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Downing, T.

Publications and source records attributed to Downing, T..

15 recordsLinked to original sources
bioRxiv2026

Insights into goatpox virus and sheeppox virus genomes from pangenome graphs

The capripoxviruses comprise three species: goatpox virus (GTPV), sheeppox virus (SPPV) and lumpy skin disease virus (LSDV). They are large double-stranded DNA viruses with highly conserved core genomes and variable terminal regions. Previous studies have described variation in Capripoxvirus gene content, their broader population structure and the contribution of non-coding and structural variation remains opaque. This study investigated the genomic diversity and evolutionary history of GTPV and SPPV using phylogenetics, pangenome variation graphs (PVGs), and gene-specific analyses. We found clear differences in population structure between the two viruses. GTPV had three deeply divergent and genetically stable lineages with limited evidence of recent gene flow, whereas SPPV had weaker clade separation consistent with an ancestral bottleneck followed by recent population expansion. PVG-based analyses indicated that GTPV has a comparatively closed pangenome, while SPPVs was open, particularly at the inverted terminal repeats (ITRs). Structural and haplotype variation was concentrated at these ITRs, which moderate host immunity and specificity. In several lineages, extended putative ORFs spanning adjacent ITR genes were observed, indicating recurrent structural plasticity at these regions. Patterns of gene-specific conservation and divergence highlighted loci under strong constraint and lineage-specific structural changes that may contribute to host specificity. Together, these results demonstrated how graph-based genome models complement gene-based analyses in resolving poxvirus genome evolution and provide a resource for improved comparative and population genomic studies of large DNA viruses. SignificanceThe capripoxviruses are economically important livestock pathogens, yet the genomic mechanisms underlying their diversification and host specificity remain poorly resolved. By applying pangenome variation graphs alongside phylogenetic and gene-level analyses, this study reveals fundamental differences in how goatpox and sheeppox viruses have evolved. Goatpox virus had a deeper, more stable lineage structure, whereas sheeppox virus was more recent and diverse. Importantly, structural variation at the inverted terminal repeats emerged as a major driver of genomic diversity, including lineage-specific haplotypes and variable gene structures. These findings demonstrated the value of graph-based genome representations for resolving complex variation in large DNA viruses and provides approaches for improving genomic surveillance, comparative analyses, and future investigations into host range, virulence and tropism.

genomics↗
bioRxiv2026

A high-quality telomere-to-telomere LSDV genome assembly

Lumpy skin disease virus (LSDV) is an emerging livestock capripoxvirus (CaPV) that continues to cause substantial economic losses across Africa, Asia and Europe. However, important uncertainties remain regarding LSDV genome structure, particularly at the telomeric inverted terminal repeats (ITRs) that are central to host interaction, replication and adaptive evolution. Structural variation at the ITRs is driven by recombination during virus replication. Previous assemblies have relied primarily on short-read sequencing, which provides limited resolution of repeat-rich telomeric regions and propagates structural ambiguities into downstream annotation and comparative analyses. Here, we present a high-quality telomere-to-telomere (T2T) assembly of the LSDV Oman 2009 isolate, generated using a hybrid approach that integrates short Illumina reads with higher-accuracy long Nanopore reads. The resulting 151,091 bp genome contains 157 annotated open reading frames and fully resolves complex repeat-rich structures at both ITRs. This new reference corrects misassemblies present in earlier LSDV genomes and confirms clade-specific gene truncations. This genome provides a robust foundation for improved genomic surveillance, accurate read mapping, mutation detection and evolutionary inference of LSDV, and demonstrates the value of long-read approaches for resolving complex CaPV genome structures.

genomics↗
bioRxiv2026

3,500 years of sheeppox virus evolution inferred from archaeological and codicological genomes

Sheeppox virus (SPPV) is a major livestock pathogen causing economic hardship through reduced production and death of vulnerable sheep, with written descriptions of sheeppox-like disease recorded since antiquity. We report 21 novel ancient SPPV genomes spanning the Eurasian steppe Bronze Age ([~]1,700 BCE) to the Early Modern period in Western Europe, including multiple genomes obtained from medieval parchment. We estimate that major capripoxvirus lineages diverged [~]11,500-3,700 years ago, overlapping known translocations and bio-cultural developments in sheep. Our dataset supports SPPV diverging first within the lineage leading to goatpox virus and lumpy skin disease virus, and that known gene inactivation events within SPPV and goatpox virus occur in our earliest SPPV genomes. These findings reveal that the food security of Eurasian communities have been threatened by sheeppox for over 3,700 years, and provide new insights to the genomic evolution and potential host adaptation of sheeppox virus. TeaserAncient viral genomes from manuscripts and teeth illuminate the evolutionary history of sheeppox virus.

genetics↗
bioRxiv2025

Using pangenome variation graphs to improve mutation detection in a large DNA virus

Accurately quantifying viral genetic diversity is essential for understanding pathogen evolution, transmission, and emergence. However, standard approaches that map sequencing reads to a single linear reference genome introduce substantial reference bias, particularly for samples that are divergent, recombinant, or belong to rare lineages. Pangenome variation graphs (PVGs) mitigate this issue by representing multiple genomes within a unified graph structure, enabling read mapping across all observed and potential haplotypes. Despite this, PVGs have rarely been applied to viruses. Here, we address this gap by constructing and evaluating the first PVG for lumpy skin disease virus (LSDV), an emerging poxvirus of global importance. We generated PVGs of different sizes and mapped Illumina datasets using Giraffe, benchmarking performance against linear reference mapping with Minimap2. A minimal three-sample PVG containing one representative from each major lineage recovered 97% of known LSDV nucleotide diversity while reducing PVG size by >95% relative to a 121-sample PVG. PVG-based mapping detected more SNPs than linear mapping, including variants supported by read evidence that was not detected when reads were mapped to a single reference genome. 27% of SNPs detected using PVG-based mapping could not be projected onto the linear reference coordinate system because they were on alternative paths absent from reference, highlighting the impacts of reference bias. Notably, these new SNPs were at genes involved in host recognition and immune evasion, and identified lineage-specific mutations that improved subclade phylogenetic structure. Our findings demonstrate that PVGs substantially enhance SNP discovery in LSDV, with direct implications for genomic surveillance, outbreak tracing, and the detection of recombinant vaccine-related lineages in LSDV and other large DNA viruses. Impact StatementGenomic surveillance of viral pathogens typically relies on mapping reads to a single reference genome, a practice that systematically misses variation in divergent or recombinant isolates. We show that pangenome variation graphs (PVGs) can reduce this limitation in DNA viruses. Using lumpy skin disease virus (LSDV) as a model system, we demonstrate that a compact PVG constructed from only three representative genomes captures most known genomic diversity and improves the detection of mutations that are difficult to identify using linear reference mapping. PVGs recover biologically meaningful variants at genes involved in immune evasion and host interaction, resolve closely related subclades, and reveal mutations that cannot be identified using a single reference genome. This work uses a population-structure-guided strategy for building reference viral PVGs that balance computational efficiency with sensitivity, offering clear benefits for genomic surveillance, outbreak reconstruction, and the detection of recombinant lineages. Data SummaryAll supporting code and protocols have been provided within the article or through supplementary data files. Supplementary tables are available at Figshare: https://figshare.com/s/7a879df5b5452d04585b with all code at https://github.com/downingtim/LSDV_pangenomics

genomics↗
bioRxiv2025

Panalyze: automated virus pangenome variation graph construction and analysis

MotivationConstructing and studying pangenome variation graphs (PVG) supports new insights into viral genomic diversity. This is because such pangenomes are less prone to reference bias, which affects mutation detection. Interpreting the information arising from this is challenging, so automating these processes to allow exploratory investigations for PVG optimisation is essential. Moreover, existing methods do not scale well to the smaller virus genome sizes and to facilitate analysis in laptop environments. To address this, we developed an easily deployable pipeline to facilitate the rapid creation of virus PVGs that applies a broad range of analyses to these PVGs. ResultsWe present panalyze, a scalable and unbiased virus PVG construction, analysis and annotation tool implemented in NextFlow and containerised in Docker. Panalyze uses NextFlow to efficiently complete tasks across multiple compute nodes and in diverse high-performance computing environments. Panalyze can also operate on a single thread on a standard laptop, and analyse sequences lengths are of any size. We illustrate how Panalyze works and the valuable outputs it can generate using a range of common viral pathogens. AvailabilityPanalyze is released under a MIT open-source license, available on GitHub with documentation accessible at https://github.com/downingtim/Panalyze/. ContactChandana.tennakoon@pirbright.ac.uk, tim.downing@pibright.ac.uk Supplementary informationSupplementary data are available online.

bioinformatics↗
bioRxiv2022

Informing plasmid compatibility with bacterial hosts using protein-protein interaction data

The compatibility of plasmids with new host cells is significant given their role in spreading antimicrobial resistance (AMR)1 and virulence factor genes. Evaluating this using in vitro screening is laborious and can be informed by computational analyses of plasmid-host compatibility through rates of protein-protein interactions (PPIs) between plasmid and host cell proteins. We identified large excesses of such PPIs in eight important plasmids, including pOXA-48, using most known bacteria (n=4,363). 23 species had high rates of interactions with four blaOXA-48-positive plasmids. We also identified 48 species with high interaction rates with plasmids common in Escherichia coli. We found a strong association between one plasmid and the fimbrial adhesin operon pil, which could enhance host cell adhesion in aqueous environments. An excess rate of PPIs could be a sign of host-plasmid compatibility, which is important for AMR control given that plasmids like pOXA-48 move between species with ease. HighlightsO_LIWe tested for protein interactions between key plasmids and 4,363 bacterial hosts C_LIO_LI23 host species had high rates of protein interactions with four blaOXA-48 plasmids C_LIO_LIPseudomonas species showed high rates of interactions with these plasmids C_LIO_LIHost-plasmid protein-protein interaction rates may be associated with compatibility C_LI

genomics↗
bioRxiv2022

Bacterial plasmid-associated and chromosomal proteins have fundamentally different properties in protein interaction networks

Plasmids facilitate horizontal gene transfer, which enables the diversification of pathogens into new anatomical and environmental niches, implying that plasmid-encoded genes can cooperate well with chromosomal genes. We hypothesise that such mobile genes are functionally different to chromosomal ones due to this ability to encode non-essential functions like antimicrobial resistance and traverse distinct host cells. The effect of plasmid-driven gene gain on protein-protein interaction network topology is an important question in this area. Moreover, the extent to which these chromosomally- and plasmid-encoded proteins interact with proteins from their own groups compared to the levels with the other group remains unclear. Here, we examined the incidence and protein-protein interactions of all known plasmid-encoded genes across representative specimens from most bacteria using all available plasmids. We found that such plasmid-encoded genes constitute [~]0.7% of the total number of genes per bacterial sample, and that plasmid genes are preferentially associated with different species but had limited taxonomical power beyond this. Surprisingly, plasmid-encoded proteins had both more protein-protein interactions compared to chromosomal proteins, countering the hypothesis that genes with higher mobility rates should have fewer protein-level interactions. Nonetheless, topological analysis and investigation of the protein-protein interaction networks connectivity and change in the number of independent components demonstrated that the plasmid-encoded proteins had limited overall impact in >96% of samples. This paper assembled extensive data on plasmid-encoded proteins, their interactions and associations with diverse bacterial specimens that is available for the community to investigate in more detail. Significance statementIt is well-established that plasmids drive new traits in their bacterial hosts, but the extent to which host-plasmid co-evolution is evident at the level of protein-protein interactions remains unclear. To address this, we compiled and analysed all available valid bacterial plasmids and associated proteins to explore the compositional differences between chromosomal and plasmid-encoded proteins and their interaction levels. We found that plasmid-encoded genes were highly correlated across the bacterial samples such that they had a high association with taxonomic context. Contrasting with the complexity hypothesis, plasmid-encoded proteins had far more interactions on average than chromosomal ones, though they had minimal effects on protein-protein interaction network structure. This demonstrated that host-plasmid co-evolution is evident and detectable at the level of protein interactions.

genomics↗
bioRxiv2021

High genome plasticity and frequent genetic exchange in Leishmania tropica isolates from Afghanistan, Iran and Syria

BackgroundThe kinetoplastid protozoan Leishmania tropica mainly causes cutaneous leishmaniasis in humans in the Middle East, and relapse or treatment failure after treatment are common in this area. L. tropicas digenic life cycle includes distinct stages in the vector sandfly and the mammalian host. Sexual reproduction and genetic exchange appear to occur more frequently than in other Leishmania species. Understanding these processes is complicated by chromosome instability during cell division that yields aneuploidy, recombination and heterozygosity. This combination of rare recombination and aneuploid permits may reveal signs of hypothetical parasexual mating, where diploid cells fuse to form a transient tetraploid that undergoes chromosomal recombination and gradual chromosomal loss. Methodology/Principal FindingsThe genome-wide SNP diversity from 22 L. tropica isolates showed chromosome-specific runs of patchy heterozygosity and extensive chromosome copy number variation. All these isolates were collected during 2007-2017 in Sweden from patients infected in the Middle East and included isolates from a patient possessing two genetically distinct leishmaniasis infections three years apart with no evidence of re-infection. We found differing ancestries on the same chromosome (chr36) across multiple samples: matching the reference genome with few derived alleles, followed by blocks of heterozygous SNPs, and then by clusters of homozygous SNPs with specific recombination breakpoints at an inferred origin of replication. Other chromosomes had similar marked changes in heterozygosity at strand-switch regions separating polycistronic transcriptional units. Conclusion/SignificanceThese large-scale intra- and inter-chromosomal changes in diversity driven by recombination and aneuploidy suggest multiple mechanisms of cell reproduction and diversification in L. tropica, including mitotic, meiotic and parasexual processes. It underpins the need for more genomic surveillance of Leishmania, to detect emerging hybrids that could spread more widely and to better understand the association between genetic variation and treatment outcome. Furthering our understanding of Leishmania genome evolution and ancestry will aid better diagnostics and treatment for cutaneous leishmaniasis caused by L.tropica in the Middle East. Author SummaryCutaneous leishmaniasis is mainly caused by Leishmania tropica in the Middle East, where it is known for treatment failure and a need for prolonged and/or multiple treatments. Several factors affect the clinical presentation and treatment outcome, such as host genetic variability and specific immune response, as well as environmental factors and the vector species. Little is known about the parasite genome and its influence on treatment response. By analysing the genome of 22 isolates of L. tropica, we have revealed extensive genomic variation and a complex population structure with evidence of genetic exchange within and among the isolates, indicating a possible presence of sexual or parasexual mechanisms. Understanding the Leishmania genome better may improve future treatment and better understanding of treatment failure and relapse.

genetics↗
bioRxiv2020

Plasmids shape the diverse accessory resistomes of Escherichia coli ST131

The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes that exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host cell adhesion like type 1 fimbriae. The extent to which commensal E. coli and uropathogenic ExPEC ST131 share AMR genes remains understudied at a genomic level, and here we examined this using a preterm infant resistome. Here, individual ST131 had small differences in AMR gene content relative to a larger shared resistome. Comparisons with a range of plasmids common in ST131 showed that AMR gene composition was driven by conjugation, recombination and mobile genetic elements. Plasmid pEK499 had extended regions in most ST131 Clade C isolates, and it had evidence of a co-evolutionary signal based on protein-level interactions with chromosomal gene products, as did pEK204 that had a type IV fimbrial pil operon. ST131 possessed extensive diversity of selective type 1, type IV, P and F17-like fimbriae genes that was highest in subclade C2. The structure and composition of AMR genes, plasmids and fimbriae vary widely in ST131 Clade C and this may mediate pathogenicity and infection outcomes. Data SummaryThe following files are available on the FigShare project "Plasmids_ST131_resistome_2020" : O_LI The set of 794 AMR genes derived from [74] are available (with their protein sequence translation) at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961402. C_LIO_LI The AMR gene profiles per sample determined by their BLAST sequence similarity results against CARD are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961612. This dataset includes the PlasmidFinder results. It also includes other AMR database comparisons (ARG-ANNOT, ResFinder, MegaRes, VFDB and VirulenceFinder). C_LIO_LI The BLAST sequence similarity results for the fim, pil, pap and ucl operons genes versus 4,071 E. coli ST131 assemblies from Decano & Downing (2019) are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961711. C_LIO_LI The genome sequences and annotation files for reference genomes NCTC13441, EC958 and SE15, along with the assembled contigs for 83972 and 3_2_53FAA are available at FigShare at doi: dx.doi.org/10.6084/m9.figshare.11961813. C_LIO_LI The 4,071 E. coli ST131 genome assemblies from Decano & Downing (2019) are available at FigShare at doi: 10.6084/m9.figshare.11962278 (the first 1,680 assemblies) and at doi: dx.doi.org/10.6084/m9.figshare.11962557 (the second 2,391 assemblies). C_LI

genomics↗
bioRxiv2019

Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones

Escherichia coli sequence type 131 (ST131) is a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. Here, we investigated an outbreak of E. coli ST131 producing extended spectrum {beta}-lactamases (ESBLs) in a long-term care facility (LTCF) in Ireland by combining data from this LTCF (n=69) with other Irish (n=35) and global (n=690) ST131 genomes to reconstruct the evolutionary history and understand changes in population structure and genome architecture over time. This required a combination of short and long-read genome sequencing, de novo assembly, read mapping, ESBL gene screening, plasmid alignment and temporal phylogenetics. We found that clade C was the most prevalent (686 out of 794 isolates, 86%) of the three major ST131 clades circulating worldwide (A, B, C), and was associated with the presence of different ESBL alleles, diverse plasmids and transposable elements. Clade C was estimated to have emerged in [~]1985 and subsequently acquired different ESBL gene variants (blaCTX-M-14 vs blaCTX-M-15). An ISEcp1- mediated transposition of the blaCTX-M-15 gene further increased the diversity within Clade C. We discovered a local clonal expansion of a rare C2 lineage (C2_8) with a chromosomal insertion of blaCTX-M-15 at the mppA gene. This was acquired from an IncFIA plasmid. The C2_8 lineage clonally expanded in the Irish LTCF from 2006, displacing the existing C1 strain (C1_10) and highlighting the potential for novel ESBL-producing ST131 with a distinct genetic profile to cause outbreaks strongly associated with specific healthcare environments.\n\nImportanceExtraintestinal pathogenic E. coli (ExPEC) ST131 is adapting in the context of antibiotic exposure, resulting in a pandemic with distinct genetic subtypes. Here, we track the evolution of antibiotic-resistance gene variants originally discovered in an ExPEC ST131 outbreak that was identified in a LTCF in Ireland. Analysis of 794 global ST131 genomes show that subclade C1 was associated with the initial infection outbreak, but that a new lineage from subclade C2 successfully displaced C1. This genetically distinct C2 subclade with a chromosomal insertion of a key antibiotic-resistance gene had clonally expanded within the LTCF. We provide new insights into the timing of genetic events driving the diversification of C2 subclades to show that that outbreak C2 strain likely evolved elsewhere before spreading to the LTCF. This study highlights the scope of antibiotic-resistance gene rearrangement within ST131, reinforcing the need to integrate genomic, epidemiological and microbiological approaches to understand ST131 transmission.

genomics↗
bioRxiv2019

An Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates

Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131s origin, adaptation and spread is essential. E. coli ST131s ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131s population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels. Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.

genomics↗
bioRxiv2019

Global genome diversity of the Leishmania donovani complex

Protozoan parasites of the Leishmania donovani complex - L. donovani and L. infantum - cause the fatal disease visceral leishmaniasis. We present the first comprehensive genome-wide global study, with 151 cultured field isolates representing most of the geographical distribution. L. donovani isolates separated into five groups that largely coincide with geographical origin but vary greatly in diversity. In contrast, the majority of L. infantum samples fell into one globally-distributed group with little diversity. This picture is complicated by several hybrid lineages. Identified genetic groups vary in heterozygosity and levels of linkage, suggesting different recombination histories. We characterise chromosome-specific patterns of aneuploidy and identified extensive structural variation, including known and suspected drug resistance loci. This study reveals greater genetic diversity than suggested by geographically-focused studies, provides a resource of genomic variation for future work and sets the scene for a new understanding of the evolution and genetics of the Leishmania donovani complex.

genomics↗
bioRxiv2019

Complete assembly of Escherichia coli ST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays and higher healthcare costs. E. coli ST131 is a major ExPEC clonal group worldwide with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-14/15/27, which are often rearranged, amplified and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long read sequencing to decipher the genome structures of six E. coli ST131 isolated from six patients. Most long read assemblies generated entire chromosomes and plasmids as single contigs, contrasting with more fragmented assemblies created with short reads alone. The long read assemblies highlighted diverse accessory genomes with blaCTX-M-15, blaCTX-M-14 and blaCTX-M-27 genes identified in three, one and one isolates, respectively. One sample had no blaCTX-M gene. Two samples had chromosomal blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B and Tn2. This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts even between closely-related isolates within a clonal group such as E. coli ST131. ImportanceDrug-resistant bacteria are a major cause of illness worldwide and a specific subtype called Escherichia coli ST131 cause a significant amount of these infections. ST131 become resistant to treatment by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to an existing approach. A combination of methods shows that drug-resistance genes on plasmids are highly mobile because they can jump into ST131s chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.

genomics↗
bioRxiv2017

Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene content evolution in the Viannia subgenus

The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3 end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.

genomics↗