Biology subjects

Yadav, I.

Publications and source records attributed to Yadav, I..

3 recordsLinked to original sources

bioRxiv2024

Multiscale topological analysis of kinetoplast DNA via high-resolution AFM

Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in-vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, selective digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena.

biophysics↗

bioRxiv2024

Guava cv. Allahabad Safeda Chromosome scale assembly and comparative genomics decodes breeder choice marker trait association for pink pulp colour

Deciphering chromosomal length genome assemblies has the potential to unravel an organisms evolutionary relationships and genetic mapping of traits of commercial importance. We assembled guava genome using a hybrid sequencing approach with [~]450x depth Illumina short reads, [~]35x PacBio long reads and Bionano maps to [~]594 MB Scaffold length on 11 pseudo chromosomes ([~]479 MB contig length). Maker pipeline predicted 17,395 genes, 23% greater from earlier draft produced in same cultivar Allahabad Safeda. The genome assembly clarified guava evolutionary history, for example revealing predominance of gene expansion by dispersed duplications, in particular contributing to abundance of monoterpene synthases; and supporting evidence of a whole genome duplication event in guava as in other Myrtaceae. Guava breeders have been aiming to reduce screening time for selecting pink pulp colour progenies using marker-trait associations, but a previous comparative transcriptomics and comparative genomics approach with draft genome assembly to identify the effector gene associated with pink pulp was unsuccessful. Here, genome re-sequencing with Illumina short reads at [~]25x depth of 20 pink fleshed and/or non-coloured guava cultivars and comprehensive analysis for genes in the carotenoid biosynthesis pathway identified structural variations in Phytoene Synthase 2. Further, ddRAD based association mapping in core-collection of 82 coloured and non-coloured genotypes from Indian sub-continent found strong association with the same causal gene. Subsequently, we developed PCR based Indel/SSR breeder friendly marker that can readily be scored in routine agarose gels and empowers accurate selection for seedlings that will produce fruits with pink pulp.

plant biology↗

bioRxiv2018

Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire

Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability of the hexaploid wheat cultivar Chinese Spring reference genome now allows a detailed study of its NLR complement. However, low NLR expression as well as high intra-family sequence homology hinders their accurate gene annotation. Here we developed NLR-Annotator for in silico NLR identification independent of transcript support. Although developed for wheat, we demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. Applying our tool to wheat and combining it with a transcript-validated subset of genes from the reference gene annotation, we characterized the structure, phylogeny and expression profile of the NLR gene family. We detected 3,400 full-length NLR loci of which 1,540 were confirmed as complete genes. NLRs with integrated domains mostly group in specific sub-clades. Members of another subclade predominantly locate in close physical proximity to NLRs carrying integrated domains suggesting a paired helper-function. Most NLRs (88%) display low basal expression (in the lower 10 percentile of transcripts), which may be tissue-specific and/or induced by biotic stress. As a case study for applying our tool to the positional cloning of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust resistance genes. Our study will support the identification of functional resistance genes in wheat to accelerate the breeding and engineering of disease resistant varieties.

plant biology↗