Biology subjects

Nepal, M. P.

Publications and source records attributed to Nepal, M. P..

6 recordsLinked to original sources

bioRxiv2026

PhytoFam: A Nextflow Pipeline for Genome-Wide Analysis of Plant Gene Families

Genome-wide identification of plant gene families is essential for functional and evolutionary studies but often requires the use of multiple independent tools for homolog detection, domain validation, orthology assignment, and phylogenetic analysis. This fragmented approach involves extensive manual scripting, complicates reproducibility and parameter tracking, and may require additional steps to remove redundant protein isoforms. To address these challenges, we developed PhytoFam, a Nextflow-based workflow that automates gene family identification from proteome input through phylogenetic reconstruction. The pipeline integrates HMMER for candidate sequence identification, isoform-aware deduplication, InterProScan for domain confirmation, BLAST reciprocal best hit (RBH) analysis for orthology assignment, MUSCLE for multiple sequence alignment with optional outgroup incorporation, TrimAl for alignment trimming, and IQ-TREE3 for phylogenetic reconstruction. PhytoFam is portable across local workstations and high-performance computing environments and supports deployment through Conda, Docker, and Singularity. We validated the workflow using the Morus alba MADS-box gene family, where the complete analysis finished in 1 h 10 min (9 CPU h). IQ-TREE3 accounted for most of the execution time, whereas InterProScan showed the highest memory requirement with a peak resident set size of 4.5 GB. PhytoFam provides a reproducible, automated, and scalable solution for plant gene family identification and phylogenetic analysis. The pipeline is freely available at https://github.com/sanamparajuli/PhytoFam.

bioinformatics↗

bioRxiv2026

Population Genetics of Native Red Mulberry at Its Northwestern Boundary Suggests Postglacial Founder Effects

Morus rubra is native to the eastern United States, with its range extending into the Upper Midwest and southern Ontario, Canada. Its present distribution suggests that past glacial events in North America may have influenced the genetic structure of populations at the species northwestern range boundary. This study assessed genetic variation among six M. rubra populations believed to have experienced postglacial colonization using published nuclear microsatellite markers and sequences from the chloroplast trnL-trnF region. Five nuclear microsatellite markers previously developed for M. alba were successfully transferred to M. rubra, while the chloroplast trnL-trnF region provided an additional marker for evaluating chlorotype diversity. Nuclear microsatellite diversity was higher in southern unglaciated populations than in northern glaciated populations, a pattern consistent with the observed distribution of chlorotype diversity. Together, these results support ancient founder effects associated with leading-edge expansion following glacial recession and suggest that postglacial colonization contributed to the present-day genetic structure of M. rubra at its northwestern range boundary. Because M. rubra hybridizes with the naturalized invasive M. alba, reduced genetic diversity in marginal populations may increase their vulnerability to genetic swamping. The markers characterized in this study provide useful tools for population genetic research in Morus, and the findings have important implications for the conservation and management of marginal and threatened M. rubra populations in the Upper Midwest.

evolutionary biology↗

bioRxiv2020

Characterization of Induced Susceptibility Effects of Soybean Aphid on Soybean

Soybean aphid (SBA) is one of the major pests of soybean (Glycine max) in the United States of America. The main objective of this research was to characterize interactions between two different biotypes of soybean aphids in susceptible and resistant soybean cultivars. Demographic and transcriptomic responses of susceptible and resistant (Rag1) soybean cultivars to aphid feeding were investigated in soybean plants colonized by aphids (biotype 1) in the presence or absence of inducer population (biotype 2) at day 1 and day 11. Leaves tissues collected at day 1 and day 11 post infestation were used for RNA sequencing, and ten RNA datasets with 266,535,654 sequence reads were analyzed. In the presence of inducer population, we found 746 and 243 differentially expressed genes (DEGs) in susceptible and resistant cultivars, respectively at day 1, whereas 981 and 377 DEGs were found in susceptible and resistant cultivars, respectively at day 11. Enrichment analysis showed a response to chitin, lignin catabolic and metabolic process, asparagine metabolic process, response to chemical unique to treatment with no inducer population, whereas, response to reactive oxygen species, photosynthesis, regulation of endopeptidase activity unique to treatment with inducer population. Furthermore, 14 DEGs were observed in Rag QTLs regions, particularly six DEGs in Rag1 containing QTL. The identified DEGs in the experiment in both resistant and susceptible cultivars during the interaction of soybean and SBA are potential candidates for furthering investigation into induced susceptibility.

plant biology↗

bioRxiv2020

Genome-wide Identification of Disease Resistance Genes (R Genes) in Wheat

Proteins encoded by plant resistance genes (R genes) detect pathogenic effectors and initiate immune responses. Although R genes in many plant genomes are identified, they are yet to be identified in wheat. The major objectives of this project were to conduct genome-wide identification of the NB-ARC-encoding R genes in wheat (Triticum aestivum L.) and assess their genomic architecture and potential functional divergence. Wheat protein sequences were obtained from the Ensembl Genomes database, and genes were identified using interpro program. Chromosomal locations of the R genes were determined and syntenic analyses were performed. Altogether, 2151 wheat NB-ARC-encoding genes were identified, among which 1298 genes formed 547 gene clusters. Many of these gene clusters included highly similar genes likely formed by tandem duplications. Among the NB-ARC-encoding genes, 1552 ([~]72%) encode Leucine-Rich Repeats (LRRs), 802 are Coiled-Coil (CC) domain-encoding CC-NBS-LRR (CNL) genes and three are Resistance to Powdery mildew 8 (RPW8) domain-encoding RPW8-NBS-LRR (RNL) genes. Surprisingly, five of the NB-ARC-encoding genes encoded a Toll/Interleukin-1 Receptor (TIR), with no LRR, known as TN genes. CNL clades formed similar nesting patterns with a large expansion of CNL-C group like previously reported findings in wheat relatives. Comparisons of the wheat genome with barley (Hordeum vulgare L.) and Tauschs goatgrass (Aegilops tauschii Coss.), showed similar locations for homologous NB-ARC-encoding genes. These results showed that R genes in wheat have diversified through duplication to encode receptors that recognize rapidly evolving pathogenic effectors. Identified R genes in this study have implications in plant breeding, as a source of resistance for crop improvement.

genomics↗

bioRxiv2019

Diversification of Disease Resistance Receptors by Integrated Domain Fusions in Wheat and its Progenitors

Pathogenic effectors inhibit plant resistance responses by interfering with intracellular signaling mechanisms. Plant Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) have evolved highly variable effector-recognition sites to detect these effectors. While many NLRs utilize variable Leucine-Rich Repeats (LRRs) to bind to effectors, some have gained Integrated Domains (IDs) necessary for receptor activation or downstream signaling. While a few studies have identified IDs within NLRs, the homology and regulation of these genes have yet to be elucidated. We identified a diverse set of wheat NLR-ID fusion proteins as candidates for NLR functional diversification through ID effector recognition or signal transduction. NLR-ID diversity corresponds directly with the various signaling components essential to defense responses, expanding the potential functions for immune receptors and removing the need for intermediate signaling factors that are often targeted by effectors. ID homologs (>80% similarity) in other grasses indicate that these domains originated as functional, non-NLR-encoding genes and were incorporated into NLR-encoding genes through duplication. Multiple NLR-ID genes encode experimentally verified alternative transcripts that include or exclude IDs. This indicates that plants employ alternative splicing to regulate IDs, possibly using them as baits, decoys, and functional signaling components. Future studies should aim to elucidate differential expression of NLR-ID alternative transcripts.

genomics↗

bioRxiv2019

Effects of Night Temperature and Water Stress on Photosynthetic Gas Exchange of Potentilla gracilis (Rosaceae)

Plants in stressful environments have evolved strategies to cope with fluctuating environmental conditions. Potentilla gracilis, also known as Alpine Cinquefoil, grows in alpine meadows of the Rocky Mountains (USA), and is subjected to wide ranges of temperature, light intensity and water availability on a time scale of minutes to days during the growing season. Leaves often freeze to a brittle state at night, are exposed to high radiation while still frosty, dehydrate to wilting during the following light period, and then repeat the cycle the following day. The main objective of this research was to determine the effect of night temperature on subsequent photosynthetic gas exchange in P. gracilis. We used a photosynthetic gas exchange system to compare assimilation and stomatal conductance from light response curves of cold-acclimated P. gracilis following warm and chilling nights, and for plants at different water potentials. From the light response curves, dark respiration, light compensation point, maximum assimilation, light saturation point, and inhibition of photosynthesis were determined and were compared among the same plants under varying conditions. Assimilation and stomatal conductance decreased with the fall in measurement temperature, following chilling nights, and with the severity of water stress. Low night temperature and high photon flux density during the daytime, which are very common during the growing season in the field, cause a reduction in photosynthesis of the plant. The probable underlying damage during inhibition is likely repairable indicating protection rather than damage. The cold nocturnal temperature, with its less efficient biochemical repair capabilities, may partly be responsible for the reduction in assimilation of the following day. P. gracilis species exhibited persistent acquired freezing tolerance; substantial photosynthetic productivity over a wide range of light intensity and temperature; and significant tolerance of, and rapid recovery from, severe drought; making a maximum use of often challenging resources.

plant biology↗