Biology subjects

Polydore, S.

Publications and source records attributed to Polydore, S..

5 recordsLinked to original sources

bioRxiv2022

Natural Variation in Brachypodium distachyon Responses to Combined Abiotic Stresses

The growing world population increases demand for agricultural production, which is more challenging as climate change increases global temperature and causes more extreme weather events. High-throughput phenotyping tools can be used to measure plant responses to the environment to identify genomic regions associated with response to stress. This study examines the phenotypic variation of 149 accessions of Brachypodium distachyon under drought, heat, and the combination of both stresses. Heat alone causes the largest amounts of tissue damage and the combination of heat and drought causes the largest decrease in plant biomass compared to other treatments. Notably, Bd21-0, the reference line for B. distachyon, was identified as not having very robust growth under stress conditions, especially in the heat-drought combined treatment. Climate data from the collection locations of these accessions (climate of origin) was used to assess whether climate of origin was correlated with responses to stresses and it was found to be significantly associated with height and percent of plant tissue damage. Additionally, genome wide association mapping found a number of genetic loci associated with changes in plant height, biomass, and the amount of damaged tissue under stress. Some SNPs found to be significantly associated with a response to heat or drought are also significantly associated in the combination of stresses, while others are not, and some significantly associated SNPs were only identified in the combined stress treatment. This, combined with the phenotypic data, indicates that the effects of these abiotic stresses are not simply additive, and the responses of B. distachyon to the combined stresses differ from drought and heat alone. Significant SNPs were closely located to genes known to be involved in plant responses to abiotic stresses.

plant biology↗

bioRxiv2021

Large structural variations in the haplotype-resolved African cassava genome.

Cassava (Manihot esculenta Crantz, 2n=36) is a global food security crop. Cassava has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultra-long-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed more than 5,000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele specific expression was further explored. RNA-seq data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava. Significance statementThe cassava varieties grown by subsistence farmers in Africa largely differ from the inbred reference genome due to their highly heterozygous nature. We used multiple sequencing technologies to assemble and resolve both haplotypes in TME7, a farmer-preferred cassava line, enabling us to study the considerable haplotypic structural variation in this line.

genomics↗

bioRxiv2019

Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants

Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but comprise only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large dataset of published and newly generated sRNA sequencing data (1,333 sRNA-seq libraries containing over 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding over 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24 nucleotide and 21 nucleotide siRNAs, respectively. 24 nucleotide-dominated siRNA loci usually occurred in intergenic regions, especially at the 5-flanking regions of protein-coding genes. In contrast, 21 nucleotide-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21 nucleotide-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, while mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible at http://plantsmallrnagenes.science.psu.edu.

plant biology↗

bioRxiv2018

Several phased siRNA annotation methods can produce frequent false-positives for 24 nucleotide RNA-dominated loci in plants

Small RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further sub-divided into transposon/repetitive region-localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA-mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt-dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt-dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt-dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently mis-identified as 24 nt-dominated PHAS loci using multiple PHAS-detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS-detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt-dominated loci.

plant biology↗

bioRxiv2017

Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci

Plant small RNAs regulate key physiological mechanisms through post-transcriptional and transcriptional silencing of gene expression. sRNAs fall into two major categories: those that are reliant on RNA Dependent RNA Polymerases (RDRs) for biogenesis and those that arent. Known RDR-dependent sRNAs include phased and repeat-associated short interfering RNAs, while known RDR-independent sRNAs are primarily microRNAs and other hairpin-derived sRNAs. In this study, we produced and analyzed small RNA-seq libraries from rdr1/rdr2/rdr6 triple mutant plants. Only a small fraction of all sRNA loci were RDR1/RDR2/RDR6-independent; most of these were microRNA loci or associated with predicted hairpin precursors. We found 58 previously annotated microRNA loci that were reliant on RDR1, -2, or -6 function, casting doubt on their classification. We also found 38 RDR1/2/6-independent small RNA loci that are not MIRNAs or otherwise hairpin-derived, and did not fit into other known paradigms for small RNA biogenesis. These 38 small RNA-producing loci have novel biogenesis mechanisms, and are frequently located in the vicinity of protein-coding genes. Altogether, our analysis suggest that these 38 loci represent one or more new types of small RNAs in Arabidopsis thaliana.\n\nSignificance StatementSmall RNAs regulate gene expression in plants and are produced through a variety of previously-described mechanisms. Here, we examine a set of previously undiscovered small RNA-producing loci that are produced by novel mechanisms.

plant biology↗