Genome-Wide Identification and Evolutionary Analysis of Gossypium Tubby-Like Protein (TLP) Gene Family and Expression Analyses During Salt and Drought Stress

Abstract

Tubby-like proteins (TLPs) possess a highly conserved closed β barrel tubby domain at C-terminal and N-terminal F-box. The role of TLP gene family members has been widely discussed in numerous organisms; however, the detailed genome-wide study of this gene family in Gossypium species has not been reported till date. Here, we systematically identified 105 TLP gene family members in cotton (Gossypium arboreum, Gossypium raimondii, Gossypium hirsutum, and Gossypium barbadense) genomes and classified them into eight phylogenetic groups. Cotton TLP12 gene family members clustered into two groups, 4 and 8. They experienced higher evolutionary pressure in comparison to others, indicating the faster evolution in both diploid as well as in tetraploid cotton. Cotton TLP gene family members expanded mainly due to segmental duplication, while only one pair of tandem duplication was found in cotton TLPs paralogous gene pairs. Subsequent qRT-PCR validation of seven putative key candidate genes of GhTLPs indicated that GhTLP11A and GhTLP12A.1 genes were highly sensitive to salt and drought stress. The co-expression network, pathways, and cis-regulatory elements of GhTLP11A and GhTLP12A.1 genes confirmed their functional importance in salt and drought stress responses. This study proposes the significance of GhTLP11A and GhTLP12A.1 genes in exerting control over salt and drought stress responses in G. hirsutum and also provides a reference for future research, elaborating the biological roles of G. hirsutum TLPs in both stress responses.

Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.)

“…Triplicate leaf samples were collected for each time point and treatment and frozen in liquid nitrogen. The samples were stored in an ultra-low temperature freezer at −80 °C ( Bano et al, 2021 ; Han, Wu & Li, 2021 ).…”

Genome-wide identification and expression analysis of the HD2 protein family and its response to drought and salt stress in Gossypium species

“…In transgenic Arabidopsis , over-expression of GRAS improves salt stress tolerance and plant growth ( Zhang et al., 2020 ). The expression of lateral organ boundaries (LOB) has been found to be upregulated in Vitis vinifera under salt stress via treatment with ABA ( Grimplet et al., 2017 ), while tubby-like protein transcription factor (TLP TF) has been reported to play an important role in increasing tolerance to salt stress ( Bano et al., 2021 ) ( Supplementary Figure 1D ). PageMan pathways analysis of the NCoEGs of GhHDT3D.2 revealed the presence of phenylpropanoid, resulting in elevated salt stress tolerance ( Sharma et al., 2019 ).…”

Genome-wide analyses of the Tubby-like proteins in Brassica napus revealed their potential roles in the abiotic stress response

“…BRAD was used to obtained the protein sequences of B. rapa and B. oleracea. According to previous reports, the full-length protein sequences of rice (Liu, 2008), cotton (Bano et al, 2021), maize (Chen et al, 2016), wheat (Hong et al, 2015), and soybean (Xu et al, 2022) were obtained from NCBI (http://www.ncbi.nlm.nih.gov/). The ClustalW default parameter setting was used to align the above protein sequences.…”

“…Plants activate various defence mechanisms in vivo to alter their metabolism, tissue, and plant morphology to adapt to and cope with a variety of harmful environments (Ding et al, 2020;Kleyn et al, 1996;Luo et al, 2017;van et al, 2020). The tubbylike protein (TLP) gene family, a transcription factor family in plants, can participate in the plant response to various abiotic stresses (Bano et al, 2021;Bao et al, 2014;. The study of the TLP gene family is critical for understanding plant molecular mechanisms in response to various abiotic stresses (Jing et al, 2021;Zhu et al, 2020).…”