Biology subjects

Taranto, A. P.

Publications and source records attributed to Taranto, A. P..

3 recordsLinked to original sources

bioRxiv2025

A Chromosome-scale Reference Genome of Meloidogyne hapla reveals localized recombination hotspots enriched with Effector Proteins

Root-knot nematodes (Meloidogyne spp.) are among the most destructive agricultural pests that cause significant yield losses across a wide range of crops. Meloidogyne hapla, a diploid species, is a valuable model for studying root-knot nematodes due to its parasitic diversity, small genome, and a reproductive strategy that facilitates genetic analysis. Here, we present a high-quality chromosome-scale assembly of M. hapla, generated using multiple sequencing platforms-PacBio HiFi, ONT, Illumina and HiC. The 59 Mb assembly comprises 16 chromosome-length scaffolds, notably lacking canonical telomeric repeats. Instead, we identified a tandem 16-mer repeat mainly present at scaffold ends, suggesting an alternative system for chromosome-end maintenance. Genetic linkage analysis of F2 populations derived from crosses between M. hapla strains validated the assembly but also revealed anomalies indicating chromosome structure differences between parental isolates such as fissions, fusions, and rearrangements. This analysis also revealed sharply delineated zones of high recombination on most chromosome arms. We also identified 1,258 genes encoding putative secreted proteins (PSP), which should be enriched in genes involved in host interaction and pathogenicity. Most of the PSP genes had orthologs in other plant parasitic nematode species, and the majority were pioneers, lacking known functional domains. Notably, we found that PSPs are significantly enriched in high-recombination zones, possibly facilitating their rapid evolution. Overall, our study provides new insights into the genome structure of diploid root-knot nematodes and highlights the interplay between genome architecture, recombination, and parasitism. These findings raise new questions about how genetic and genomic adaptations drive the success of rootknot nematodes as plant parasites.

plant biology↗

bioRxiv2023

Phased chromosome-scale genome assembly of an asexual, allopolyploid root-knot nematode reveals complex subgenomic structure

We present the chromosome-scale genome of the allopolyploid root-knot nematode Meloidogyne javanica. We show that the M. javanica genome is predominantly allotetraploid, comprising two subgenomes, A and B, that most likely originated from hybridisation of two ancestral parental species. The assembly is annotated using full-length non-chimeric transcripts, comparison to reference databases, and ab initio prediction techniques, and the subgenomes are phased using ancestral k-mer spectral analysis. Subgenome B appears to show greater fission of chromosomal contigs, and while there is substantial synteny between subgenomes, we also identify regions lacking synteny that may have diverged in the ancestral genomes prior to or following hybridisation. Indels are common both between alleles within a subgenome, and between the A and B subgenomes, suggesting the M. javanica genome exists in a dynamic hypo-tetraploidy where copy number can vary along the chromosome. This annotated and phased genome assembly forms a significant resource for understanding the origins and genetics of these globally important plant pathogens. Author SummaryRoot-knot nematodes represent one of the most significant crop parasites globally. Despite their agricultural importance, only rudimentary genomic resources have been published to date, leaving a gap in the understanding of genetic mechanisms driving genome evolution and crop virulence. Here, we have used modern genomic and bioinformatic approaches to create a chromosome-scale reference genome to investigate the origins and genomic constitution of the root-knot nematode species Meloidogyne javanica. This species reproduces by ameiotic parthenogenesis and has an allopolyploid genome and is among the most damaging plant parasitic nematodes with a large and evolving plant host range. Utilising modern long-range DNA sequencing and bioinformatics approaches, we successfully phased the genome into its constituent subgenomes, a first for this agriculturally important clade. While we find the genomic landscape is mostly syntenic between subgenomes, we identified regions of minimal similarity, and highlight structural divergence between subgenomes. We demonstrate that this species was originally tetraploid, but insertions and deletions have been the major force in generating diversity, resulting in a hypo-tetraploid genome with local variations in ploidy.

genomics↗

bioRxiv2019

Transposon mediated horizontal transfer of the host-specific virulence protein ToxA between three fungal wheat pathogens

Most known examples of horizontal gene transfer (HGT) between eukaryotes are ancient. These events are identified primarily using phylogenetic methods on coding regions alone. Only rarely are there examples of HGT where non-coding DNA is also reported. The gene encoding the wheat virulence protein ToxA and surrounding 14 kb is one of these rare examples. ToxA has been horizontally transferred between three fungal wheat pathogens (Parastagonospora nodorum, Pyrenophora tritici-repentis and Bipolaris sorokiniana) as part of a conserved [~]14kb element, which contains coding and non-coding regions. Here we use long-read sequencing to define the extent of HGT between these three fungal species. Construction of near-chromosomal level assemblies enabled identification of terminal inverted repeats on either end of the 14kb region, typical of a Type II DNA transposon. This is the first description of ToxA with complete transposon features, which we call ToxhAT. In all three species, ToxhAT resides in a large (140-250 kb) transposon-rich genomic island which is absent in toxA- isolates. We demonstrate that the horizontal transfer of ToxhAT between Pyrenophora tritici-repentis and P. nodorum occurred as part of a large [~]80kb HGT which is now undergoing extensive decay. In contrast, in B. sorokiniana ToxhAT and its resident genomic island are mobile within the genome. Together these data provide insight into the non-coding regions that facilitate HGT between eukaryotes and the genomic processes which mask the extent of HGT between these species.\n\nIMPORTANCEThis work dissects the tripartite horizontal transfer of ToxA; a gene that has a direct negative impact on global wheat yields. Defining the extent of horizontally transferred DNA is important because it can provide clues as to the mechanisms that facilitate HGT. Our analysis of ToxA and its surrounding 14kb suggests that this gene was horizontally transferred in two independent events, with one event likely facilitated by a Type II DNA transposon. These horizontal transfer events are now in various processes of decay in each species due to the repeated insertion of new transposons and subsequent rounds of targeted mutation by a fungal genome defense mechanism known as repeat induced point-mutation. This work highlights the role that HGT plays in the evolution of host adaptation in eukaryotic pathogens. It also increases the growing body of evidence that transposons facilitate adaptive HGT events between fungi present in similar environments and hosts.\n\nDATA AVAILABILITYAll raw sequencing data is available under NCBI BioProject PRJNA505097.\n\nThe P. nodorum SN15 Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession SSHU00000000. The version SSHU01000000 is described in this paper. The P. nodorum SN79-1087 Whole Genome Shotgun project has been deposited under the accessions CP039668-CP039689. The Whole Genome shotgun project and accession numbers for B. sorokiniana isolates are as follows: CS10; SRZH00000000, CS27; SRZG00000000, WAI2406; SRZF00000000, WAI2411; SRZE00000000. Transposon annotations, CS10 and CS27 gene annotations are available at https://github.com/megancamilla/Transposon-Mediated-transfer-of-ToxA

genomics↗