Biology subjects

Shakya, P.

Publications and source records attributed to Shakya, P..

5 recordsLinked to original sources

bioRxiv2026

Resistance Breaking in Root-knot Nematodes Carries a Fitness Cost Associated with Defective Feeding Site Development

Root-knot nematodes (RKNs) cause an estimated 157 billion dollars in annual yield losses worldwide. In tomato, resistance to RKNs is conferred by the single dominant resistance gene Mi-1, which has been widely integrated into commercial cultivars. Prolonged and widespread use of Mi-1 has led to the emergence of resistance-breaking populations in tomato fields worldwide; however, the consequences of resistance breaking for nematode performance on susceptible hosts remain poorly understood. Here, we compared infection outcomes of two closely related strains of Meloidogyne javanica, VW4 (Mi-1-avirulent; wild-type) and VW5 (Mi-1-virulent; resistance-breaking), on three susceptible hosts: tomato, cucumber, and rice. Across all hosts, VW5 produced significantly fewer eggs than VW4, revealing a fitness cost associated with Mi-1 virulence. Light and transmission electron microscopy of tomato and cucumber galls revealed impaired feeding site establishment by VW5. Consistent with these observations, transcriptomic profiling showed that VW5 infection induced weaker host transcriptional reprogramming and lacked gene expression signatures associated with effective suppression of plant defense responses. Together, these findings demonstrate that adaptation to Mi-1-mediated resistance incurs a fitness cost on susceptible plants and is accompanied by impaired feeding site formation and altered host reprogramming. Furthermore, these results establish VW4 and VW5 as a powerful resource for understanding nematode genes and pathways required for successful parasitism and feeding site development.

plant biology↗

bioRxiv2026

RLBWT-Based LCP Computation in Compressed Space for Terabase-Scale Pangenome Analysis

Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this problem. In particular, run-length Burrows-Wheeler transform (RLBWT) based compressed full text indexes have seen wide development and adoption. However, the construction of these RLBWT-based compressed full text indexes is still computationally expensive, sometimes prohibitively so, even for current dataset sizes. Therefore, we present algorithms for the construction of RLBWT-based compressed full text indexes and their supporting data structures in compressed space. The algorithms have a space complexity of O(r) words and run in O(n) time for repetitive datasets, where r is the number of runs in the BWT, n is the length of the text, and repetitive datasets implies the average run length is at least log n. We provide the first algorithm to compute LCP-related information for repetitive datasets in optimal time and O(r) space, greatly reducing memory requirements. The key idea behind this algorithm is the utilization of r samples of the inverse suffix array at regular intervals. For example, on the Human Pangenome Reference Consortium Release 2 dataset, this reduces peak memory from 2,135 GiB to 170 GiB (12.6x reduction) compared to the previous best method (pfp-thresholds). AvailabilityThe implementation is available at https://github.com/ucfcbb/TeraTools. Supplementary InformationSupplementary Material is available online at bioRxiv.

bioinformatics↗

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↗

bioRxiv2025

Dynamic μ-PBWT: Dynamic Run-length Compressed PBWT for Biobank Scale Data

Durbins positional Burrows-Wheeler transform (PBWT) supports efficient haplotype matching and queries given a panel of haplotypes. It has been widely used for statistical phasing, imputation and identity-by-descent (IBD) detection. However, the original PBWT panel doesnt support dynamic updates when haplotypes need to be added or deleted from the panel. Dynamic-PBWT (d-PBWT) solved this problem but it is not memory efficient. While the memory constraint problem of the PBWT has been tackled by Syllable-PBWT and {micro}-PBWT, these are static data structures that do not allow updates. Additionally, Syllable-PBWT only supports long-match query and {micro}-PBWT only supports set-maximal match query, limiting their functionality in the compressed form. In this paper, we present Dynamic {micro}-PBWT (which can also be seen as compressed d-PBWT) that is memory efficient and supports dynamic updates. We run-length compress PBWT to achieve better compression rate and store the runs in the self-balancing trees to enable dynamic updates. We show that the number of updates per insertion or deletion in the tree at each site is constant regardless of the number of haplotypes in the panel and the updates can be made without decompressing the index. In addition, we use orders of magnitude less memory than d-PBWT. We also provide a long match query algorithm that can easily be extended back to the original {micro}-PBWT. Overall, the flexibility and space-efficiency of Dynamic {micro}-PBWT makes it a potential index data structure for biobank scale genetic data analyses. The source code for Dynamic {micro}-PBWT is available at https://github.com/ucfcbb/Dynamic-mu-PBWT.

bioinformatics↗

bioRxiv2022

mcPBWT: Space-efficient Multi-column PBWT Scanning Algorithm for Composite Haplotype Matching

Positional Burrows-Wheeler Transform (PBWT) is a data structure that supports efficient algorithms for finding matching segments in a panel of haplotypes. It is of interest to study the composite patterns of multiple matching segments or blocks arranged contiguously along a same haplotype as they can indicate recombination crossover events, gene-conversion tracts, or, some-times, errors of phasing algorithms. However, current PBWT algorithms do not support search of such composite patterns efficiently. Here, we present our algorithm, mcPBWT (multi-column PBWT), that uses multiple synchronized runs of PBWT at different variant sites providing a "look-ahead" information of matches at those variant sites. Such "look-ahead" information allows us to analyze multiple contiguous matching pairs in a single pass. We present two specific cases of mcPBWT, namely double-PBWT and triple-PBWT which utilize two and three columns of PBWT respectively. double-PBWT finds two matching pairs combinations representative of crossover event or phasing error while triple-PBWT finds three matching pairs combinations representative of gene-conversion tract.

bioinformatics↗