Genome-Wide Identification and Expression Analysis of the TCP Gene Family Related to Developmental and Abiotic Stress in Ginger.

Ginger (Zingiber officinale Roscoe), a widely consumed edible and medicinal plant, possesses significant nutritional and economic value. Abiotic stresses such as drought and low temperatures can impact the growth and development of ginger. The plant-specific transcription factor Teosinte branched1/cycloidea/proliferating cell factor (TCP) has progressively been identified in various plants for its role in regulating plant growth and development as well as conferring resistance to abiotic stresses. However, limited information on the TCP family is available in ginger. In this study, we identified 20 TCP members in the ginger genome, which were randomly distributed across 9 chromosomes. Based on phylogenetic analysis, these ginger TCP were classified into two subfamilies: Class I (PCF) and Class II (CIN, CYC/TB). The classification of the identified ginger TCPs was supported by a multi-species phylogenetic tree and motif structure analysis, suggesting that the amplification of the ginger TCP gene family occurred prior to the differentiation of angiosperms. The promoter region of ginger TCP genes was found to contain numerous cis-acting elements associated with plant growth, development, and abiotic stress response. Among these elements, the stress response element, anaerobic induction, and MYB binding site play a dominant role in drought responsiveness. Additionally, expression pattern analysis revealed variations in the expression of ginger TCP gene among different tissues and in response to diverse abiotic stresses (drought, low temperature, heat, and salt). Our research offers a thorough examination of TCP members within the ginger plant. This analysis greatly contributes to the understanding of how TCP genes regulate tissue development and response to stress, opening up new avenues for further exploration in this field.

Influence of High-Temperature and Intense Light on the Enzymatic Antioxidant System in Ginger (Zingiber officinale Roscoe) Plantlets.

Environmental stressors such as high temperature and intense light have been shown to have negative effects on plant growth and productivity. To survive in such conditions, plants activate several stress response mechanisms. The synergistic effect of high-temperature and intense light stress has a significant impact on ginger, leading to reduced ginger production. Nevertheless, how ginger responds to this type of stress is not yet fully understood. In this study, we examined the phenotypic changes, malonaldehyde (MDA) content, and the response of four vital enzymes (superoxide dismutase (SOD), catalase (CAT), lipoxygenase (LOX), and nitrate reductase (NR)) in ginger plants subjected to high-temperature and intense light stress. The findings of this study indicate that ginger is vulnerable to high temperature and intense light stress. This is evident from the noticeable curling, yellowing, and wilting of ginger leaves, as well as a decrease in chlorophyll index and an increase in MDA content. Our investigation confirms that ginger plants activate multiple stress response pathways, including the SOD and CAT antioxidant defenses, and adjust their response over time by switching to different pathways. Additionally, we observe that the expression levels of genes involved in different stress response pathways, such as SOD, CAT, LOX, and NR, are differently regulated under stress conditions. These findings offer avenues to explore the stress mechanisms of ginger in response to high temperature and intense light. They also provide interesting information for the choice of genetic material to use in breeding programs for obtaining ginger genotypes capable of withstanding high temperatures and intense light stress.

Exploring the Heat Shock Transcription Factor (HSF) Gene Family in Ginger: A Genome-Wide Investigation on Evolution, Expression Profiling, and Response to Developmental and Abiotic Stresses.

Ginger is a valuable crop known for its nutritional, seasoning, and health benefits. However, abiotic stresses, such as high temperature and drought, can adversely affect its growth and development. Heat shock transcription factors (HSFs) have been recognized as crucial elements for enhancing heat and drought resistance in plants. Nevertheless, no previous study has investigated the HSF gene family in ginger. In this research, a total of 25 ZoHSF members were identified in the ginger genome, which were unevenly distributed across ten chromosomes. The ZoHSF members were divided into three groups (HSFA, HSFB, and HSFC) based on their gene structure, protein motifs, and phylogenetic relationships with Arabidopsis. Interestingly, we found more collinear gene pairs between ZoHSF and HSF genes from monocots, such as rice, wheat, and banana, than dicots like Arabidopsis thaliana. Additionally, we identified 12 ZoHSF genes that likely arose from duplication events. Promoter analysis revealed that the hormone response elements (MEJA-responsiveness and abscisic acid responsiveness) were dominant among the various cis-elements related to the abiotic stress response in ZoHSF promoters. Expression pattern analysis confirmed differential expression of ZoHSF members across different tissues, with most showing responsiveness to heat and drought stress. This study lays the foundation for further investigations into the functional role of ZoHSFs in regulating abiotic stress responses in ginger.

The complete chloroplast genome of Zingiber striolatum Diels (Zingiberaceae).

The chloroplast genome of Zingiber striolatum Diels was sequenced using the MGI paired-end sequencing method and assembled. The chloroplast genome was 163,711 bp in length, containing a large single-copy (LSC) region of 88,205 bp, a small single-copy (SSC) region of 15,750 bp, and two inverted repeat (IR) regions of 29,752 bp. The overall GC content was 36.1%, whereas the corresponding value in the IR regions was 41.1%, which was higher than that in the LSC region (33.8%) and SSC region (29.6%). A total of 136 complete genes were annotated in the chloroplast genome of Z. striolatum, including 87 protein-coding genes (79 protein-coding gene species), 40 tRNA genes (29 tRNA species), and 8 rRNA genes (4 rRNA species). A phylogenetic tree was constructed using the maximum likelihood (ML) method, and the results showed that the phylogeny of Zingiber was well resolved with high support values, and Z. striolatum was sister to Z. mioga. The assembly and sequence analysis of the chloroplast genome can provide a basis for developing high-resolution genetic makers.

Complete chloroplast genomes provide insights into evolution and phylogeny of Zingiber (Zingiberaceae).

BACKGROUND: The genus Zingiber of the Zingiberaceae is distributed in tropical, subtropical, and in Far East Asia. This genus contains about 100-150 species, with many species valued as important agricultural, medicinal and horticultural resources. However, genomic resources and suitable molecular markers for species identification are currently sparse. RESULTS: We conducted comparative genomics and phylogenetic analyses on Zingiber species. The Zingiber chloroplast genome (size range 162,507-163,711 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 86,986-88,200 bp), a small single copy (SSC, 15,498-15,891 bp) and a pair of inverted repeats (IRs, 29,765-29,934 bp). The genomes contain 113 unique genes, including 79 protein coding genes, 30 tRNA and 4 rRNA genes. The genome structures, gene contents, amino acid frequencies, codon usage patterns, RNA editing sites, simple sequence repeats and long repeats are conservative in the genomes of Zingiber. The analysis of sequence divergence indicates that the following genes undergo positive selection (ccsA, ndhA, ndhB, petD, psbA, psbB, psbC, rbcL, rpl12, rpl20, rpl23, rpl33, rpoC2, rps7, rps12 and ycf3). Eight highly variable regions are identified including seven intergenic regions (petA-pabJ, rbcL-accD, rpl32-trnL-UAG, rps16-trnQ-UUG, trnC-GCA-psbM, psbC-trnS-UGA and ndhF-rpl32) and one genic regions (ycf1). The phylogenetic analysis revealed that the sect. Zingiber was sister to sect. Cryptanthium rather than sect. Pleuranthesis. CONCLUSIONS: This study reports 14 complete chloroplast genomes of Zingiber species. Overall, this study provided a solid backbone phylogeny of Zingiber. The polymorphisms we have uncovered in the sequencing of the genome offer a rare possibility (for Zingiber) of the generation of DNA markers. These results provide a foundation for future studies that seek to understand the molecular evolutionary dynamics or individual population variation in the genus Zingiber.

Interplay of Ecological Opportunities and Functional Traits Drives the Evolution and Diversification of Millettiod Legumes (Fabaceae).

Understanding the striking diversity of the angiosperms is a paramount issue in biology and of interest to biologists. The Millettiod legumes is one of the most hyper-diverse groups of the legume family, containing many economically important medicine, furniture and craft species. In the present study, we explore how the interplay of past climate change, ecological opportunities and functional traits' evolution may have triggered diversification of the Millettiod legumes. Using a comprehensive species-level phylogeny from three plastid markers, we estimate divergence times, infer habit shifts, test the phylogenetic and temporal diversification heterogeneity, and reconstruct ancestral biogeographical ranges. We found that three dramatic accumulations of the Millettiod legumes occurred during the Miocene. The rapid diversification of the Millettiod legumes in the Miocene was driven by ecological opportunities created by the emergence of new niches and range expansion. Additionally, habit shifts and the switch between biomes might have facilitated the rapid diversification of the Millettiod legumes. The Millettiod legumes provide an excellent case for supporting the idea that the interplay of functional traits, biomes, and climatic and geographic factors drives evolutionary success.

Genome-Wide Identification, Characterization, and Expression Analysis of GRAS Gene Family in Ginger (Zingiber officinale Roscoe).

GRAS family proteins are one of the most abundant transcription factors in plants; they play crucial roles in plant development, metabolism, and biotic- and abiotic-stress responses. The GRAS family has been identified and functionally characterized in some plant species. However, this family in ginger (Zingiber officinale Roscoe), a medicinal crop and non-prescription drug, remains unknown to date. In the present study, 66 GRAS genes were identified by searching the complete genome sequence of ginger. The GRAS family is divided into nine subfamilies based on the phylogenetic analyses. The GRAS genes are distributed unevenly across 11 chromosomes. By analyzing the gene structure and motif distribution of GRAS members in ginger, we found that the GRAS genes have more than one cis-acting element. Chromosomal location and duplication analysis indicated that whole-genome duplication, tandem duplication, and segmental duplication may be responsible for the expansion of the GRAS family in ginger. The expression levels of GRAS family genes are different in ginger roots and stems, indicating that these genes may have an impact on ginger development. In addition, the GRAS genes in ginger showed extensive expression patterns under different abiotic stresses, suggesting that they may play important roles in the stress response. Our study provides a comprehensive analysis of GRAS members in ginger for the first time, which will help to better explore the function of GRAS genes in the regulation of tissue development and response to stress in ginger.