains a few SNPs, and a third is highly diverged with hundreds of SNPs). To handle these, we need to model genetic variation that occurs at different length-scales (SNPs to large structural variants) and that occurs on alternate backgrounds. We refer to these together as multiscale variation. ResultsWe model the genome as a directed acyclic graph consisting of successive hierarchical subgraphs ("sites") that naturally incorporate multiscale variation, and introduce an algorithm for genotyping, implemented in the software gramtools. This enables variant calling on different sequence backgrounds. In addition to producing regular VCF files, we introduce a JSON file format based on VCF, which records variant site relationships and alternate sequence backgrounds. We show two applications. First, we benchmark gramtools against existing state-of-the-art methods in joint-genotyping 17 M. tuberculosis samples at long deletions and the overlapping small variants that segregate in a cohort of 1,017 genomes. Second, in 706 African and SE Asian P. falciparum genomes, we analyse a dimorphic surface antigen gene which possesses variation on two diverged backgrounds which appeared to not recombine. This generates the first map of variation on both backgrounds, revealing patterns of recombination that were previously unknown. ConclusionsWe need new approaches to be able to jointly analyse SNP and structural variation in cohorts, and even more to handle variants on different genetic backgrounds. We have demonstrated that by modelling with a directed, acyclic and locally hierarchical genome graph, we can apply new algorithms to accurately genotype dense variation at multiple scales. We also propose a generalisation of VCF for accessing multiscale variation in genome graphs, which we hope will be of wide utility.

bioinformatics↗

bioRxiv2020

Nucleotide-resolution bacterial pan-genomics with reference graphs

BackgroundBacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core); the union of these is the pan-genome. The alignable fraction of two genomes from a single species can be low (e.g. 50-70%), such that no single reference genome can access all single nucleotide polymorphisms (SNPs). The pragmatic solution is to choose a close reference, and analyse SNPs only in the core genome. Given much bacterial adaptability hinges on the accessory genome, this is an unsatisfactory limitation. ResultsWe present a novel pan-genome graph structure and algorithms implemented in the software pandora, which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. The method takes fastq as input and outputs a multi-sample VCF with respect to an inferred data-dependent reference genome, and is available at https://github.com/rmcolq/pandora. Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show pandora recovers at least 13k more rare SNPs than single-reference based tools, achieves equal or better error rates with Nanopore as with Illumina data, 6-24x lower Nanopore error rates than other tools, and provides a stable framework for analysing diverse samples without reference bias. We also show that our inferred recombinant VCF reference genome is significantly better than simply picking the closest RefSeq reference. ConclusionsThis is a step towards comprehensive cohort analysis of bacterial pan-genomic variation, with potential impacts on genotype/phenotype and epidemiological studies.

bioinformatics↗