Biology subjects

Geniza, M.

Publications and source records attributed to Geniza, M..

4 recordsLinked to original sources

bioRxiv2023

Comparative Analysis of Salinity Response Transcriptomes in Salt-Tolerant Pokkali and Susceptible IR29 Rice

Rice is a major cereal crop responsible for feeding the worlds population. To improve grain yield and quality, meet growing demand, and face the challenges posed by abiotic and biotic stress, it is imperative to explore genetic diversity in rice for candidate genes and loci that may contribute to stress tolerance. High salinity abiotic stress in the rice growth environment affects growth, yield, and quality. Therefore, we conducted a salt stress-responsive RNA-Seq-based transcriptome study of two rice (Oryza sativa) varieties, the salt-tolerant Pokkali and the salt-sensitive breeding line IR29. To identify early and late salinity response genes, we collected samples from the treated and untreated plants in this study at 1, 2, 5, 10, and 24 hours after treatment with 300 mM NaCl solution. We identified 7,209 and 6,595 salt-induced differentially expressed transcripts from Pokkali and IR29, respectively, over all time points. We identified [~]190,000 single nucleotide polymorphism (SNP) sites and [~]40,000 simple sequence repeat (SSR) sites, allowing analysis of their consequences on genetic diversity, transcript structure, gene function, and differential expression. We identified and validated the polymorphic SSRs in the differentially expressed salt-responsive genes Respiratory Burst Oxidase Homolog B (RBOHB) and Rice Salt Sensitive 1 (RSS1) that underly nearby salt tolerance QTLs. This study provides insight into transcriptional programming during salt stress, evidence for improving Oryza genome annotations, and reveals SNP and SSR sites associated with differential gene expression and potential gene function.

plant biology↗

bioRxiv2020

NASA GeneLab RNA-Seq Consensus Pipeline: Standardized Processing of Short-Read RNA-Seq Data

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility and reusability of pipeline data, to provide a template for data processing of future spaceflight-relevant datasets, and to encourage cross-analysis of data from other databases with the data available in GeneLab.

bioinformatics↗

bioRxiv2020

Chia (Salvia hispanica) gene expression atlas elucidates dynamic spatio-temporal changes associated with plant growth and development

Chia (Salvia hispanica L.), now a popular superfood, is one of the richest sources of dietary nutrients such as protein, fiber, and polyunsaturated fatty acids. At present, the genomic and genetic information available in the public domain for this crop is scanty, which hinders understanding its growth and developmental processes and impedes genetic improvement through genomics-assisted methods. We report RNA-seq based comprehensive transcriptome atlas of Chia across 13 different tissue types covering vegetative and reproductive growth stages. We generated [~]394 million raw reads from transcriptome sequencing, of which [~]355 million high-quality reads were used to generate de novo reference transcriptome assembly and the tissue-specific transcript assemblies. After quality assessment of merged assemblies and using redundancy reduction methods, 82,663 reference transcripts were identified. Of these, 53,200 transcripts show differential expression in at least one sample and provide information on spatio-temporal modulation of gene expression in Chia. We identified genes involved in the biosynthesis of omega-3 and omega-6 polyunsaturated fatty acids, and various terpenoid compounds. The study also led to the identification of 633 differentially expressed transcription factors from 53 gene families. The coexpression analysis suggested that members of the B3, bZIP, ERF, WOX, AP2, MYB, C3H, EIL, LBD, DBB, Nin-like, and HSF transcription factor gene families play key roles in the regulation of target gene expression across various developmental stages. This study also identified 2,411 simple sequence repeat (SSRs) as potential genetic markers residing in the transcribed regions. The transcriptome atlas provides essential genomic resources for basic research, applications in plant breeding, and annotation of the Chia genome.

genomics↗

bioRxiv2019

Loss of premature stop codon in the Wall-Associated Kinase 91 (OsWAK91) gene confers sheath blight disease resistance in rice

The genetic arms race between pathogen and host plant is a tug of war that has been ongoing for millennia. The \"battles\" are those of disruption, restoration of signaling and information transmission on a subcellular level. One such battle occurs between rice an important crop that feeds 50% of the world population and the sheath blight disease (SB) caused by the fungus Rhizoctonia solani. It results in 10{square}30% global yield loss annually and can reach 50% under severe outbreak. Many Receptor{square}like kinases (RLKs) are recruited as soldiers in these battles. Wall Associated Receptor Kinases (WAKs) a subfamily of receptor-like kinases have been shown to play a role in fungal defense. Here we show that rice gene OsWAK91, present in the major SB resistance QTL region on Chromosome{square}9 is a key component in defense against rice sheath blight. An SNP mutation C/T separates susceptible variety, Cocodrie (CCDR) from the resistant line MCR010277 (MCR). The resistant allele C results in the stop codon loss that results in 68 amino acids longer C{square}terminus carrying longer protein kinase domain and phosphorylation sites. Our genotype and phenotype analysis of the top 20 individuals of the double haploid SB population shows a strong correlation with the SNP. The susceptible allele appears as a recent introduction found in the japonica subspecies reference genome and a majority of the tropical and temperate japonica lines sequenced by the 3000 rice genome project. Multiple US commercial varieties with japonica background carry the susceptible allele and are known for SB susceptibility. This discovery opens the possibility of introducing resistance alleles into high yielding commercial varieties to reduce yield losses incurred by the disease.

plant biology↗