Comparative genome-wide analysis of CAD (Cinnamyl Alcohol Dehydrogenase) gene family in Medicago truncatula and Lotus japonicus and their expression profiles in response to various abiotic abiotic stresses
These genes may serve as promising candidates for improving abiotic stress tolerance and provide molecular insights into their functional roles for future crop improvement programs and experimental validation.
Abstract
The CAD (Cinnamyl Alcohol Dehydrogenase) gene family is a key determinant for lignin biosynthesis in plants. In legumes, CAD enzymes are involved in the development of vascular tissues such as xylem and Casparian strip and they contribute to the production of antimicrobial and antifungal compounds. Thereby, it offers defense against pathogens and pests. Despite their biological significance, a comparative genome-wide analysis of the CAD gene family in Medicago truncatula and Lotus japonicus has not been explored. Therefore, we conducted a comparative genome-wide study to investigate the characteristics and potential role of CAD genes in these two model legume species. A total of 51 CAD genes were identified in M. truncatula (MtCAD) and 35 in L. japonicus (LjCAD). The CAD proteins are prominently characterized by ADH_N and ADH_zinc_N domains that were distributed in 8 and 6 chromosomes of MtCAD and LjCAD, respectively. Structural organization and conserved motif analysis indicated notable similarities between MtCAD and LjCAD proteins. However, considering the ancestry and functionality and based on the evolutionary analysis, LjCAD showed more similarities with Arabidopsis than MjCAD. Gene duplication analysis identified twelve duplicated gene pairs in MtCAD and eight in LjCAD, including both tandem and segmental duplication events. Most MtCAD and LjCAD were found in the cytoplasm with some of the cis-acting regulatory elements associated with stress responses. Gene Ontology annotation suggested that most MtCAD genes were associated with biological processes whereas LjCAD genes are mainly enriched in molecular functions. Both MtCAD and LjCAD showed potential roles in secondary metabolite production. Three substantial transcription factor families such as bZIP, C2H2, and ERF and several unique microRNAs were predicted to target MtCAD and LjCAD in regulating their gene expression against certain abiotic stressors for instance cold, freezing, drought, and heat. The MtCAD and LjCAD expressed highly in stress-responsive tissues such as nodule, root, immature flower, seed, and leaf. Meanwhile, RNA-sequencing data further highlighted several potential stress-responsive genes. In M. truncatula, The MtCAD1, MtCAD3, MtCAD9, MtCAD15, MtCAD23, MtCAD27, and MtCAD47 exhibited higher expression under cold, drought, and freezing stress compared with control conditions. Whereas in L. japonicus, LjCAD6, LjCAD8, and LjCAD11 showed higher expression under cold, drought, and heat stress. Thus, these genes may serve as promising candidates for improving abiotic stress tolerance and provide molecular insights into their functional roles for future crop improvement programs and experimental validation.
The expansin (EXs) gene family plays a crucial role in the growth and development of various plants, as well as responses to biotic and abiotic stresses. However, genome-wide analysis of the EX gene family and their functions in drought and salt stress tolerance has not been examined in Rosa rugosa. In this study, a total of 30 RrEX genes were identified and located on seven different chromosomes. Phylogenetic analysis classified these genes into four subfamilies: EXPA (24 members), EXPB (3 members), EXLA (1 member), and EXLB (2 members). The average amino acid length was 269.17 aa, with isoelectric points ranging from 4.79 to 9.97. Most members exhibited high aliphatic indices and protein stability, suggesting their adaptability to diverse environments. The synteny analysis provided insights into the evolution of the EXs gene family in rose. Toxicity and autoactivation assays confirmed that BD-RrEXPA1 was non-toxic to yeast cells and lacked autoactivation activity, indicating its suitability for yeast two-hybrid screening. The transgenic Arabidopsis lines overexpressing RrEXPA1 improved seed germination and root length under abiotic stress. In addition, the overexpression lines showed reduced malondialdehyde (MDA) levels and increased chlorophyll content and superoxide dismutase (SOD) activity. These results suggest that RrEXPA1 may enhance stress tolerance by promoting root elongation and modulating physiological responses. This study provides important insights into the role of RrEXs in salt and drought stress and lays the foundation for further studies on the regulatory mechanisms of abiotic stress.
Na Sang, Xiao-Xiao Hong, Xi Liu et al.· Gene· 0 citations
This study systematically characterized the Aux/IAA gene family in pumpkin, highlighting its evolutionary diversity, structural conservation, and distinct regulatory features and inform the potential roles of CmIAA genes in abiotic stress responses.
expression analysis indicated tissue-specific expression patterns, with higher expression levels observed in roots and qRT-PCR profiling detected increased expression of multiple candidate PtrCOMT genes upon high-salt treatment, hinting that members of this family may be implicated in plant salt stress regulatory processes.
A genome-wide analysis of the DIR gene family was undertaken to characterize these genes and to gain insights into their potential involvement in stress responses, with the aim of supporting the development of improved stress-resistant banana cultivars.
Anuradha Chelliah, B. Suthanthiram, C. Arumugam et al.· 3 Biotech· 0 citations
Fructose-1,6-bisphosphate aldolases (FBAs; EC 4.1.2.13) are core enzymes involved in glycolysis, gluconeogenesis, and the Calvin cycle, exerting vital functions in carbon allocation, plant growth and development, as well as the adaptation to abiotic stresses. Although the
FBA
gene family has been systematically characterized in a variety of plant species, a comprehensive characterization of FBAs in soybean (
Glycine max
) remains unreported to date, restricting the elucidation of the conserved and legume-specific functions of
GmFBA
genes in stress adaptation. In the present study, a total of 13
FBA
genes, designated as
GmFBA1
to
GmFBA13
, were identified in the soybean genome, which were unevenly distributed across 9 out of the 20 soybean chromosomes. Subcellular localization prediction showed that six GmFBA proteins were localized in the chloroplast, while the remaining seven were distributed in the cytoplasm. Phylogenetic analysis classified these genes into four distinct classes, and members within the same class shared similar gene structural features. Synteny analysis demonstrated that segmental duplication events served as a major driving force for the expansion of the
GmFBA
gene family. Promoter sequence analysis revealed that the upstream regulatory regions of
GmFBA
genes contained a variety of
cis
-acting elements associated with hormone responses and stress tolerance, suggesting that the expression of
GmFBA
genes might be modulated by diverse developmental cues and environmental stresses. Expression profiling indicated that
GmFBA
genes displayed differential expression patterns in various organs and tissues of soybean, and a number of
GmFBA
genes showed significant expression changes under biotic and abiotic stress conditions. Transcriptome analysis revealed distinct expression patterns of
GmFBA
genes in response to salt-alkali stress. Furthermore, quantitative real-time PCR assays indicated a significant upregulation of two specific
GmFBA
genes,
GmFBA2
and
GmFBA11
. These findings suggest that
GmFBA2
and
GmFBA11
may serve as candidate genes potentially involved in the adaptive response to salt-alkali stress. Collectively, this study presents the first comprehensive characterization of the
FBA
gene family in soybean, puts forward putative candidate genes for salt-alkali tolerance breeding, and lays a foundation for subsequent functional investigations.
Xin-Yan Zhao, Ya-Wen Zhan, Shuang-Jin Fan et al.· Frontiers in Plant Science· 0 citations
Background Superoxide dismutases (SODs) are crucial metalloenzymes that constitute the first line of defense against reactive oxygen species in plants under abiotic stress. Wolfberry (Lycium barbarum) is an economically important medicinal plant with notable stress tolerance, however, a comprehensive genome-wide analysis of its SOD gene family has not yet been performed. Results We identified ten wolfberry SOD genes (LbaSODs) and classified them into three subfamilies: iron-SODs (Fe-SODs), manganese-SODs (Mn-SODs), and copper/zinc-SODs (Cu/Zn-SODs). Members within each subfamily shared conserved gene structures and motifs. Segmental duplication was the primary driver of LbaSOD expansion, with three paralogous pairs identified. Analysis of cis-regulatory elements in the promoter region revealed a predominance of stress- and hormone-responsive cis-elements, particularly ABA-responsive elements (ABREs) (22 copies) and LTR (17 copies) motifs. Tissue-specific expression profiling revealed that LbaSOD2 and LbaSOD5 expression peaked during early fruit development, whereas LbaSOD6, LbaSOD9, and LbaSOD10 were progressively upregulated through fruit maturation. Under abiotic conditions, Fe-SOD members were markedly suppressed during prolonged drought, whereas LbaSOD9 and LbaSOD10 were rapidly induced in response to salt stress. Among the phytohormone treatments, methyl jasmonate (MeJA) elicited the most pronounced response, with LbaSOD5 expression increasing by approximately 60-fold after 24 hours. Notably, abscisic acid (ABA) triggered an exceptionally strong transcriptional induction of LbaSOD5 (2.5 × 105-fold), LbaSOD10 (6 × 105-fold), and LbaSOD6 (70-fold). In addition, LbaSOD3 and LbaSOD7 transcripts were undetectable in any of the tested conditions. Conclusions This study provides the first comprehensive characterization of the LbaSOD gene family and elucidates its hormone- and stress-responsive regulatory landscape, providing a valuable foundation for future functional investigations of LbaSOD genes in abiotic stress adaptation. The extraordinarily strong ABA-mediated induction of specific LbaSOD members, together with their tissue- and stress-specific expression patterns, highlights their potential as targets for genetic improvement of stress tolerance in wolfberry.
Xiao-Yu Cao, Xiao-Rong Bai, Ying-Wu-Di Li et al.· Frontiers in Plant Science· 0 citations
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