Paeonia delavayi var. lutea, Paeonia delavayi var. angustiloba, and Paeonia ludlowii are Chinese endemics that belong to the Paeoniaceae family and have vital medicinal and ornamental value. It is often difficult to classify Paeoniaceae plants based on their morphological characteristics, and the limited genomic information has strongly hindered molecular evolution and phylogenetic studies of Paeoniaceae. In this study, we sequenced, assembled, and annotated the chloroplast genomes of P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii. The chloroplast genomes of these strains were comparatively analyzed, and their phylogenetic relationships and divergence times were inferred. These three chloroplast genomes exhibited a typical quadripartite structure and were 152,687–152,759 bp in length. Each genome contains 126–132 genes, including 81–87 protein-coding genes, 37 transfer RNAs, and 8 ribosomal RNAs. In addition, the genomes had 61–64 SSRs, with mononucleotide repeats being the most abundant. The codon bias patterns of the three species tend to use codons ending in A/U. Six regions of high variability were identified (psbK-psbL, trnG-UCC, petN-psbM, psbC, rps8-rpl14, and ycf1) that can be used as DNA molecular markers for phylogenetic and taxonomic analysis. The Ka/Ks ratio indicates positive selection for the rps18 gene associated with self-replication. The phylogenetic analysis of 99 chloroplast genomes from Saxifragales clarified the phylogenetic relationships of Paeoniaceae and revealed that P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii are monophyletic groups and sisters to P. delavayi. Divergence time estimation revealed two evolutionary divergences of Paeoniaceae species in the early Oligocene and Miocene. Afterward, they underwent rapid adaptive radiation from the Pliocene to the early Pleistocene when P. delavayi var. lutea, P. delavayi var. angustiloba, and P. ludlowii formed. The results of this study enrich the chloroplast genomic information of Paeoniaceae and reveal new insights into the phylogeny of Paeoniaceae.

Background: GRAS transcription factors are crucial for plant development and stress responses but remain poorly characterized in citrus. Soil salinization increasingly threatens sweet orange (Citrus sinensis) yield. Identifying salt-responsive GRAS genes could reveal key tolerance determinants for breeding resistant cultivars. Methods: We systematically identified and analyzed sweet orange GRAS transcription factors using bioinformatics. Results: Forty-three CsGRAS genes were identified, phylogenetically classified into ten subfamilies, and found to be structurally conserved. A promoter analysis revealed a high prevalence (58.78%) of hormone- and stress-responsive cis-elements. These genes reside on nine chromosomes, with segmental duplication being the primary evolutionary driver (eight duplicated pairs). Functional enrichment implicated hormone signaling pathways in regulating growth under stress. Transcriptome profiling identified 42 differentially expressed CsGRAS genes (19 upregulated and 23 downregulated) under salt stress. qRT-PCR validated the expression patterns of selected genes (e.g., CsGRAS15 and CsGRAS27). Notably, DELLA subfamily members CsGRAS15 and CsGRAS27, key negative regulators in gibberellin (GA) signaling, were differentially expressed. Modulating these DELLA proteins presents a promising strategy to enhance sweet orange salt tolerance by mitigating GA-mediated growth inhibition during stress. Conclusion: This study identifies salt-responsive CsGRAS genes, highlighting CsGRAS15 and CsGRAS27 as potential targets for improving salt tolerance in citrus.

Drought can limit plant growth. The ABRE binding factor (ABF) gene family is extensively involved in multifarious bioregulatory processes in plants. However, kiwifruit has not yet been systematically analyzed. This study analyzed the response of kiwifruit AcABF genes to drought stress. Eleven AcABF genes were distributed on nine chromosomes and clustered into three subfamilies with Arabidopsis AtABF genes, AcABF2, AcABF3, AcABF8, AcABF9, and AcABF10, which have drought resistance functions, and AtABF1, AtABF2, AtABF3, and AtABF4 were clustered in Group I. The structural domains of the nine ABF genes in Group I were highly conserved, and the protein structures were highly similar. In the analysis of the five AcABF genes in Group I, all of their cis-acting elements were related to ABA, the content of ABA-like hormones was significantly increased after drought stress, and most of the GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment results were related to hormonal processes. A total of six AcABF genes were upregulated under drought stress. qRT-PCR was performed to validate the AcABF genes of Group I. The correlation coefficients of the results with the transcriptome data were all above 0.70, and the expression level of ABA increased under drought treatment. These results indicated that the five AcABF genes were positively correlated with ABA under drought stress and that, by synthesizing ABA and facilitating the expression of ABF gene family members, the tolerance of kiwifruit increased. These results provide a solid foundation for further research on improving drought tolerance in kiwifruit.

Drought stress severely restricts the growth, development, yield, and fruit quality of Actinidia chinensis, making it urgent to explore drought resistance genes and their regulatory mechanisms. Trehalose-6-phosphate synthase (TPS) genes are key genes involved in trehalose synthesis and metabolism, playing important roles in plant abiotic stress tolerance. Based on the genome database, transcriptome data, and leaf soluble sugar content analysis of A. chinensis, we investigated the response of A. chinensis and its AcTPS gene family to drought stress. Through bioinformatics and phylogenetic analysis, 13 AcTPS genes were identified, which were divided into two subfamilies and unevenly distributed across 11 chromosomes. Under drought stress, seven AcTPS genes showed significant expression changes, and five randomly selected genes were validated by qRT-PCR, with results highly consistent with the transcriptome data. Drought stress severely inhibited seedling growth, reduced leaf relative water content, and significantly promoted the accumulation of trehalose in A. chinensis leaves, indicating that the plant adapts to drought by regulating soluble sugar metabolism. Integrated transcriptomic and metabolomic analyses indicate that AcTPS1 may be related to trehalose biosynthesis, and a potential time-lag effect between trehalose content and AcTPS1 gene expression was observed. This study is limited to bioinformatics and omics analyses; AcTPS1 may be related to drought resistance in kiwi, but further functional validation is still required.

Drought stress is one of the primary environmental factors affecting plant survival rates and productivity, and it is a key bottleneck restricting the development of the world kiwifruit industry. Therefore, studying the drought resistance-related genes and drought resistance mechanisms of kiwifruit is essential. The bHLH (basic helix-loop-helix) TF family plays a crucial role in the resistance of kiwifruit to abiotic stresses such as drought stress. In this study, we analyzed the response of the AcbHLH gene in kiwifruit under drought stress based on the kiwifruit genome database, transcriptome data, and metabolome data. One hundred eighty-seven AcbHLH genes were identified via bioinformatics and divided into eighteen subfamilies via phylogenetic analysis. The cis-acting elements of the AcbHLH gene are mainly hormone-related cis-acting elements. Under drought stress, 64 AcbHLH genes were significantly different, 5 AcbHLH genes whose expression significantly differed were randomly selected for qRT-PCR verification, and the correlation between the qRT-PCR results and the transcriptome data was high. The determination of plant hormone contents revealed that the contents of plant hormones, such as JA, changed markedly before and after drought stress. Through the combined analysis of transcriptome and metabolome data, it was speculated that AcbHLH84 and AcbHLH97 have functions similar to those of the MYC2 transcription factor and are the main downstream effectors in the JA signaling pathway; these functions could be activated and participate in the JA signaling pathway and that the activation of the JA signaling pathway would inhibit the production of reactive oxygen species. In turn, the drought resistance of kiwifruit is improved. The AcbHLH84 and AcbHLH97 genes could be candidate genes for breeding new transgenic drought-resistant kiwifruit varieties.

Sweet orange (Citrus sinensis) is an important commercial fruit tree, and anthracnose associated with Colletotrichum spp. severely affects yield and fruit