Biology subjects

Rane, R. V.

Publications and source records attributed to Rane, R. V..

6 recordsLinked to original sources

bioRxiv2023

Exhaustive benchmarking of de novo assembly methods for eukaryotic genomes

The assembly of reference-quality, chromosome-resolution genomes for both model and novel eukaryotic organisms is an increasingly achievable task for single research teams. However, the overwhelming abundance of sequencing technologies, assembly algorithms, and post-assembly processing tools currently available means that there is no clear consensus on a best-practice computational protocol for eukaryotic de novo genome assembly. Here, we provide a comprehensive benchmark of 28 state-of-the-art assembly and polishing packages, in various combinations, when assembling two eukaryotic genomes using both next-generation (Illumina HiSeq) and third-generation (Oxford Nanopore and PacBio CLR) sequencing data, at both controlled and open levels of sequencing coverage. Recommendations are made for the most effective tools for each sequencing technology and the best performing combinations of methods, evaluated against common assessment metrics such as contiguity, computational performance, gene completeness, and reference reconstruction, across both organisms and across sequencing coverage depth.

bioinformatics↗

bioRxiv2023

Pyro: A Comprehensive Pipeline for Eukaryotic Genome Assembly

1The assembly of reference-quality, chromosome-level genomes for both model and novel eukaryotic organisms is an increasingly achievable task for single research teams. However, the broad variety of sequencing technologies, assembly algorithms, and post-assembly processing tools currently available means that there is no clear consensus on a best-practice computational protocol for eukaryotic de novo genome assembly. An ever-increasing field of algorithms and packages with unique parameters, setup requirements, and environments makes it difficult for groups to pick up and test new tools, despite potential benefits. Here, we present a comprehensive Snakemake-based pipeline for eukaryotic genome assembly, Pyro, to further assist future de novo assembly and benchmarking projects. Pyro combines 20 assembly and eight polishing packages, comprising 30 different assembly approaches and up to 48 different polishing approaches in combination. These are available across Illumina short-read, Nanopore and PacBio CLR long-read technologies in one container, complete with data preparation, quality metric calculation and result reporting. We demonstrate Pyro effectiveness by running Pyro on publicly available Illumina, Nanopore and PacBio CLR read sets for Arabidopsis thaliana, producing 12 candidate assembly options with minimal initial input or configuration, each with extremely high contiguity and completeness. Pyro is highly customizable to expert needs, while also providing an accessible suggested set of tools for more casual users based on simple inputs. Pyro is available as a Singularity container suitable for execution on any Unix-compatible OS, and is freely available on GitHub (https://github.com/genomeassembler/pyro). This pipeline provides a one-stop solution for a variety of de novo eukaryotic genome assembly needs, and will also assist in the assessment of new tools as a convenient benchmark-generating platform.

bioinformatics↗

bioRxiv2022

Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum

The genome of the major agricultural weed species, annual ryegrass (Lolium rigidum) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N50=361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.

genomics↗

bioRxiv2022

Resistance bioassays and allele characterisation inform Spodoptera frugiperda (Lepidoptera: Noctuidae) management and introduction pathways in Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda is present in over 70 countries in Africa, Asia, and Oceania. Its rapid dispersal since 2016 when it was first reported in western Africa, and associated devastation to agricultural productivity, highlight the challenges posed by this pest. Currently, its management largely relies on insecticide sprays and transgenic Bacillus thuringiensis toxins, therefore understanding their responses to these agents and characteristics of any resistance genes enables adaptive strategies. In Australia, S. frugiperda was reported at the end of January 2020 in northern Queensland and by March 2020, also in northern Western Australia. As an urgent first response we undertook bioassays on two Australian populations, one each from these initial points of establishment. To assist with preliminary sensitivity assessment, two endemic noctuid pest species, Helicoverpa armigera and Spodoptera litura, were concurrently screened to obtain larval LC50 estimates against various insecticides. We characterised known resistance alleles from the VGSC, ACE-1, RyR, and ABCC2 genes to compare with published allele frequencies and bioassay responses from native and invasive S. frugiperda populations. An approximately 10x LC50 difference for indoxacarb was detected between Australian populations, which was approximately 28x higher than that reported from an Indian population. Characterisation of ACE-1 and VGSC alleles provided further evidence of multiple introductions in Asia, and multiple pathways involving genetically distinct individuals into Australia. The preliminary bioassay results and resistance allele patterns from invasive S. frugiperda populations suggest multiple introductions have contributed to the pests spread and challenge the axiom of its rapid west-to-east spread.

evolutionary biology↗

bioRxiv2019

Genomic analyses of sibling honey bee ectoparasitic mite species show divergent strategies of adaptation

Multispecies host-parasite evolution is common, but how parasites evolve after speciating remains poorly understood. Shared evolutionary history and physiology may propel species along similar evolutionary trajectories whereas pursuing different strategies can reduce competition. We test these scenarios in the economically important association between honey bees and ectoparasitic mites by sequencing the genomes of the sister mite species Varroa destructor and Varroa jacobsoni. These genomes were closely related, with 99.7% sequence identity. Among the 9,628 orthologous genes, 4.8% showed signs of positive selection in at least one species. Divergent selective trajectories were discovered in conserved chemosensory gene families (IGR, SNMP), and Halloween genes (CYP) involved in moulting and reproduction. However, there was little overlap in these gene sets and associated GO terms, indicating different selective regimes operating on each of the parasites. Based on our findings, we suggest that species-specific strategies may be needed to combat evolving parasite communities.

genomics↗

bioRxiv2019

The spread of resistance to imidacloprid is restricted by thermotolerance in natural populations of Drosophila melanogaster

Imidacloprid, the worlds most utilised insecticide1, has raised considerable controversy due to its harmful effects on non-pest species2-6 and there is increasing evidence showing that insecticides have become the primary selective force in many insect species7-14. The genetic response to insecticides is heterogeneous across population and environment15-17, leading to more complex patterns of genetic variation than previously thought. This motivated the investigation of imidacloprid resistance at different temperatures in natural populations of Drosophila melanogaster originating from four climate extremes replicated across two continents. Population and quantitative genomic analysis, supported by functional tests, demonstrated a polygenic basis to resistance and a major trade-off with thermotolerance. Reduced genetic differentiation at resistance-associated loci indicate enhanced gene flow at these loci. Resistance alleles showed stronger evidence of positive selection in temperate populations compared to tropical populations. Polygenic architecture and ecological factors should be considered when developing sustainable management strategies for both pest and beneficial insects.

evolutionary biology↗