Zingibereae is a large tribe in the family Zingiberaceae, which contains plants with important medicinal, edible, and ornamental values. Although tribes of Zingiberaceae are well circumscribed, the circumscription of many genera within Zingibereae and the relationships among them remain elusive, especially for the genera of Boesenbergia, Curcuma, Kaempferia and Pyrgophyllum. In this study, we investigated the plastome variation in nine species representing five genera of Zingibereae. All plastomes showed a typical quadripartite structure with lengths ranging from 162,042 bp to 163,539 bp and contained 132–134 genes, consisting of 86–88 coding genes, 38 transfer RNA genes and eight ribosomal RNA genes. Moreover, the characteristics of the long repeats sequences and simple sequence repeats (SSRs) were detected. In addition, we conducted phylogenomic analyses of the Zingibereae and related taxa with plastomes data from additional 32 species from Genbank. Our results confirmed that Stahlianthus is closely related to Curcuma, supporting the idea of merging it into Curcuma. Kaempferia, Boesenbergia and Zingiber were confirmed as close relatives and grouped together as the Kaempferia group. Pyrgophyllum is not allied with the Curcuma clade but instead is embedded within the Hedychium clade. Our results demonstrate the power of plastid phylogenomics in improving the phylogenetic relationships within Zingibereae and provide a new insight into plastome evolution in Zingibereceae.

Clarifying the genetic relationship and divergence among Curcuma L. (Zingiberaceae) species around the world is intractable, especially among the species located in China. In this study, Reduced Representation Sequencing (RRS), as one of the next generation sequences, has been applied to infer large scale genotyping of major Chinese Curcuma species which present little differentiation of morphological characteristics and genetic traits. The 1295 high-quality SNPs (reduced-filtered SNPs) were chosen from 997,988 SNPs of which were detected from the cleaned 437,061 loci by RRS to investigate the phylogeny and divergence among eight major Curcuma species locate in the Hengduan Mountains of the Qinghai–Tibet Plateau (QTP) in China. The results showed that all the population individuals were clustered together within species, and species were obviously separated; the clustering results were recovered in PCA (Principal Component Analysis); the phylogeny was (((((C. Phaeocaulis, C. yunnanensis), C. kwangsiensis), (C. amarissima, C. sichuanensis)), C. longa), (C. wenyujin, C. aromatica)); Curcuma in China originated around ~7.45 Mya (Million years ago) in the Miocene, and interspecific divergence appeared at ca. 4–2 Mya, which might be sped up rapidly along with the third intense uplift of QTP.

Exogenous biostimulants (EB) are crucial for reducing abiotic stress in plants. It is currently unclear how EB such as melatonin (MT), betaine (BA), and salicylic acid (SA) regulate the stress in Camellia oleifera seedlings under alkali stress (XP). This study demonstrates the moderating effect of SA (0.5, 1, and 2 mmol/L), BA (0.2, 0.4, and 0.8 g/L), and MT (200, 400, and 800 μmol/L) on the relative chlorophyll content, photosynthetic parameters, chlorophyll fluorescence parameters, osmoregulatory substances, and antioxidant enzymes in C. oleifera seedlings under XP. The results showed that spraying different types and different concentrations of EB under alkali stress had a certain alleviating effect on the phenotype of C. oleifera seedlings. Whether 7 or 15 days after the application of EB, the relative chlorophyll content (SPAD) and the degree of yellowish-green in the control group were different from those in the other 10 treatment groups, but the difference in brightness was not significant. As far as the malondialdehyde (MDA) content is concerned, the SA2, BA3, MT2, and MT3 treatment groups can significantly reduce the MDA content on the 7th day of EB application. The electrolytic leakage (EL) is also significantly reduced by MT2 and MT3. It was found that treatment groups SA3 and MT2 could improve the photosynthetic parameters of C. oleifera seedlings to different degrees on the 7th day of EB application. On the 15th day of EB application, treatment groups SA1, SA3, BA1, and BA2 all increased the photosynthetic rate of C. oleifera compared to the XP treatment group, but other treatments did not increase. At the same time, the results showed that the fluorescence parameters of the seedlings showed different degrees of improvement under different EB spraying conditions. Under alkali stress, soluble proteins (SP) and soluble sugars (SS) increased in the XP group, but it was found that the SA3, BA3, and MT2 treatment groups could reduce the content of osmoregulatory substances both on the 7th and 15th days of EB application. In terms of proline (Pro) content, BA1, BA2, and MT2 treatment groups could reduce Pro content on the 7th and 15th days of EB spraying, respectively. As for the antioxidant enzymes, the SA2, BA3, MT2, and MT3 treatment groups could basically increase the activity of antioxidant enzymes and further reduce oxidative damage on the 7th day of application of EB. According to the comprehensive results of the membership function, whether on the 7th or 15th day of EB spraying, the MT2 treatment group has the best overall mitigation effect of the three EB applications, ranking in the top three. This study will help to improve the scientific understanding of C. oleifera’s alkali resistance and interaction with EB while filling the knowledge gap on the physiological response to oleofylline stress.

Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.

Environmental stresses significantly influence crop growth and productivity, acting as powerful selective pressures in plant evolution. The AP2/ERF superfamily is crucial for plant development and stress responses, orchestrating key regulatory pathways. This study explores the adaptive evolution of AP2/ERF genes across 15 key plant species, focusing on expansion and contraction patterns driven by amplification through multi-omics analyses. Across 15 plant genomes, we identified 1495 AP2/ERF genes. AP2/ERF genes demonstrated preferential retention following amplification, underscoring their importance in genomic stability and functional adaptation. Notably, the amplification-associated AP2 subfamily exhibited substantial expansion in quinoa (CqAP2/ERFs), emphasizing its role in stress adaptation. Robust regulatory networks were identified between CqAP2/ERFs, AtAP2/ERFs, and fatty acid pathways, highlighting their contributions to stress resilience. Transcriptomic analyses in Arabidopsis thaliana further validated the conserved correlation of these networks. Functional predictions based on phenotypic and RNA-seq data revealed the involvement of AP2/ERFs in key stress response and developmental processes. By integrating genomic, metabolomic, phenotypic, transcriptomic, and protein interaction data, this study uncovers novel regulators and adaptive pathways of AP2/ERFs, providing insights into their evolutionary diversification post-amplification. These findings establish a comprehensive framework for understanding the pivotal roles of AP2/ERFs in enhancing plant stress tolerance.