RAD gene family analysis in cotton provides some key genes for flowering and stress tolerance in upland cotton G. hirsutum

Abstract

Background RADIALIS (RAD), belongs to the MYB gene family and regulates a variety of functions including floral dorsoventral asymmetry in Antirrhinum majus and development of fruit proteins in Solanum lycopersicum. RAD genes contain an SNF2_N superfamily domain. Here, we comprehensively identified 68 RAD genes from six different species including Arabidopsis and five species of cotton. Results Phylogenetic analysis classified RAD genes into five groups. Gene structure, protein motifs and conserved amino acid residues indicated that GhRAD genes were highly conserved during the evolutionary process. Chromosomal location information showed that GhRAD genes were distributed unevenly on different chromosomes. Collinearity and selection pressure analysis indicated RAD gene family expansion in G. hirsutum and G. barbadense with purifying selection pressure. Further, various growth and stress related promotor cis-acting elements were observed. Tissue specific expression level indicated that most GhRAD genes were highly expressed in roots and flowers (GhRAD2, GhRAD3, GhRAD4 and GhRAD11). Next, GhRAD genes were regulated by phytohormonal stresses (JA, BL and IAA). Moreover, Ghi-miRN1496, Ghi-miR1440, Ghi-miR2111b, Ghi-miR2950a, Ghi-miR390a, Ghi-miR390b and Ghi-miR7495 were the miRNAs targeting most of GhRAD genes. Conclusions Our study revealed that RAD genes are evolutionary conserved and might be involved in different developmental processes and hormonal stress response. Data presented in our study could be used as the basis for future studies of RAD genes in cotton.

Comparative transcriptome analysis, unfolding the pathways regulating the seed-size trait in cultivated lentil (Lens culinaris Medik.)

“…The miR3457 is known to regulate the WSC domain–containing protein having a function in cell wall formation ( Tarver et al, 2015 ), whereas miR7743 was found associated with dormancy release ( Zhang et al, 2018 ). miR1440 was identified which functions by targeting the RAD (RADIALIS) gene of the MYB gene family and thereby regulates cell proliferation and cell cycles ( Kabir et al, 2022 ). In addition, many developmental pathways are found regulated by miR902 and miR7511 ( Berruezo et al, 2017 ; Zhang et al, 2019 ) and miR5543, having a role in cell transport ( Achakzai et al, 2018 ).…”

Analysis of Methylesterase Gene Family in Fragaria vesca Unveils Novel Insights into the Role of FvMES2 in Methyl Salicylate-Mediated Resistance against Strawberry Gray Mold

“…In response to environmental stresses, stress-responsive CAEs enhance plant resistance through the activation of various stressrelated genes. 44 In the promoter region of FvMES genes, several CAEs, including STRE, ARE, MYB (MYB, MYB-like, and MBS), and WRKY (W-box), have been identified. Previous literatures had shown that these CAEs are responsive to abiotic stresses, including drought, gibberellic acid (GA), and abscisic acid (ABA) in various plant species.…”

Recent genome resequencing paraded COBRA-Like gene family roles in abiotic stress and wood formation in Poplar

“…Pseudogenes emerge from neutral selection when the Ka/Ks ratio is 1, purifying selection favors duplicated genes with a Ka/Ks ratio below 1, and positive selection of rapid evolution is shown with a Ka/Ks ratio above 1. All the COBLs have Ka/Ks ratios below 1, suggesting that the COBL gene family was subject to purifying selection over the course of evolution ( Niu et al., 2015 ; Bano et al., 2021 ; Kabir et al., 2022 ). The Ka/Ks ratios for PtrCOBL12-PtrCOBL3 and PtrCOBL8-PtrCOBL10 were the lowest among the paralogous genes, indicating these genes were able to keep their original roles despite their shorter divergence dates.…”

“…Gene expression control occurs primarily via transcriptional regulation, which requires interaction between transcription factors and promoter binding sites ( Wang et al., 2022 ). Specific and consistent cis-acting elements in promoter regions are required for different external signals to activate inducible promoters; for example, auxin-induced promoters typically contain cis-acting elements of the AuxRE, and light-induced promoters typically contain cis-acting elements rich in the AT-rich motif, the I-box, the G-box, and the GT1-motif ( Kabir et al., 2022 ; Wang et al., 2022 ). Similarly, drought-induced promoters included the cis-acting elements CACG and CATGTG.…”