Biology subjects

Despot-Slade, E.

Publications and source records attributed to Despot-Slade, E..

5 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↗

bioRxiv2024

Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species

Tandemly repeated satellite DNAs (satDNAs) are among the most abundant and fastest-evolving eukaryotic sequences, but the way they model genomes is still elusive. Here, we investigated the evolutionary dynamics of satDNAs in the extremely satDNA-rich genomes of two closely related Tribolium insects that produce sterile hybrids. In Tribolium freemani, we identified 135 satDNAs, accounting for 38.7% of the genome. Comparative analysis with the Tribolium castaneum satellitome revealed that the drastic difference happened in their centromeric regions, which share orthologous organization hallmarked by totally different major satDNAs but related minor satDNAs. The T. freemani male sex chromosome, which lacks the major satDNA but contains a minor-like satDNA, further heightened the question of which satDNA is centromere-competent. By analyzing the long-range organization of the centromeric regions, we revealed that both the major and minor satDNA arrays exhibit a strong tendency toward macro-dyad symmetry, suggesting that the secondary structures in the centromeres may be more important than the primary sequence itself. We found evidence that the centromeric satDNAs of T. freemani occur in extrachromosomal circular DNAs, which may contribute to their expansion and homogenization between non-homologous chromosomes. We also identified numerous low-copy-number satDNAs that are orthologous between the siblings, some of which are associated with transposable elements, highlighting transposition as a mechanism of their spreading. The dynamic evolution of satDNAs has clearly influenced the differentiation of Tribolium genomes, but the question remains whether the differences in their satDNA profiles are a cause or consequence of speciation.

genomics↗

bioRxiv2024

SatXplor - A comprehensive pipeline for satellite DNA analyses in complex genome assemblies

Satellite DNAs (satDNAs) are tandemly repeated sequences that make up a significant portion of almost all eukaryotic genomes. Although satDNAs have been shown to play a very important role in genome organization and evolution, they are relatively poorly analysed even in model. One of the main reasons for the current lack of in-depth studies on satDNAs is their underrepresentation in genome assemblies. The complexity and highly repetitive nature of satDNAs make their analysis challenging, and there is a need for efficient tools that can ensure accurate annotation and analysis of satDNAs. We present a novel pipeline, named Satellite DNA Exploration (SatXplor), designed to robustly characterize satDNA elements and analyse their arrays and flanking regions. SatXplor is benchmarked against curated satDNA datasets from diverse species, showcasing its versatility across genomes with varying complexities and different satDNA profile. Component algorithms excel in the identification of tandemly repeated sequences and for the first time enable evaluation of satDNA variation and array annotation with the addition of information about surrounding genomic landscape. SatXplor is an innovative pipeline for satDNA analysis that can be paired with any tool used for satDNA detection, offering insights into the structural characteristics, array determination and genomic context of satDNA elements. By integrating various computational techniques, from sequence analysis and homology investigation to advanced clustering and graph-based methods, it provides a versatile and comprehensive approach to explore the complexity of satDNA organization and to understand the underlying mechanisms and evolutionary aspects. It is open-source and freely accessible at https://github.com/mvolar/SatXplor.

bioinformatics↗

bioRxiv2023

Long-read genome assembly of the insect model organism Tribolium castaneum reveals extensive propagation of satellite DNA long arrays in gene-rich regions

Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly repeated sequences which are mostly underrepresented in genome assemblies. Here we combined Nanopore long-read sequencing with a reference-guided assembly approach, to generate an improved, high-quality genome assembly TcasONT of the model beetle Tribolium castaneum. Enriched by 45 Mb in the repetitive part, the new assembly comprises almost the entire genome sequence. We used the enhanced assembly to conduct global and in-depth analyses of abundant euchromatic satDNAs, Cast1-Cast9. Contrary to the commonly adopted view, our finding showed the extensive spread of satDNAs in gene-rich regions, including long arrays. The results of the principal component analysis of monomers and sequence similarity relationships between satDNA arrays, revealed an occurrence of recent satDNAs array exchange between different chromosomes. We proposed a scenario of their genome dynamics characterized by repeated bursts of satDNAs spreading through euchromatin, followed by a process of elongation and homogenization of arrays. We also found that suppressed recombination on the X chromosome has no significant effect on the spread of satDNAs, but rather tolerates the amplification of these satDNAs into longer arrays. Analyses of arrays neighboring regions showed a tendency of one Cast satDNA to be associated with transposon-like elements. Using 2D electrophoresis followed by Southern blotting, we proved Cast satDNAs presence in the fraction of extrachromosomal circular DNA (eccDNA). We point to two mechanisms that enable the said satDNA spread to occur: transposition by transposable elements and insertion mediated by eccDNA. The presence of such a large proportion of satDNA in gene-rich regions inevitably gives rise to speculation about their possible influence on gene expression.

genomics↗

bioRxiv2023

Unzipped assemblies of polyploid root-knot nematode genomes reveal new kinds of unilateral complex telomeric repeats

Telomeres play central roles in senescence, aging and chromosome integrity. Using ONT long read sequencing we have assembled the genomes of Meloidogyne incognita, M. javanica and M. arenaria, the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats mostly present at one end of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using FISH we confirmed these repeats were present at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles and opens new perspectives towards the development of more specific control methods against these pests.

genomics↗