Genome-wide identification of the auxin/indole-3-acetic acid (Aux/IAA) gene family in pepper, its characterisation, and comprehensive expression profiling under environmental and phytohormones stress

Abstract

Auxin is an essential phytohormone that plays a crucial role in the growth and development of plants in stressful environments. Here, we analysed the auxin/indole-3-acetic acid (Aux/IAA) gene family, which produces auxin in pepper, and succeeded in identifying 27 putative members containing four conserved domains (I. II. III and IV) in their protein sequences. Sequence analysis, chromosomal mapping and motif prediction of all identified CaAux/IAA genes were performed. It was observed that these genes contained four conserved motifs divided into nine different groups and distributed across nine chromosomes in pepper plants. RNA-seq analysis revealed the organ specific expression of many CaAux/IAA genes. However, the majority of genes were expressed with high expression levels in the early stages of fruit development. However, the maximum expression level of the CA03g34540 gene was observed in the breaker stage. Moreover, thirteen CaAux/IAA genes were labelled as early responsive genes to various phytohormone and abiotic stresses. Furthermore, RNA-seq analysis in response to pathogen inoculation (PepMoV, TMV strains P0/P1, and Phytophthora capsici) showed distinct expression profiles of all identified genes, suggesting the diverse expression nature of genes under these stress conditions. Overall, this study provides insight into the dynamic response of CaAux/IAA genes under environmental and phytohormones stress conditions, providing bases to further explore the importance of these genes through mutant/transgenic analysis in pepper.

The DUF221 domain-containing (DDP) genes identification and expression analysis in tomato under abiotic and phytohormone stress

“… 1 The availability of the plant genome enables us to identify and characterize various gene families under abiotic and biotic stresses. For instance, several gene families have been identified and characterized, such as NAC, 2 , 3 bHLH, 4 MAPK, 5 bZIP, 6–8 GRAS, 9 Aux/IAA, 10 TIFY, 11 FKBP, 12 PEPC, 13 and HSF transcription factors. 14 In addition, plants’ genomes contained plenty of stress-responsive proteins with highly conserved domain 15 , 16 and play critical roles in various plant biological processes during stress conditions.…”

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

“…Our results revealed two BAHD genes, tcBAHD13 (a vinorine synthase) and tcBAHD26 (an Omega-hydroxypalmitate Oferuloyl transferase) that were upregulated specifically in resistant cultivars, indicating that these two genes are potentially involved in the P. megakarya fungi response. Although, these results were not validated from qualitative PCR (qPCR), previous studies reported high consistency between the result of RNAseq and qPCR, i.e., in the GASA gene family in soybean (Ahmad et al, 2019) and apple (Fan et al, 2017), extensin genes in tomato (Ding et al, 2020), papain-like cysteine proteases in rice (Niño et al, 2020) and cotton (Zhang et al, 2019), and auxin/indole-3-acetic acid in pepper (Waseem et al, 2018). Nevertheless, a functional study is required to draw a complete conclusion.…”

Function identification of MdTIR1 in apple root growth benefited from the predicted MdPPI network

“…In this process, MdIAA45 , MdIAA46 , and MdIAA47 were not anchored to any chromosome due to anomalies in the apple genome sequence (Figure 4A). To determine further the reliability of the screening members, we used protein sequences of IAA members from Arabidopsis (29) (Okushima et al, 2005), Oryza sativa (31) (Jain et al, 2006), Zea mays (31) (Wang et al, 2010), Carica papaya (18) (Liu et al, 2017a), and Capsicum annuum (27) (Waseem et al, 2018) for multiple alignments. The results of a WebLogo annotation showed that the apple IAA protein sequences containing four conserved domains, defined as domains I to IV, had high similarity to their homologs from the other five species (Figure 4B), further confirming the reliability of the MdIAA identification.…”