Chloroplast (Cp) Transcriptome of P. davidiana Dode×P. bolleana Lauch provides insight into the Cp drought response and Populus Cp phylogeny

Comparative and Phylogenetic Analysis of the Chloroplast Genomes of Four Wild Species of the Genus Prunus

BACKGROUND

Prunus armeniaca, Prunus divaricata, Prunus tianshanica, and Prunus domestica are valuable ancient tree species that have persisted since the end of the Tertiary period within the Tianshan wild fruit forest. However, the evolutionary relationships among Prunus species in the Tianshan wild fruit forest have long posed a challenge.

METHODS

We sequenced and assembled the chloroplast genomes of P. armeniaca, P. divaricata, and P. tianshanica, and incorporated the chloroplast genome data of P. domestica for comparative analysis to elucidate their phylogenetic positions within the genus Prunus.

RESULTS

The lengths of these chloroplast genomes ranged from 157,395 bp to 158,090 bp, with a total of 130 to 131 genes annotated, comprising 85 to 86 protein-coding genes, 8 rRNA genes, and 35 to 36 tRNA genes. Notably, the four wild Prunus species predominantly used high-frequency codons ending in A/U. Additionally, we identified 300 simple repetitive sequences and 166 long repetitive sequences across the four wild Prunus species. The mutation sites were mainly found in the non-coding regions, with seven regions of high mutation frequency identified. The phylogenetic tree revealed five branches: subgenus Armeniaca, subgenus Microcerasus, subgenus Prunus, subgenus Amygdalus, and subgenus Cerasus. The estimated deviation time for the crown group of Prunus is roughly 61.41 million years ago.

CONCLUSIONS

This study provides exhaustive genetic evidence for the classification and systematic relationships of the four wild Prunus species and establishes a crucial foundation for subsequent research into the diversity and evolutionary history of the Prunus genus.

Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae.

Comprehensive analysis of the first complete mitogenome and plastome of a traditional Chinese medicine Viola diffusa

BACKGROUND

Viola diffusa is used in the formulation of various Traditional Chinese Medicines (TCMs), including antiviral, antimicrobial, antitussive, and anti-inflammatory drugs, due to its richness in flavonoids and triterpenoids. The biosynthesis of these compounds is largely mediated by cytochrome P450 enzymes, which are primarily located in the membranes of mitochondria and the endoplasmic reticulum.

RESULTS

This study presents the complete assembly of the mitogenome and plastome of Viola diffusa. The circular mitogenome spans 474,721 bp with a GC content of 44.17% and encodes 36 unique protein-coding genes, 21 tRNA, and 3 rRNA. Except for the RSCU values of 1 observed for the start codon (AUG) and tryptophan (UGG), the mitochondrial protein-coding genes exhibited a codon usage bias, with most estimates deviating from 1, similar to patterns observed in closely related species. Analysis of repetitive sequences in the mitogenome demonstrated potential homologous recombination mediated by these repeats. Sequence transfer analysis revealed 24 homologous sequences shared between the mitogenome and plastome, including nine full-length genes. Collinearity was observed among Viola diffusa species within the other members of Malpighiales order, indicated by the presence of homologous fragments. The length and arrangement of collinear blocks varied, and the mitogenome exhibited a high frequency of gene rearrangement.

CONCLUSIONS

We present the first complete assembly of the mitogenome and plastome of Viola diffusa, highlighting its implications for pharmacological, evolutionary, and taxonomic studies. Our research underscores the multifaceted importance of comprehensive mitogenome analysis.

Tree species and drought: Two mysterious long-standing counterparts

Around 252 million years ago (Late Permian), Earth experienced one of its most significant drought periods, coinciding with a global climate crisis, resulting in a devastating loss of forest trees with no hope of recovery. In the current epoch (Anthropocene), the worsening of drought stress is expected to significantly affect forest communities. Despite extensive efforts, there is significantly less research at the molecular level on forest trees than on annual crop species. Would it not be wise to allocate equal efforts to woody species, regardless of their importance in providing essential furniture and sustaining most terrestrial ecosystems? For instance, the poplar genome is roughly quadruple the size of the Arabidopsis genome and has 1.6 times the number of genes. Thus, a massive effort in genomic studies focusing on forest trees has become inevitable to understand their adaptation to harsh conditions. Nevertheless, with the emerging role and development of high-throughput DNA sequencing systems, there is a growing body of literature about the responses of trees under drought at the molecular and eco-physiological levels. Therefore, synthesizing these findings through contextualizing drought history and concepts is essential to understanding how woody species adapt to water-limited conditions. Comprehensive genomic research on trees is critical for preserving biodiversity and ecosystem function. Integrating molecular insights with eco-physiological analysis will enhance forest management under climate change.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Function of MYB8 in larch under PEG simulated drought stress

Larch, a prominent afforestation, and timber species in northeastern China, faces growth limitations due to drought. To further investigate the mechanism of larch's drought resistance, we conducted full-length sequencing on embryonic callus subjected to PEG-simulated drought stress. The sequencing results revealed that the differentially expressed genes (DEGs) primarily played roles in cellular activities and cell components, with molecular functions such as binding, catalytic activity, and transport activity. Furthermore, the DEGs showed significant enrichment in pathways related to protein processing, starch and sucrose metabolism, benzose-glucuronic acid interconversion, phenylpropyl biology, flavonoid biosynthesis, as well as nitrogen metabolism and alanine, aspartic acid, and glutamic acid metabolism. Consequently, the transcription factor T_transcript_77027, which is involved in multiple pathways, was selected as a candidate gene for subsequent drought stress resistance tests. Under PEG-simulated drought stress, the LoMYB8 gene was induced and showed significantly upregulated expression compared to the control. Physiological indices demonstrated an improved drought resistance in the transgenic plants. After 48 h of PEG stress, the transcriptome sequencing results of the transiently transformed LoMYB8 plants and control plants exhibited that genes were significantly enriched in biological process, cellular component and molecular function. Function analyses indicated for the enrichment of multiple KEGG pathways, including energy synthesis, metabolic pathways, antioxidant pathways, and other relevant processes. The pathways annotated by the differential metabolites mainly encompassed signal transduction, carbohydrate metabolism, amino acid metabolism, and flavonoid metabolism.

Phylogenetics Study to Compare Chloroplast Genomes in Four Magnoliaceae Species

Magnoliaceae, a family of perennial woody plants, contains several endangered species whose taxonomic status remains ambiguous. The study of chloroplast genome information can help in the protection of Magnoliaceae plants and confirmation of their phylogenetic relationships. In this study, the chloroplast genomes were sequenced, assembled, and annotated in Woonyoungia septentrionalis and three Michelia species (Michelia champaca, Michelia figo, and Michelia macclurei). Comparative analyses of genomic characteristics, repetitive sequences, and sequence differences were performed among the four Magnoliaceae plants, and phylogenetic relationships were constructed with twenty different magnolia species. The length of the chloroplast genomes varied among the four studied species ranging from 159,838 bp (Woonyoungia septentrionalis) to 160,127 bp (Michelia macclurei). Four distinct hotspot regions were identified based on nucleotide polymorphism analysis. They were petA-psbJ, psbJ-psbE, ndhD-ndhE, and rps15-ycf1. These gene fragments may be developed and utilized as new molecular marker primers. By using Liriodendron tulipifera and Liriodendron chinense as outgroups reference, a phylogenetic tree of the four Magnoliaceae species and eighteen other Magnoliaceae species was constructed with the method of Shared Coding Sequences (CDS). Results showed that the endangered species, W. septentrionalis, is relatively genetically distinct from the other three species, indicating the different phylogenetic processes among Magnoliaceae plants. Therefore, further genetic information is required to determine the relationships within Magnoliaceae. Overall, complete chloroplast genome sequences for four Magnoliaceae species reported in this paper have shed more light on phylogenetic relationships within the botanical group.

Comparative Analysis of the Chloroplast Genome of Sicyos angulatus with Other Seven Species of Cucurbitaceae Family

Sicyos angulatus (SA) is an annual plant from the Cucurbitaceae family that is native to the eastern part of North America. This study aims to assemble and annotate the chloroplast genome of S. angulatus, and then compare it with plastomes of the other species representing the Cucurbitaceae family. The chloroplast genome size of S. angulatus is 154,986 bp, including a pair of inverted repeats (IR) of 26,276 bp, and small single-copy region (SSC) of 18,079 bp and large single-copy region (LSC) of 84,355 bp. Compared to other Cucurbitaceae species, the chloroplast genome of S. angulatus is almost 4222 bp smaller than the plastome Gynostemma pentaphyllum. All other seven species have an identical set of tRNA (37), except Citrullus laevigata, which contains 36 tRNA. The IRa/LSC junction in all eight species is located upstream of rpl2 and downstream of trnH gene. Moreover, variation in the size of the gene and the presence of pseudogene ycf1 has been seen because of the IR contraction and expansion. The highest number of tandem repeats was seen in G. pentaphyllum, and then Corynocarpus leavigata. The sequence divergence analysis and topology of the phylogenetic tree indicate that S. angulatus is more similar to genus Citrullus as compared to genus Gynostemma. These findings contribute to developing the genomic marker for the purpose of future genetic studies.

Complete Chloroplast Genome of Gladiolus gandavensis (Gladiolus) and Genetic Evolutionary Analysis

Gladiolus is an important ornamental plant that is one of the world's four most-grown cut flowers. Gladiolus gandavensis has only been found in the Cangnan County (Zhejiang Province) of China, which is recorded in the "Botanical". To explore the origin of G. gandavensis, chloroplast genome sequencing was conducted. The results indicated that a total of 151,654 bp of circular DNA was obtained. The chloroplast genome of G. gandavensis has a quadripartite structure (contains a large single-copy (LSC) region (81,547 bp), a small single-copy region (SSC) (17,895 bp), and two inverted repeats (IRs) (IRa and IRb, 52,212 bp)), similar to that of other species. In addition, a total of 84 protein-coding genes, 8 rRNA-encoding genes, and 38 tRNA-encoding genes were present in the chloroplast genome. To further study the structural characteristics of the chloroplast genome in G. gandavensis, a comparative analysis of eight species of the Iridaceae family was conducted, and the results revealed higher similarity in the IR regions than in the LSC and SSC regions. In addition, 265 simple sequence repeats (SSRs) were detected in this study. The results of the phylogenetic analysis indicated that the chloroplast genome of G. gandavensis has high homology with the Crocus cartwrightianus and Crocus sativus chloroplast genomes. Genetic analysis based on the rbcl sequence among 49 Gladiolus species showed that samples 42, 49, 50, and 54 had high homology with the three samples from China (64, 65, and 66), which might be caused by chance similarity in genotypes. These results suggest that G. gandavensis may have originated from South Africa.

Comparative Analyses of Six Complete Chloroplast Genomes from the Genus Cupressus and Juniperus (Cupressaceae)

Cupressaceae is a conifer family distributed around the world. Cupressus and Juniperus are the main genera of the Cupressaceae family and have important medicinal value. This leads to confusion between Cupressus and Juniperus due to similar morphologies. Here, the complete cp genomes of two Cupressus (C. duclouxiana and C. funebri) and four Juniperus (J. chinensis, J. gaussenii J. pingii and J. procumbens) were sequenced. The results revealed that the length of the cp genomes ranged from 126,996 bp to 129,959 bp, with 119 genes comprising 82 protein-coding genes, 33 transfer RNAs and 4 ribosomal RNAs. All chloroplast genomes of Cupressus and Juniperus lost whole IR regions, which is consistent with gymnosperm cp genome studies. In addition, the number of SSRs per species ranged from 54 to 73 and was dominated by mononucleotide repeats. In the six cp genomes of Cupressus and Juniperus, five highly divergent regions, including accD, accD-rpl2, ycf1, ycf2 and rrn23-rrn4.5, can be used as DNA barcodes of interspecific relationships and potential genetic markers. We compared the gene selection pressures (C. chengiana as reference species), and 6 genes underwent positive selection, the majority of which were related to photosynthesis. Phylogenetic results showed that the monophyly of Cupressus and Juniperus supported most bootstrap support. Cupressus funebris and J. chinensis were resolved to be early diverging species within Cupressus and Juniperus, and the two genera were sister groups to each other. This research revealed a new understanding of the structural pluralism and phylogenetic relationships of Cupressaceae cp genomes. These results will facilitate comprehension of the complexity and diversity of conifer cp genomes. SIGNIFICANCE:: Phylogenetic relationships among Cupressus, Juniperus, and their closest relatives are controversial, and generic delimitations have been in flux for the past decade. To address relationships and attempt to produce a more robust classification, we sequenced 6 new plastid genomes (plastomes) from the two variously described genera in this complex (Cupressus and Juniperus) and compared them with additional plastomes from diverse members of Cupressaceae. Our study corroborated the accD of Cupressophytes have a tendency to expand in size and strongly supported a sister relationship between Cupressus and Juniperus. The disparity in these results could be traced to the facts that the chloroplast genome is uniparentally inherited, also the usage of the whole chloroplast genome for this research is of a better advantage compared to usage of selected genes or portion of the plastome. The complete CP genomic data will provide useful information for studying genetic diversity and species identification, which is important for the overarching goal of biodiversity conservation.

Research progress on the response of tea catechins to drought stress

Drought stress (DS) is the most important abiotic stress affecting yield and quality of tea worldwide. DS causes oxidative stress to cells due to the accumulation of reactive oxygen species (ROS). As non-enzymatic antioxidants, tea catechins can scavenge excess ROS in response to DS. Further, catechin accumulation contributes to the formation of oxidative polymerization products (e.g. theaflavins and thearubigins) that improve the quality of black tea. However, there are no systematic reports on the response of tea catechins to DS. First, we reviewed the available literature on the response of tea plants to DS. Second, we summarized the current knowledge of ROS production in tea leaves under DS and typical antioxidant response mechanisms. Third, we conducted a detailed review of the changes in catechin levels in tea under different drought conditions. We found that the total amounts of catechin and o-quinone increased under DS conditions. We propose that the possible mechanisms underlying tea catechin accumulation under DS conditions include (i) autotrophic formation of o-quinone, (ii) polymerization of proanthocyanidins that directly scavenge excess ROS, and (iii) formation of metal ion complexes and by influencing the antioxidant systems that indirectly eliminate excess ROS. Finally, we discuss ways of potentially improving black tea quality using drought before picking in the summer/fall dry season. In summary, we mainly discuss the antioxidant mechanisms of tea catechins under DS and the possibility of using drought to improve black tea quality. Our review provides a theoretical basis for the production of high-quality black tea under DS conditions. © 2021 Society of Chemical Industry.