Taste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain unclear. The goal of this study was to identify candidate genes for flavor compound metabolism and to construct a regulatory transcriptional network. We characterized the transcriptome of the ‘Jianali’ apricot cultivar, which exhibits substantial changes in flavor during ripening, at 50 (turning), 73 (commercial maturation) and 91 (full ripe) days post anthesis (DPA) using RNA sequencing (RNA-Seq). A weighted gene co-expression network analysis (WGCNA) revealed that four of 19 modules correlated highly with flavor compound metabolism (P < 0.001). From them, we identified 1237 differentially expressed genes, with 16 intramodular hubs. A proposed pathway model for flavor compound biosynthesis is presented based on these genes. Two SUS1 genes, as well as SPS2 and INV1 were correlated with sugar biosynthesis, while NADP-ME4, two PK-like and mitochondrial energy metabolism exerted a noticeable effect on organic acid metabolism. CCD1 and FAD2 were identified as being involved in apocarotenoid aroma volatiles and lactone biosynthesis, respectively. Five sugar transporters (Sweet10, STP13, EDR6, STP5.1, STP5.2), one aluminum-activated malate transporter (ALMT9) and one ABCG transporter (ABCG11) were associated with the transport of sugars, organic acids and volatiles, respectively. Sixteen transcription factors were also highlighted that may also play regulatory roles in flavor quality development. Apricot RNA-Seq data were obtained and used to generate an annotated set of predicted expressed genes, providing a platform for functional genomic research. Using network analysis and pathway mapping, putative molecular mechanisms for changes in apricot fruit taste and aroma during ripening were elucidated.

Primulina Hance is an emerging model for studying evolutionary divergence, adaptation and speciation of the karst flora. However, phylogenetic relationships within the genus have not been resolved due to low variation detected in the cpDNA regions. Chloroplast genomes can provide important information for phylogenetic and population genetic studies. Recent advances in next-generation sequencing (NGS) techniques greatly facilitate sequencing whole chloroplast genomes for multiple individuals. Consequently, novel strategies for development of highly polymorphic loci for population genetic and phylogenetic studies based on NGS data are needed. For development of high polymorphic loci for population genetic and phylogenetic studies, two novel strategies are proposed here. The first protocol develops lineage-specific highly variable markers from the true high variation regions (Con_Seas) across whole cp genomes, instead of traditional noncoding regions. The pipeline has been integrated into a single perl script, and named "Con_Sea_Identification_and_PIC_Calculation". The second method assembles chloroplast fragments (poTs) and sub-super-marker (CpContigs) through our "SACRing" pipeline. This approach can fundamentally alter the strategies used in phylogenetic and population genetic studies based on cp markers, facilitating a transition from traditional Sanger sequencing to RAD-Seq. Both of these scripts are available at https://github.com/scbgfengchao/ . Three complete Primulina chloroplast genomes were assembled from genome survey data, and then two novel strategies were developed to yield highly polymorphic markers. For experimental evaluation of the first protocol, a set of Primulina species were used for PCR amplification. The results showed that these newly developed markers are more variable than traditional ones, and seem to be a better choice for phylogenetic and population studies in Primulin a. The second method was also successfully applied in population genetic studies of 21 individuals from three natural populations of Primulina. These two novel strategies may provide a pathway for similar research in other non-model species. The newly developed high polymorphic loci in this study will promote further the phylogenetic and population genetic studies in Primulina and other genera of the family Gesneriaceae.

The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental fluctuations—remains unresolved in evolutionary biology. Here, we present chromosome-scale genomes for three ecologically divergent species (including both arborescent and nonarborescent growth forms) within Cyatheaceae, an ancient tree fern family characterized by morphological conservation dating back to the Jurassic era. Our results revealed substantial yet cryptically regulated genomic dynamism. A shared Jurassic whole-genome duplication (∼154 Ma) conferred dual adaptive advantages: initially buffering tree ferns against Late Jurassic climatic extremes through retention of stress-response genes, and subsequently facilitating niche diversification and phenotypic innovation via lineage-specific repurposing of duplicate genes. Arborescent lineages preferentially retained duplicates involved in cell wall biogenesis, essential for structural reinforcement and lignification, while nonarborescent forms conserved paralogs linked to metabolic resilience and defense. Alongside slow substitution rates, we detected cryptic genome dynamism mediated primarily by bursts of transposable elements, leading to genome size variations, chromosomal rearrangements, and localized innovation hotspots with elevated evolutionary rates. The concerted expansion and expression of lignification-related genes, coordinated with light signaling components, suggest a potential evolutionary mechanism integrating light perception with shade adaptation and lignification, facilitating arborescent adaptation in angiosperm-dominated understories. Our findings redefine evolutionary stasis as a dynamic equilibrium, sustained by regulatory plasticity and localized genomic innovation within a conserved morphological framework. This study offers a novel genomic perspective on the long-term persistence and evolution of ancient plant lineages, demonstrating how regulated genomic dynamism enables adaptive diversification while sustaining morphological conservatism.

Primulina, a genus of >200 species specialized to extreme soils, provides a model for edaphic adaptation. We assemble seven genomes and construct a pan-genome spanning nine species from karst, Danxia, and acidic soils. Comparative analyses reveal that karst-adapted species have smaller genomes. Two lineage-specific whole-genome duplications (WGDs) exhibit biased duplicate loss in large gene families but preferential retention of transcription factors, indicating combined adaptive and nonadaptive forces. Pan-genome analyses identify ion channel and transporter genes enriched in variant hotspots and under positive selection in karst lineages. Candidate genes for drought and salt stress tolerance include ABC transporters and ion channels. Notably, an ABC transporter shows positive selection in karst species and unique structural variation in non-karst species. Together, our findings show that genome downsizing, biased post-WGD retention, and evolution of ion-transport pathways shape adaptation to extreme soils. The Primulina pan-genome provides a resource for dissecting mechanisms underlying edaphic specialization.

Premise of the Study: Euchresta horsfieldii (Fabaceae) is a rare and endangered medicinal plant in Indonesia with restricted distribution. Single‐copy nuclear DNA (scn DNA ) markers were developed for this species to facilitate further investigation of genetic diversity and population structure. Methods and Results: We performed RNA ‐Seq and de novo assembly of the transcriptome. Ten primer sets were developed for E. horsfieldii , all of which also amplified in E. japonica and E. tubulosa . Conclusions: These scn DNA markers will be an important resource for the study of genetic diversity and population structure of E. horsfieldii and other species in the genus Euchresta .