Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads

Farooq, Muhammad; Naqvi, Rubab Zahra; Amin, Imran; Rehman, Atiq Ur; Asif, Muhammad; Mansoor, Shahid

doi:10.1016/j.gene.2022.147065

Cited by 2 publications

(2 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The latest bioinformatics tools also provide help in the identification of hub genes through weighted co-expression analysis and genome-wide analysis of gene families ( Zaidi et al., 2020 ; Ehsan et al., 2023 ). Alternative splicing studies through transcriptomics allow the investigation of genetic diversity in different crops ( Glushkevich et al., 2022 ; Farooq et al., 2023 ). The innovations in NGS technology have empowered gene expression profiling and annotation of transcriptomes in major food and feed crops, including wheat, rice, maize, potato, tomato, cotton, and cassava, under different conditions and stimuli.…”

Section: Transcriptomics As a Tool To Discover Vital Genesmentioning

confidence: 99%

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

Naqvi,

Mahmood,

Mansoor

et al. 2024

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.

show abstract

Section: Transcriptomics As a Tool To Discover Vital Genesmentioning

confidence: 99%

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

Naqvi,

Mahmood,

Mansoor

et al. 2024

Front. Plant Sci.

Self Cite

View full text Add to dashboard Cite

show abstract

“…In Arabidopsis [ 13 ] and rice [ 14 ], more than 60% and 48% of mature mRNAs are generated by RNA splicing, respectively [ 15 ], and more new splice sites appear under stress conditions [ 16 , 17 ]. Alternative splicing is significantly altered during abiotic and biotic stress, which is a novel regulation mechanism to rapidly reprogram gene expression [ 18 – 21 ].…”

Section: Introductionmentioning

confidence: 99%

AtSNU13 modulates pre-mRNA splicing of RBOHD and ALD1 to regulate plant immunity

Jiang,

Yue,

et al. 2024

BMC Biol

View full text Add to dashboard Cite

Pre-mRNA splicing is a significant step for post-transcriptional modifications and functions in a wide range of physiological processes in plants. Human NHP2L binds to U4 snRNA during spliceosome assembly; it is involved in RNA splicing and mediates the development of human tumors. However, no ortholog has yet been identified in plants. Therefore, we report At4g12600 encoding the ortholog NHP2L protein, and AtSNU13 associates with the component of the spliceosome complex; the atsnu13 mutant showed compromised resistance in disease resistance, indicating that AtSNU13 is a positive regulator of plant immunity. Compared to wild-type plants, the atsnu13 mutation resulted in altered splicing patterns for defense-related genes and decreased expression of defense-related genes, such as RBOHD and ALD1. Further investigation shows that AtSNU13 promotes the interaction between U4/U6.U5 tri-snRNP-specific 27 K and the motif in target mRNAs to regulate the RNA splicing. Our study highlights the role of AtSNU13 in regulating plant immunity by affecting the pre-mRNA splicing of defense-related genes.

show abstract

Transcriptome diversity assessment of Gossypium arboreum (FDH228) leaves under control, drought and whitefly infestation using PacBio long reads

Cited by 2 publications

References 41 publications

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

Omics-driven exploration and mining of key functional genes for the improvement of food and fiber crops

AtSNU13 modulates pre-mRNA splicing of RBOHD and ALD1 to regulate plant immunity

Contact Info

Product

Resources

About