Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Abstract

Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.

Genome-wide analysis of NPR1-like genes in citrus species and expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri)

“…The MEME Suite, accessible at https://meme-suite.org/meme/tools/meme , was utilized to identify protein motifs encoded by these genes. Additionally, an online tool was employed to pinpoint the locations of these motifs within the peptide sequences ( Haider et al., 2023b ).…”

“…The Ka/Ks ratio was assessed to elucidate the molecular evolutionary rates of each gene pair. Generally, a Ka/Ks value <1 suggests purifying selection in evolution, Ka/Ks equals to 1 indicates neutral selection, while Ka/Ks >1 signifies positive selection ( Haider et al., 2023b ). Furthermore, the calculation of the divergence time for these gene pairs was conducted using the formula t = Ks/2r, with r (1.5 × 10 −8 ) serving as the representative value for neutral substitution rates ( Campos et al., 2023 ).…”

“…PlantCARE database ( http://bioinformatics.pAb.ugent.be/webtools/plantcare/htmL/ ) ( Haider et al., 2023b ) was used to identify Cis-regulatory elements. The promoter sequences of NPR1 -like genes were extracted from genome sequences of 10 citrus species by TBtools software.…”

“…Phylogenic classification, characterization on molecular basis conserved motifs, residues of amino acids, distribution on chromosomes, and composition of protein domains were investigated. Furthermore, the stress-related expression pattern of citrus-resistant genes in different regions was also analyzed using citrus species sequencing of RNA (RNA-seq) datasets ( Haider et al., 2023b ). The findings underscore the need for substantial support to facilitate applied research and in-depth exploration of resistant genes in citrus species and related plant families.…”

Genome wide analysis of carotenoid cleavage oxygenases (CCO) gene family in Arachis hypogaea (peanut) under biotic stress

“…In tomato, this led to greater water usage efficiency due to an increase in root hydraulic conductivity and a decrease in stomatal conductance (g s ) [ 21 ]. In rice, the NCED genes OsNCED6 and OsNCED10 defend against salt stress, whereas OsCCD7 and OcCCD8 are involved in grain and inflorescence development [ 22 ].The genes HaNCED16 and HaNCED19 were expressed in response to drought stress revealed in recent studies [ 23 ].…”