Molecular phylogenetic relationships based on chloroplast genomes of Zingiberaceae species: Insights into evolution and adaptation to extreme environments

IntroductionThe Zingiberaceae family, which includes numerous economically and medicinally important species, exhibits considerable phylogenetic and genetic diversity. Chloroplast genomes are valuable resources for studying evolutionary relationships, genetic diversity, and adaptive evolution in plants. While many Zingiberaceae chloroplast genomes have been sequenced, the evolutionary mechanisms—including structural variation, codon usage bias, selection pressures, and divergence history—remain to be comprehensively investigated. Methodswe performed a comparative analysis of 11 newly identified species (Aframomum alboviolaceum, Amomum longipetiolatum, Amomum petaloideum, Amomum velutinum, Cautleya spicata, Cornukaempferia larsenii, Globba atrosanguinea, Globba variabilis, Hedychium aureum, Riedelia arfakensis, and Zingiber citriodorum) and 110 published data from the Zingiberaceae family, including their structure, codon usage, nucleotide polymorphisms, divergence time, and selection pressures.ResultsThe chloroplast genomes of Zingiberaceae species exhibited a highly conserved structure with no significant expansion or contraction during diversification. Analysis revealed four hypervariable protein-coding genes (atpH, rpl32, ndhA, and ycf1) and one intergenic region (psac-ndhE), which are proposed as potential molecular markers for future phylogeographic and population genetic studies. Codon usage bias was found to be predominantly shaped by natural selection. Phylogenetic analysis strongly supported the division of Zingiberaceae into two primary subfamilies (Alpinioideae and Zingiberoideae) and clarified key relationships, revealing that Globba is more closely related to Curcuma than to Hedychium, and Hedychium is more closely related to the Pommereschea-Rhynchanthus clade than to Cautleya. Divergence time estimation indicated two rapid diversification events within Zingiberoideae, coinciding with the rapid uplift of the Tibetan Plateau and a Late Miocene cooling event linked to declining CO₂ levels. Ancestral range reconstruction suggested an African origin during the Cretaceous period, followed by dispersal to Southeast Asia and India. Selection pressure analysis showed that most protein-coding genes are under negative selection. In contrast, the ycf2 gene was found to be under relaxed selection. Furthermore, two genes (matK and ndhB) were identified to be under positive selection in high-altitude species of Roscoea, suggesting a role in adaptation to alpine environments.DiscussionThis study provides a comprehensive genomic analysis of the Zingiberaceae family, highlighting the conserved nature of chloroplast genome structure despite extensive diversification. The identified mutation hotspots present valuable tools for developing high-resolution markers for species identification and biogeographic studies. The phylogenetic results resolve longstanding uncertainties in the relationships among key genera. The inferred divergence times and ancestral range suggest that the evolutionary history of Zingiberaceae was significantly influenced by major geological and climatic events, notably the uplift of the Tibetan Plateau and global cooling in the Late Miocene. The prevalence of negative/purifying selection across most genes indicates strong evolutionary constraints to maintain core photosynthetic functions. The discovery of positively selected genes in high-altitude Roscoea species provides insights into adaptive evolution to environmental stressors. These findings offer foundational knowledge for future efforts in crop improvement, species identification, and the conservation of genetic diversity within the Zingiberaceae family

Comparative analysis of the organelle genomes of seven Rosa species (Rosaceae): insights into structural variation and phylogenetic position

IntroductionThe genus Rosa belongs to the family Rosaceae within the order Rosales, which is one of the more ancient plant lineages. At present, the complete mitochondrial genome of Rosa spp. is still rarely reported, and studies on the mitochondrial genome of Rosa spp. are limited.MethodsIn this study, the R. laevigata mitochondrial genome was sequenced using both Pacbio Sequel II and DNB-SEQ-T7 platforms. The second- and third-generation data for the other five Rosa species were downloaded from the NCBI database. Genome annotation was performed using Geneious, with structural visualization via CPGview. In-depth analyses were conducted, including assessments of non-synonymous/synonymous mutation ratios (Ka/Ks), codon usage bias, collinearity, and the identification of homologous fragments between chloroplast and mitochondrial genomes. Finally, we employed the maximum likelihood (ML) methods to analyze the phylogenetic relationships among R. laevigata and other Rosa species.ResultsThe chloroplast genome sizes ranged from 156,342 bp (R. laevigata) to 157,214 bp (R. agrestis). The GC content varied from 37.2% to 37.3%, and the number of genes ranged from 129 to 131. The mitochondrial genomes were all circular, with lengths between 271,191 bp and 338,975 bp, containing 52 to 59 genes. Codon usage analysis indicated a preference for A/T-ending codons in both chloroplast and mitochondrial genes. Four highly differentiated regions (rps19, ndhF, ycf1, and psbM-trnD-GUC) in the plastomes of the 7 Rosa species were identified, which can serve as molecular markers for future species identification and studies of genetic diversity. Compared to PCGs of plastome, mitochondrial PCGs displayed a higher non-synonymous to synonymous ratio. We also observed extensive gene transfer between the mitochondria and chloroplasts, particularly with the rrn16 and rpl23 genes, which are commonly found in Rosa species. These gene transfer events likely occurred in the ancestor of Rosa around 4.46 Mya. Estimates of divergence events indicate that rapid differentiation among Rosa species took place around 4.46 Mya, potentially influenced by the uplift of the Qinghai-Tibet Plateau during the Late Miocene.DiscussionThis study enriches the genetic resources of the Rosa genus and lays the groundwork for the development of molecular markers, phylogenetic analyses, and research into the evolution of organelle genomes

Demonstration of the frequency-drift-induced self-comparison measurement error in optical lattice clocks

Abstract The frequency-drift-induced self-comparison measurement error was experimentally demonstrated by measuring the frequency difference between two interleaved clock loops with the same systemic parameters in the 87Sr optical lattice clock at the National Time Service Center of China. Combining the experimental and simulated results, this error was precisely determined by the total clock laser frequency drift during the time interval between two adjacent operations of interleaved clock loops.</jats:p

An Evaluation of the Zeeman Shift of the 87Sr Optical Lattice Clock at the National Time Service Center

The Zeeman shift plays an important role in the evaluation of optical lattice clocks since a strong bias magnetic field is applied for departing Zeeman sublevels and defining a quantization axis. We demonstrated the frequency correction and uncertainty evaluation due to Zeeman shift in the 87Sr optical lattice clock at the National Time Service Center. The first-order Zeeman shift was almost completely removed by stabilizing the clock laser to the average frequency of the two Zeeman components of mF = ±9/2. The residual first-order Zeeman shift arose from the magnetic field drift between measurements of the two stretched-state center frequencies; the upper bound was inferred as 4(5) × 10−18. The quadratic Zeeman shift coefficient was experimentally determined as –23.0(4) MHz/T2 and the final Zeeman shift was evaluated as 9.20(7) × 10−17. The evaluation of the Zeeman shift is a foundation for overall evaluation of the uncertainty of an optical lattice clock. This measurement can provide more references for the determination of the quadratic coefficient of 87Sr.</jats:p

An Evaluation of the Zeeman Shift of the 87Sr Optical Lattice Clock at the National Time Service Center

The Zeeman shift plays an important role in the evaluation of optical lattice clocks since a strong bias magnetic field is applied for departing Zeeman sublevels and defining a quantization axis. We demonstrated the frequency correction and uncertainty evaluation due to Zeeman shift in the 87Sr optical lattice clock at the National Time Service Center. The first-order Zeeman shift was almost completely removed by stabilizing the clock laser to the average frequency of the two Zeeman components of mF = &plusmn;9/2. The residual first-order Zeeman shift arose from the magnetic field drift between measurements of the two stretched-state center frequencies; the upper bound was inferred as 4(5) &times; 10&minus;18. The quadratic Zeeman shift coefficient was experimentally determined as &ndash;23.0(4) MHz/T2 and the final Zeeman shift was evaluated as 9.20(7) &times; 10&minus;17. The evaluation of the Zeeman shift is a foundation for overall evaluation of the uncertainty of an optical lattice clock. This measurement can provide more references for the determination of the quadratic coefficient of 87Sr

Distribution and Potential Metabolic Functions of Soil Actinobacteria in Degraded Alpine Grassland on the Northern Tibetan Plateau

Actinobacteria play major roles in human health and soil nutrient biogeochemical cycles, which are important for environmental protection. On the northern Qinghai&ndash;Tibet Plateau, the Qiangtang Alpine Grasslands have recently become degraded to varying degrees due to global climate changes and human disturbances. Here, we compared the community diversity, composition, and potential metabolic functions of Actinobacteria in soil from different degradation conditions through Illumina MiSeq sequencing. The soil Actinobacteria community structure in the Qiangtang Alpine Grasslands of northern Tibet was dominated by Nocardioides, Gaiella, Solirubrobacter, and Pseudonocardia, with evidence of previously unidentified taxa. Compared with non-degraded and severely degraded grasslands, the moderately degraded grassland had the highest soil Actinobacteria alpha-diversity, and the community composition showed significant differences between degraded grasslands with different degrees of degradation. The interactions between Actinobacteria and KO functions predominantly show negative correlations, but significant positive correlations outnumber significant negative ones. This study showed that Actinobacteria diversity and potential ecological functions in the alpine grasslands of northern Tibet decreased with grassland degradation due to the loss of vegetation cover. Therefore, it is necessary to effectively manage and protect the Qiangtang Alpine Grasslands on the northern Tibetan Plateau