Biology subjects

Dhakal, R.

Publications and source records attributed to Dhakal, R..

6 recordsLinked to original sources

bioRxiv2026

PanvaR: An R package for fine-mapping and visualizing results from genome-wide association studies

Genome-wide association studies (GWAS) use statistical models to correlate single nucleotide polymorphisms (SNPs) to a phenotype of interest. This scan of the entire genome identifies regions of association with a phenotype, but due to linkage disequilibrium (LD), GWAS on their own cannot identify single genes responsible for phenotypic variation. Rather, fine-mapping of GWAS regions is required, necessitating the use of additional tools and software. With the introduction of more pangenomic resources in a number of crops (Guo et al. 2025; Hufford et al. 2021), the fidelity of these fine-mapping efforts is growing, presenting the opportunity to leverage new information about allelic variation towards gene discovery (Shi et al. 2023; Della Coletta et al. 2021). Panvar is a tool developed to integrate existing software and resources to perform GWAS and fine-mapping in one seamless step. For each identified GWAS peak, panvaR outputs information about LD and SNP effect prediction for each SNP and by layering locations of nearby genes, creates a refined list of possible candidate genes. We have implemented Panvar as an R package, "panvaR", which runs the analysis functions, creates interactive and static visualizations, and outputs results tables. This tool seeks to bridge the gap between GWAS and gene speeding up an important step of quantitative genetic studies.

genomics↗

bioRxiv2025

mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing

The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel genomics tools and algorithms. In this work, we introduce mim: a lightweight, auxiliary index that enables fast, parallel, and highly-scalable parsing of compressed fastq.gz files. The creation of the mim index for a file is a one-time operation that can be performed in time comparable to that of simply decompressing and parsing the file (index creation induces [~] 20% overhead) and with minimal working memory. The mim index itself is very small, usually about [Formula]th of the size of the original compressed file, and can be easily stored along side the file or fetched from a remote location when it is needed. Further, the mim index is purely additive -- it does not modify the original gzipped FASTQ file in any way, nor require that the file be recompressed or rewritten -- and thus it does not require converting the massive back catalog of existing raw sequencing data. To demonstrate the feasibility and utility of the mim index, we benchmark construction of the mim index on a variety of existing gzipped FASTQ data, and also measure thread-scaling of mim index-assisted parallel FASTQ parsing on a simple parsing/ decompression-related task. We find that, for the one-time cost of index creation, and a small fraction of extra storage space, the mim index can massively accelerate the ingestion and parsing of gzipped FASTQ data, exhibiting near linear thread scaling in our experiments. mim is written in C++17, and is available as open source software under a BSD 3-clause license at https://github.com/COMBINE-lab/mim.

bioinformatics↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, Quercus virginiana

Hybridization is a major force driving diversification, migration, and adaptation in Quercus species. While population genetics and phylogenetics have traditionally been used for studying these processes, advances in sequencing technology now enable us to incorporate comparative and pan-genomic approaches as well. Here we present a highly contiguous, chromosome-scale and haplotype-resolved genome assembly for the southern live oak, Quercus virginiana, the first reference genome for section Virentes, as part of the American Campus Tree Genomes (ACTG) program. Originating from a clone of Auburn Universitys historic "Toomers Oak," this assembly contributes to the pool of genomic resources for investigating recombination, haplotype variation, and structural genomic changes influencing hybridization potential in this clade and across Quercus. It also provides insights into the architecture of the putative centromeric regions within the genus. Alongside other oak references, the Q. virginiana genome will support research into the evolution and adaptation of the Quercus genus.

genomics↗

bioRxiv2024

Chromosome Numbers and Reproductive Life Cycles in Green Plants: A Genomic Perspective

The strong correlation between reproductive life cycle type and chromosome numbers in green plants has been a long-standing mystery in evolutionary biology. Within green plants, the derived condition of heterosporous reproduction has emerged from the ancestral condition of homospory in disparate locations on the phylogenetic tree at least 11 times, of which 3 lineages are extant. In all green plant lineages where heterospory has emerged, there has been a significant downsizing in chromosome numbers (refer to figure 1). This dynamic has been investigated without clear answers for many decades. In this study, we combine known ideas from existing literature with novel methods, tools, and data to generate fresh insights into an old question. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/604804v3_fig1.gif" ALT="Figure 1"> View larger version (8K): org.highwire.dtl.DTLVardef@fcc574org.highwire.dtl.DTLVardef@10759bforg.highwire.dtl.DTLVardef@1950e33org.highwire.dtl.DTLVardef@d7718d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:-C_FLOATNO A simplified phylogeny of green plants/Embryophytes with the respective group and their average chromosome numbers in each group. Heterosporous lineages highlighted in green. C_FIG Using gene family evolution models and selection analyses, we identified gene families that have undergone significant expansion, contraction, or selection in heterosporous lineages. Our results reveal both shared and lineage-specific genomic changes associated with the evolution of heterospory. We found expansions in gene families related to developmental regulation, signaling pathways, and stress responses across heterosporous groups. Notably, the MATE efflux family showed consistent expansion and evidence of selection in heterosporous lineages, suggesting a potentially conserved role in heterospory evolution. These findings highlight novel insights that may underpin the association between heterospory and reduced chromosome numbers. The general importance of chromosome numbers, structure, and sizes in cellular biology notwithstanding, the association between the emergence of heterosporous reproduction and chromosome number reduction/genome downsizing is not fully understood. It remains unclear why there exists an association between aspects of biology at such disparate levels as reproductive life-cycles and chromosome numbers/genome size. Exploring and answering this conundrum of evolutionary biology can add to our broader understanding of life sciences and of biology at different levels. Applying the novel tools and methods emerging from ongoing progress in biotechnology and computational sciences presents an opportunity to make new inroads into this long-standing question.

bioinformatics↗

bioRxiv2020

STRATEGIC IDENTIFICATION OF NEW GENETIC DIVERSITY TO EXPAND LENTIL (Lens culinaris Medik.) PRODUCTION USING NEPAL AS AN EXAMPLE

This article is written to disseminate descriptive results obtained from field experiments conducted at Bardiya, Nepal, during winter 2016 and 2017 on 324 diverse lentil (L. culinaris Medik.) genotypes obtained from genebanks and breeding programs around the world. Lentil genotypes were examined for phenological traits related to adaptation, and recommendations for potential incorporation of new exotic genotypes into Nepalese breeding programs are presented. In addition, predictions of days to flowering based on temperature and photoperiod are used to identify genotypes that hold suitability for specific growing regions in Nepal, allowing for the potential expansion of growing regions. From this study we found many potentially adapted genotypes for terai, mid-hill and high hill growing regions, the list consists of a number of large-seeded lines with yellow cotyledons, an entirely new market class of lentils in Nepal. This paper primarily targets lentil breeders and agronomists; furthermore, it can be equally informative to extension workers involved in the pulse crop research and development in Nepal and other countries with similar climatic conditions.

plant biology↗

bioRxiv2020

Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

O_LILentil (Lens culinaris Medik.) is cultivated under a wide range of environmental conditions, which led to diverse phenological adaptations and resulted in a decrease in genetic variability within breeding programs due to reluctance in using genotypes from other environments. C_LIO_LIWe phenotyped 324 genotypes across nine locations over three years to assess their phenological response to the environment of major lentil production regions and to predict days from sowing to flowering (DTF) using a photothermal model. C_LIO_LIDTF was highly influenced by the environment and is sufficient to explain adaptation. We were able to predict DTF reliably in most environments using a simple photothermal model, however, in certain site-years, results suggest there may be additional environmental factors at play. Hierarchical clustering of principal components revealed the presence of eight groups based on the responses of DTF to contrasting environments. These groups are associated with the coefficients of the photothermal model and revealed differences in temperature and photoperiod sensitivity. C_LIO_LIExpanding genetic diversity is critical to the success of a breeding program; understanding adaptation will facilitate the use of exotic germplasm. Future climate change scenarios will result in increase temperature and/or shifts in production areas, we can use the photothermal model to identify genotypes most likely to succeed in these new environments. C_LI

plant biology↗