Identification and Functional Analysis of CAD Gene Family in Pomegranate (Punica granatum)

Abstract

[Objective] Cinnamyl alcohol dehydrogenase (CAD) is a key enzyme in lignin biosynthesis. The aim of this study was to identify CAD gene family members in pomegranate and its expression correlation with seed hardness. [Methods] Based on the reported CAD sequence of Arabidopsis, the CAD gene family of pomegranate was identified by homologous comparison, and then phylogenetic, molecular characterization, and expression profile analysis were performed. [Results] Pomegranate CAD gene family has 25 members, distributed on seven chromosomes of pomegranate. All pomegranate CAD proteins have similar physical and chemical properties. We divide the family into four groups based on evolutionary relationships. The member of group I, called bona fide CAD, was involved in lignin synthesis. Most of the members of group II were involved in stress resistance. The functions of groups III and IV need to be explored. We found four duplicated modes (whole genome duplication or segmental (WGD), tandem duplication (TD), dispersed duplication (DSD), proximal duplication (PD) in this family; TD (36%) had the largest number of them. We predicted that 20 cis-acting elements were involved in lignin synthesis, stress resistance, and response to various hormones. Gene expression profiles further demonstrated that the PgCAD gene family had multiple functions. [Conclusions] Pomegranate CAD gene family is involved in lignin synthesis of hard-seeded cultivar Hongyushizi and Baiyushizi, but its role in seed hardness of soft-seeded cultivar Tunisia needs to be further studied.

Genome-wide identification of the walnut MYC gene family and functional characterization of Xinjiang wild walnut under low-temperature stress

“…Plant growth and development, adversity stress, biosynthesis and other biological processes. In addition, 18 genes encoded cis -acting elements involved in the response to low-temperature stress, among which jasmonic acid-related genes were the most widely distributed (12), and it was hypothesized that these genes might be induced by jasmonic acid in response to low-temperature stress, which is in line with the findings of studies on tomato ( Miura et al, 2012 ), pomegranate ( Sayyari et al, 2011 ), mango ( González-Aguilar et al, 2000 ), and poplar ( Hu et al, 2023 ). The predicted protein interactions of walnut MYC transcription factor family members revealed that walnut JrMYC25 and JrMYC29 had the strongest interactions and shared high homology with MYC2 and MYC3 in Arabidopsis thaliana , and MYC2 and MYC3 worked together to activate the relevant transcription factors of the jasmonic acid signaling pathway in response to adversity ( Cheng et al, 2011 ).…”

“…The screening of walnut genome-wide data based on MYC transcription factors with a conserved bHLH structural domain at the C-terminus and a bHLH_MYC_N structural domain at the N-terminus, excluding proteins with deletions or non-full-length fragments, yielded 30 JrMYC genes, named JrMYC1 to JrMYC30, with a greater number of members than in the model plants Arabidopsis thaliana (8 AtMYC genes) and poplar (10 AtMYC genes) ( Hu et al, 2023 ).…”

“…Can respond to high salt and drought stresses. PtrMYC2b gene expression is induced by jasmonic acid and responds to low temperature and high salt stresses ( Hu et al, 2023 ). The evolutionary tree shows that JrMYC22 and JrMYC23 have high homology with PtrMYC2b , and it is hypothesized that JrMYC22 and JrMYC23 may have both cold resistance and salt resistance.…”

“…MYC transcription factors play important regulatory roles in plant growth and development and the response to adverse stresses, and one of them plays a key role in the response to low-temperature stress. Currently, the MYC transcription factor family has been identified in plants such as wheat ( Bai et al, 2019 ), tomato ( Feng et al, 2023 ), poplar ( Hu et al, 2023 ), and tea tree ( Chen et al, 2021 ). However, bioinformatic analysis of the MYC transcription factor family in walnut has not been reported.…”

Unraveling the Pomegranate Genome: Comprehensive Analysis of R2R3-MYB Transcription Factors

“…Pomegranates have been cultivated and evolved in China for more than 2000 years to form numerous varieties with rich genetic diversity [1,2]. Pomegranate is generally considered a healthy fruit [3]. Pomegranate seeds are rich in nutrients, including organic acids, sugars, minerals, and many other nutrients [4,5].…”