Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species

Comprehensive analysis of the multi-rings mitochondrial genome of Populus tomentosa

BACKGROUND

Populus tomentosa, known as Chinese white poplar, is indigenous and distributed across large areas of China, where it plays multiple important roles in forestry, agriculture, conservation, and urban horticulture. However, limited accessibility to the mitochondrial (mt) genome of P. tomentosa impedes phylogenetic and population genetic analyses and restricts functional gene research in Salicaceae family.

RESULTS

Single-molecule real-time (SMRT) sequencing technology was used to sequence, assemble, and annotate the mt genome of P. tomentosa. This genome has a complex structure composed of four circular molecules ranging from 153,004 to 330,873 base pairs (bp). Each of these four circular molecules contains unique gene sequences that constitute the mt genome of P. tomentosa. The mt genome comprises 69 functional genes, including 38 protein-coding genes (PCGs), 26 tRNA genes, and 5 rRNA genes. After removing duplications, 19 different tRNA coding genes remain, though only 10 amino acids can be recognized. The noncoding region constitutes 93.38% of the mt genome, comprising a large number of repetitive sequences, gene spacer regions, and insertion from chloroplast sequences. Specifically, 40 chloroplast-derived sequences, with a total length of 24,381 bp, were identified in P. tomentosa.

CONCLUSIONS

In the current study, the results provide mitochondrial genomic evidence for the maternal origin of P. tomentosa and enhance understanding of the gene dialog between organelle genomes, contributing to the conservation and utilization of the genetic resources of P. tomentosa.

The Identification and Characterization of the PeGRF Gene Family in Populus euphratica Oliv. Heteromorphic Leaves Provide a Theoretical Basis for the Functional Study of PeGRF9

Populus euphratica Oliv. typically has four kinds of heteromorphic leaves: linear (Li), lanceolate (La), ovate (Ov) and broad ovate (Bo). Heteromorphic leaves help P. euphratica adapt to extreme desert environments and further contribute to protection against land desertification in Northwest China. In the authors' previous research, growth-regulating factors (GRFs) were speculated to be related to the development of P. euphratica heteromorphic leaves via multi-omics integrated analysis. However, the genomic features and biological role of the P. euphratica GRF gene family in heteromorphic leaves are still unclear. In this study, 19 PeGRF genes were genome-widely identified and characterized in P. euphratica, and their physicochemical properties, gene structure and phylogenetic evolution were analyzed. An analysis of the research showed that PeGRFs were unevenly distributed on 11 chromosomes and that PeGRF proteins contained conserved motif 1 (WRC) and motif 2 (QLQ). Moreover, 19, 15, 19 and 22 GRFs were identified in Populus deltoides Marshall, Populus pruinosa Schrenk, Salix sinopurpurea C. Wang et C. Y. Yang and Salix suchowensis W. C. Cheng, respectively. A collinearity analysis showed that the PeGRF family evolved slowly within Populus species. A phylogenetic tree of the GRF family was also constructed, and GRFs were divided into four subfamilies. A large number of cis-acting elements were related to plant growth and development, plant hormone response and stress response on the promoter of PeGRFs. The expression pattern of PeGRFs showed significant up-regulation in broad leaves (Ov and Bo) compared with narrow leaves (Li and La). In combination with the predicted gene regulatory network, PeGRF9 (PeuTF06G01147.1) may have an important contribution to the leaf shape development of P. euphratica. The heterologous expression of PeGRF9 in wild-type plants (Col-0) of Arabidopsis thaliana (L.) Heynh was also studied, showing a significant increase in the leaf area of overexpressing plants compared with the wild type. Nineteen PeGRF gene members were identified and characterized in P. euphratica, and a comparison of the genomic analysis of Populus GRF members revealed their evolutionary features. The further overexpression of PeGRF9 in A. thaliana revealed its biological role in the heteromorphic leaves of P. euphratica. This study not only provides new insights into the evolution and function of PeGRFs in P. euphratica heteromorphic leaves but also helps in an understanding of the adaptive evolution of P. euphratica in drought desert environments.

Effects of copper sulphate stress on the morphological and biochemical characteristics of Spinacia oleracea and Avena sativa

Plants are subjected to various biotic and abiotic stresses that significantly impact their growth and productivity. To achieve balanced crop growth and yield, including for leafy vegetables, the continuous application of micronutrient is crucial. This study investigates the effects of different concentrations of copper sulphate (0, 75, 125, and 175 ppm) on the morphological and biochemical features of Spinacia oleracea and Avena sativa. Morphological parameters such as plant height, leaf area, root length, and fresh and dry weights were optimized at a concentration of 75 ppm copper sulfate. At this concentration, chlorophyll a & b levels increased significantly in Spinacia oleracea (462.9 and 249.8 𝜇𝑔/𝑔), and Avena sativa (404.7 and 437.63𝜇𝑔/𝑔). However, carotenoid content and sugar levels in Spinacia oleracea were negatively affected, while sugar content in Avena sativa increased at 125 ppm (941.6 µg/ml). Protein content increased in Spinacia oleracea (75 ppm, 180.3 µg/ml) but decreased in Avena sativa. Phenol content peaked in both plants at 75 ppm (362.2 and 244.5 µg/ml). Higher concentrations (175 ppm) of copper sulfate reduced plant productivity and health. Plants exposed to control and optimal concentrations (75 and 125 ppm) of copper sulpate exhibited the best health and growth compared to those subjected to higher concentrations. Maximum plant height, leaf area, root length, fresh and dry weights were observed at lower concentrations (75 and 125 ppm) of copper sulfate, while higher concentrations caused toxicity. Optimal copper sulfate levels enhanced chlorophyll a, chlorophyll b, total chlorophyll, protein, and phenol contents but inhibited sugar and carotenoid contents in both Spinacia oleracea and Avena sativa. Overall, increased copper sulfate treatment adversely affected the growth parameters and biochemical profiles of these plants.

Green synthesis of Zn-doped TIO2 nanoparticles from Zanthoxylum armatum

Green synthesis is an easy, safe, and environmentally beneficial nanoparticle creation method. It is a great challenge to simultaneously improve the capping and stabilizing agent carrier separation efficiency of photocatalysts. Herein, Zn-doped Titanium dioxide (TiO2) nanoparticles with high exposure of 360 nm using a UV/visible spectrophotometer were prepared via a one-step hydrothermal decomposition method. A detailed analysis reveals that the electronic structures were modulated by Zn doping; thus, the responsive wavelength was extended to 600 nm, which effectively improved the visible light absorption of TiO2. We have optimized the different parameters like concentration, time, and temperature. The peak for TiO2 is located at 600 cm-1 in FTIR. A scanning electron microscope revealed that TiO2 has a definite shape and morphology. The synthesized Zn-doped TiO2NPs were applied against various pathogens to study their anti-bacterial potentials. The anti-bacterial activity of Zn-doped TiO2 has shown robust against two gram-ve bacteria (Salmonella and Escherichia coli) and two gram + ve bacteria (Staphylococcus epidermidis and Staphylococcus aureus). Synthesized Zn-doped TiO2 has demonstrated strong antifungal efficacy against a variety of fungi. Moreover, doping TiO2 nanoparticles with metal oxide greatly improves their characteristics; as a result, doped metal oxide nanoparticles perform better than doped and un-doped metal oxide nanoparticles. Compared to pure TiO2, Zn-doped TiO2 nanoparticles exhibit considerable applications including antimicrobial treatment and water purification.

A Fruit-Expressed MYB Transcription Factor Regulates Anthocyanin Biosynthesis in Atropa belladonna

Anthocyanins are water-soluble flavonoid pigments that play a crucial role in plant growth and metabolism. They serve as attractants for animals by providing plants with red, blue, and purple pigments, facilitating pollination and seed dispersal. The fruits of solanaceous plants, tomato (Solanum lycopersicum) and eggplant (Solanum melongena), primarily accumulate anthocyanins in the fruit peels, while the ripe fruits of Atropa belladonna (Ab) have a dark purple flesh due to anthocyanin accumulation. In this study, an R2R3-MYB transcription factor (TF), AbMYB1, was identified through association analysis of gene expression and anthocyanin accumulation in different tissues of A. belladonna. Its role in regulating anthocyanin biosynthesis was investigated through gene overexpression and RNA interference (RNAi). Overexpression of AbMYB1 significantly enhanced the expression of anthocyanin biosynthesis genes, such as AbF3H, AbF3'5'H, AbDFR, AbANS, and Ab3GT, leading to increased anthocyanin production. Conversely, RNAi-mediated suppression of AbMYB1 resulted in decreased expression of most anthocyanin biosynthesis genes, as well as reduced anthocyanin contents in A. belladonna. Overall, AbMYB1 was identified as a fruit-expressed R2R3-MYB TF that positively regulated anthocyanin biosynthesis in A. belladonna. This study provides valuable insights into the regulation of anthocyanin biosynthesis in Solanaceae plants, laying the foundation for understanding anthocyanin accumulation especially in the whole fruits of solanaceous plants.

Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny

Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.

Structural Characterization of the Acer ukurunduense Chloroplast Genome Relative to Related Species in the Acer Genus

Acer ukurunduense refers to a deciduous tree distributed in Northeast Asia and is a widely used landscaping tree species. Although several studies have been conducted on the species’ ecological and economic significance, limited information is available on its phylo-genomics. Our study newly constitutes the complete chloroplast genome of A. ukurunduense into a 156,645-bp circular DNA, which displayed a typical quadripartite structure. In addition, 133 genes were identified, containing 88 protein-coding genes, 37 tRNA genes, and eight rRNA genes. In total, 107 simple sequence repeats and 49 repetitive sequences were observed. Thirty-two codons indicated that biased usages were estimated across 20 protein-coding genes (CDS) in A. ukurunduense. Four hotspot regions (trnK-UUU/rps16, ndhF/rpl32, rpl32/trnL-UAG, and ycf1) were detected among the five analyzed Acer species. Those hotspot regions may be useful molecular markers and contribute to future population genetics studies. The phylogenetic analysis demonstrated that A. ukurunduense is most closely associated with the species of Sect. Palmata. A. ukurunduense and A. pubipetiolatum var. pingpienense diverged in 22.11 Mya. We selected one of the hypervariable regions (trnK-UUU/rps16) to develop a new molecular marker and designed primers and confirmed that the molecular markers could accurately discriminate five Acer species through Sanger sequencing. By sequencing the cp genome of A. ukurunduense and comparing it with the relative species of Acer, we can effectively address the phylogenetic problems of Acer at the species level and provide insights into future research on population genetics and genetic diversity.

Chloroplast Genomic Variation in Euonymus maackii Rupr. and Its Differentiation Time in Euonymus

Euonymus maackii Rupr. is a small deciduous tree belonging to family Celastraceae. It is an important ornamental tree and a potential medicinal plant resource. Here, we assembled and annotated the chloroplast (cp) genome of E. maackii. By combining this genome with seven available cp genomes from Euonymus species, we performed plastome variation analysis of E. maackii and Euonymus. Furthermore, we reconstructed a phylogenetic tree and estimated the differentiation time of E. maackii. The newly assembled cp genome of E. maackii was 157,551 bp in size and had a typical quadripartite structure, which consisted of one large single-copy (LSC 86,524 bp) region, one small single-copy (SSC 18,337 bp) region, and a pair of inverted repeat regions (26,345 bp). A total of 652 single nucleotide polymorphisms (SNPs) and 65 insertions/deletions (indels) were detected between the two cp genomes of E. maackii, with overall genetic variation of 4.1 SNPs per kb or a π value of 0.00443, reflecting a high level of intraspecific variation. Some coding and noncoding regions with higher variation were identified, including trnV-UAC, petN, ycf1-ndhF, trnM-CAU-atpE, rpl2-rpl23, psbZ-trnG-GCC, trnY-GUA-trnE-UUC, trnW-CCA-trnP-UGG, rps16-trnQ-UUG, and psbC-trnS-UGA. The hypervariable coding and noncoding regions in E. maackii were not the same as those in Euonymus. The phylogenetic tree and divergence time based on the whole cp genomes showed that the seven Euonymus species formed a clade, which was sister to that formed with Catha edulis and Maytenus guangxiensis, and they separated 24.74 million years ago. E. maackii and E. hamiltonianus were most closely related, having separated from each other only approximately 2.68 million years ago. Our study provides important genetic information for further studies of E. maackii, such as studies on its phylogeography, population genetics and molecular ecology, and provides new insights into the evolution of the cp genome in Euonymus.