Browsing by Author "Suresh, Gokul Babu"

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Genome-wide identification, characterization, and expression analysis of Clavata3 Insensitive receptor Kinases (CIKs) on developmental tissues and under temperature stress conditions in Brassica oleracea
(Springer Nature Publishing AG, 2025) Suresh, Gokul Babu; Baskar, Harssitha; Subramaniam, Geethanjali; Soundararajan, Prabhakaran
Unprecedented climate changes are one of the major global threats to agriculture. Though cauliflower is grown worldwide in different conditions, it is sensitive to temperature fluctuation. Clavata3 Insensitive receptor Kinase (CIK) is one of the important co-receptors involved in WUS-CLV pathway for shoot apical meristem (SAM) maintenance, floral development and environment buffering. In this study we did genome-wide identification and characterization of CIKs in Brassica oleracea var. botrytis cv. Korso. Expression analysis was conducted on developmental tissues and short-term heat and cold stress conditions. Seven fulllength BolCIKs have been identified in the Korso genome through comparison against Arabidopsis thaliana CIKs. Gene structure and motifs are distinct between each sub-class. Ka/Ks ratios showed that all CIKs underwent purifying selection. Abundance of stress-responsive cis-elements, such as MYB and MYC recognition sites, showed the involvement of BolCIK in environmental stress regulation. Among the nine developmental tissues such as leaf, stem, root, curd, sepal, petal, stamen, pistil, and silique, except BolCIK4 and BolCIK5a, CIKs were merely detected in leaves. Contrastingly, expression of all BolCIKs was detected in stem, curd, and reproductive organs. Importantly, most of the BolCIKs were highly expressed in sepal, petal, pistil, and siliques. In SAM specific manner, BolCIK3 and BolCIK6 are upregulated in heat stress and cold stress, respectively. Other BolCIKs expressions are varying between tissues-types and stress conditions. Since CIKs can possibly be involved in thermomorphogenesis, results of this work may lead to further exploration of its function to improve climate resilience in cauliflower.
Pangenome-wide identification, evolutionary analysis, and characterization of WOX gene family among Brassica Triangle of U's genomes
(Elsevier B.V., 2025) Soundararajan, Prabhakaran; Vivek, AT; Suresh, Gokul Babu; Shukla, Bhavya; Singh, Kanchan B.M.; Kumar, Shailesh; Manivannan, Abinaya
WUSCHEL-related homeobox (WOX) is an evolutionarily important gene family involved in key developmental processes such as embryo patterning, stem cell regulation, apical meristem maintenance, etc. Brassica contains several widely diversified and economically important vegetables grown worldwide. In this study, a pangenome-wide identification and characterization of the WOX gene family among all the species of Brassica Triangle of U's have been performed. WOX gene family was identified from the genomes of 31 Brassica species/morphotypes. About 26–28, 28, and 26–31 copies of WOX genes are present in diploid progenitors such as B. rapa (AA), B. nigra(BB), and B. oleracea (CC), respectively. In allotetraploid species, the number of WOX genes exceeds more than 50 copies. However, their number varies between morphotypes at the pangenome level. Motif and gene structure analysis showed distinct and conserved patterns between homoeologous genes. Non-synonymous (Ka)/Synonymous (Ks) ratio indicated that more number of modern/WUS clade orthologs underwent positive selection followed by those of the intermediate clade. Interacting networks between the WOX and miRNA showed that the CC genome has more complex network pattern compared to the AA genome. Although the WOX-miRNA interactions observed in both AABB and AACC genomes were distinct, they exhibited similarity in overlapping connections. Transcriptome data, analyzed from unfertilized ovule to seven developmental stages of embryos and their seed coat, sourced from public databases across six genomes, illustrated that WOX genes are expressed in a spatio-temporal manner throughout these developmental stages. Furthermore, qPCR analysis of WOX genes at two stages, such as 2–3 days old (leaf and root primordia) and 3 weeks old seedlings (leaf and root) in B. juncea and B. oleracea provides details of stage- and tissues-specific expression patterns between AB and C genomes. Overall, the present study sheds light on evolution and characterization of the WOX gene family in Brassica at the pangenome level for further functional validation.