Biology subjects

Parajuli, S.

Publications and source records attributed to Parajuli, S..

4 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↗

bioRxiv2023

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

BackgroundBlackberries (Rubus subgenus Rubus) are a major berry crop consumed globally for being a rich source of anthocyanins and antioxidants, and their unique flavor. However, breeding for fruit improvement in blackberry has been significantly hindered by the scarcity of genomic resources and the genetic complexity of traits. The blackberry genome has been particularly challenging to assemble, largely due to its polyploid nature. FindingsWe present the first chromosome-scale and haplotype-phased genome assembly for the cultivated primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The tetraploid genome assembly was generated using the Oxford Nanopore Technology (ONT) and Hi-C scaffolding, comprising 919 Mb placed on 27 pseudochromosomes with an N50 of 35.73 Mb. The assembly covers >92% of the genome length and contains over 98% of complete BUSCOs. Repetitive sequences constitute 57% of the assembly, with the long terminal repeats (LTR) being the most abundant class. A total of 87,968 protein-coding genes were predicted, of which, 82% were functionally annotated. Gene expression analyses identified candidate genes and transcription factors related to thornlessness in blackberries, including MYB16, lysine histidine transporters, PDR1, Caffeoyl-CoA, glycosylphosphatidylinositol-anchored lipid protein transfer 1, DRN, beta-ketoacyl reductase, and homocysteine S-methyltransferase 3. ConclusionsThe utility of this genome has been demonstrated in this study by identifying candidate genes related to thornlessness in blackberry. Resequencing of tetraploid blackberry cultivars/selections with different horticultural characteristics revealed genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome will serve as a valuable resource to accelerate genetic analysis and breeding of this important berry crop, enabling the development of improved varieties with enhanced traits.

plant biology↗

bioRxiv2022

mRNAid, an Open-Source Platform for Therapeutic mRNA Design and Optimization Strategies

Recent COVID-19 vaccines unleashed the potential of mRNA-based therapeutics. mRNA optimization is indispensable for reducing immunogenicity, ensuring stability, and maximizing protein output. We present mRNAid, an experimentally validated software for mRNA optimization and visualization that generates mRNA sequences with comparable if not superior characteristics to commercially optimized sequences. To encompass all aspects of mRNA design, we also interrogated the impact of uridine content, nucleoside analogs and UTRs on expression and immunogenicity.

bioinformatics↗

bioRxiv2022

Editing the CsDMR6 Gene in Citrus Results in Resistance to the Bacterial Disease Citrus Canker

Citrus is one of the most important fruit crops in the world. Citrus production worldwide faces challenges from devastating bacterial diseases, including citrus canker caused by Xanthomonas citri ssp. citri (Xcc). Improving citrus resistance to citrus canker and other major bacterial diseases has been a top priority in citrus biotechnology. Disabling disease susceptibility genes has emerged as a novel, promising approach to engineering disease resistance. The bottleneck for applying such an approach has been the identification of proper disease susceptibility-related genes in citrus. Here we show the first successful case of editing the CsDMR6 gene in citrus and obtaining strong resistance to citrus canker in six mutants in two citrus cultivars, Duncan grapefruit and Carrizo citrange. Multiple types of deletions and insertions were induced in CsDMR6, resulting in frameshift of its coding region and presumably loss of gene function. The mutation frequency in most of the mutants reached 71.8% to 98.9%. The mutants showed 71.2% to 99.8% reduction in citrus canker lesion and greater than 99.7% or 2.45 to 4.95 Log10 unit reduction in Xcc bacterial cell population. Mutants also accumulated more salicylic acid and expressed much higher levels of the NPR1 gene than the wildtype with or without Xcc inoculation, which suggests potential resistance to other diseases in these mutants. The guide RNAs for targeting CsDMR6 were selected from highly conserved regions and have 100% nucleotide identity with DMR6 homologs in important citrus species; these guide RNAs are expected to work in other important citrus species and cultivars.

plant biology↗