Biology subjects

Heidari, P.

Publications and source records attributed to Heidari, P..

5 recordsLinked to original sources

bioRxiv2021

Phosphate transporter genes: genome-wide identification and characterization in Camelina sativa

Phosphorus is known as a key element associated with growth, energy, and cell signaling. In plants, phosphate transporters (PHTs) are responsible for moving and distributing phosphorus in cells and organs. PHT genes have been genome-wide identified and characterized in various plant species, however, these genes have not been widely identified based on available genomic data in Camellia sativa, which is an important oil seed plant. In the present study, we found 66 PHT genes involved in phosphate transporter/translocate in C. sativa. The recognized genes belonged to PHTs1, PHTs2, PHTs4, PHOs1, PHO1 homologs, glycerol-3-PHTs, sodium dependent PHTs, inorganic PHTs, xylulose 5-PHTs, glucose-6-phosphate translocators, and phosphoenolpyruvate translocators. Our finding revealed that PHT proteins are divers based on their physicochemical properties such as Isoelectric point (pI), molecular weight, GRAVY value, and exon-intron number(s). Besides, the expression profile of PHT genes in C. sativa based on RNA-seq data indicate that PHTs are involved in response to abiotic stresses such as cold, drought, salt, and cadmium. The tissue specific expression high expression of PHO1 genes in root tissues of C. sativa. In additions, four PHTs, including a PHT4;5 gene, a sodium dependent PHT gene, and two PHO1 homolog 3 genes were found with an upregulation in response to aforementioned studied stresses. In the current study, we found that PHO1 proteins and their homologs have high potential to post-translation modifications such as N-glycosylation and phosphorylation. Besides, different cis-acting elements associated with response to stress and phytohormone were found in the promoter region of PHT genes. Overall, our results show that PHT genes play various functions in C. Sativa and regulate Camellia responses to external and intracellular stimuli. The results can be used in future studies related to the functional genomics of C. sativa.

plant biology↗

bioRxiv2021

Pseudogenization of trnT-GGU in chloroplast genomes of the plant family Asteraceae

The chloroplast genome evolves through the course of evolution. Various types of mutational events are found within the chloroplast genome, including insertions-deletions (InDels), substitutions, inversions, gene rearrangement, and pseudogenization of genes. The pseudogenization of the trnT-GGU gene was previously reported in the Cryptomeria japonica (Cupressaceae), Pelargonium x hortorum (Geraniaceae), and in the two species of the tribe Gnaphalieae (Asteroideae, Asteraceae). Here, we performed a broad analysis of the trnT-GGU gene among the species of twelve subfamilies of Asteraceae and found pseudogenization of this gene is not limited to the two species of Gnaphalieae or the tribe Gnaphalieae. We report for the first time that this gene is pseudo in the species of three subfamilies of Asteraceae, including Gymnarrhenoideae, Cichorioideae and Asteroideae. The analyses of the species of 78 genera of Asteroideae revealed that this pseudogenization event is linked to the insertion within the 5' acceptor stem and not linked to the habit, habitat, and geographical distribution of the plant.

evolutionary biology↗

bioRxiv2021

The GASA Gene Family in Theobroma cacao: Genome Wide Identification and Expression Analyses

The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20-25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

plant biology↗

bioRxiv2020

Gexplora - user interface that highlights and explores the density of genomic elements along a chromosomal sequence

The density of genomic elements such as genes or transposable elements along its consecutive sequence can provide an overview of a genomic sequence while in the detailed analysis of candidate genes it may depict enriched chromosomal hotspots harbouring genes that explain a certain trait. The herein presented python-based graphical user interface Gexplora allows to obtain more information about a genome by considering sequence-intrinsic information from external databases such as Ensembl, OMA and STRING database using REST API calls to retrieve sequence-intrinsic information, protein-protein datasets and orthologous groups. Gexplora is available under https://github.com/nthomasCUBE/Gexplora.

genomics↗

bioRxiv2019

TraitCorr - correlating gene expression measurements with phenotypic data

Today, transcriptomes and microarrays can be generated and analysed in high quantity. In addition, experiments often include descriptive information about each sample which needs to be compared to the gene expression profiles. The understanding of the relationships between gene expression and phenotype is introduced as new challenge in system biology. Combining expression (RNA-seq and microarray) and phenotype data could reveal the role or effects of each gene on traits. To address all these needs, the user-interface TraitCorr was developed which allows to determine genes that are significantly correlating with a selected trait. Furthermore, it allows to determine significantly correlated genes among different traits and provides visualisation and analysis possibilities.

bioinformatics↗