The Maternal Donor of Chrysanthemum Cultivars Revealed by Comparative Analysis of the Chloroplast Genome

The chloroplast genome sequence and phylogenetic analysis of Rubia alata Wall and Rubia ovatifolia Z. Ying Zhang. (Rubiaceae)

BACKGROUND

Rubia alata Wall (R. alata) and Rubia ovatifolia Z. Ying Zhang (R. ovatifolia) are unique medicinal plants native to China. Sequencing their chloroplast genomes is important for understanding species differentiation and establishing phylogenetic relationships.

METHODS AND RESULTS

The chloroplast genomes of R. alata and R. ovatifolia were sequenced using the Illumina HiSeq platform. The chloroplast genome of R. alata is 154,973 base pairs (bp) in length, containing a large single-copy region (LSC) of 84,801 bp, a small single-copy region (SSC) of 17,138 bp, and a pair of inverted repeats (IRs) of the same length. The length of the chloroplast genome, LSC, SSC, and IR regions of R. ovatifolia is 26,517 bp, 84,716 bp, 17,116 bp and 26,517 bp, respectively. Codon usag e analysis revealed that R. alata had the highest frequency of Aspartic acid (Asp) (1650 occurrences) in protein-coding sequences (CDS), while R. ovatifolia showed the highest frequency of Tyrosine (Try) (1479 occurrences). Comparative analysis of chloroplast genomes across seven species from the genus Rubia identified the most divergent coding regions, including rps16, psbI-trns-CGA, and petN, while plastid rRNAs were the most conserved. Phylogenetic analysis showed R. alata clustering with R. cordifolia (66.3% support), and R. ovatifolia clustering with Rubia podantha (100% support).

CONCLUSIONS

These findings enhance our understanding of the chloroplast genome structure in Rubia species and provide molecular information for the future development and utilization of R. alata and R. ovatifolia resources.

Comparative and phylogenetic analysis of the chloroplast genomes of four commonly used medicinal cultivars of Chrysanthemums morifolium

'Boju' and 'Huaiju' are cultivars of the Chrysanthemum (Chrysanthemum morifolium Ramat.) in the family Asteraceae, valued for their medicinal, tea, and ornamental properties, and valued by individuals. However, the yield and quality of medicinal chrysanthemums are limited by the characteristics of the germplasm resources, including the identification at the varieties and cultivation levels. Currently, research characterizing the chloroplast genomes of medicinal Chrysanthemum flowers is relatively limited. This study conducted chloroplast whole-genome sequencing on two cultivars of Chrysanthemum, 'Boju' and 'Huaiju', and compared them with the previously published chloroplast genomes of 'Hangbaiju' and 'Gongju'. The study analyzed the chloroplast genome structures of these four medicinal Chrysanthemums, identifying mutation hotspots and clarifying their phylogenetic relationships. The chloroplast genome sizes of four medicinal Chrysanthemum cultivation products ranged from 151,057 to 151,109 bp, with GC content ranging from 37.45% to 37.76%. A total of 134 genes were identified, including 89 protein-coding genes, 37 ribosomal RNA genes, and 8 transfer RNA genes. Comparative genomic analysis revealed 159 large repeat sequences, 276 simple sequence repeats, 1 gene, and 8 intergenic regions identified as highly variable regions. Nucleotide diversity (Pi) values were high (≥ 0.004) for the petN-psbM, trnR-UCU-trnT-GGU, trnT-GGU-psbD, ndhC-trnV-UCA, ycf1, ndhI-ndhG, trnL-UGA-rpl32, rpl32-ndhF, and ndhF-ycf1 fragments, aiding in variety identification. Phylogenetic analysis revealed consistent results between maximum likelihood and Bayesian inference trees, showing that the four medicinal Chrysanthemum cultivars, along with their wild counterparts and related species, evolved as a monophyletic group, forming a sister clade to Artemisia and Ajania. Among the six Chrysanthemum species, the wild Chrysanthemum diverged first (Posterior probability = 1, bootstrap = 1,000), followed by Ajania, while C. indicum and C. morifolium clustered together (Bootstrap = 100), indicating their closest genetic relationship. The chloroplast whole-genome data and characteristic information provided in this study can be used for variety identification, genetic conservation, and phylogenetic analysis within the family Asteraceae.

High-Quality Assembly and Analysis of the Complete Mitogenomes of German Chamomile (Matricaria recutita) and Roman Chamomile (Chamaemelum nobile)

German chamomile (Matricaria chamomilla L.) and Roman chamomile (Chamaemelum nobile) are the two well-known chamomile species from the Asteraceae family. Owing to their essential oils and higher medicinal value, these have been cultivated widely across Europe, Northwest Asia, North America, and Africa. Regarding medicinal applications, German chamomile is the most commonly utilized variety and is frequently recognized as the "star among medicinal species". The insufficient availability of genomic resources may negatively impact the progression of chamomile industrialization. Chamomile's mitochondrial genome is lacking in extensive empirical research. In this study, we achieved the successful sequencing and assembly of the complete mitochondrial genome of M. chamomilla and C. nobile for the first time. An analysis was conducted on codon usage, sequence repeats within the mitochondrial genome of M. chamomilla and C. nobile. The phylogenetic analysis revealed a consistent positioning of M. chamomilla and C. nobile branches within both mitochondrial and plastid-sequence-based phylogenetic trees. Furthermore, the phylogenetic analysis also showed a close relationship between M. chamomilla and C. nobile within the clade comprising species from the Asteraceae family. The results of our analyses provide valuable resources for evolutionary research and molecular barcoding in chamomile.

Evaluation of Five Chrysanthemum morifolium Cultivars against Leaf Blight Disease Caused by Alternaria alternata at Rooting and Seedling Growth Stages

During the winter of 2018, leaf blight on florist's daisy (Chrysanthemum morifolium L.) was noticed in Egypt. The disease, which was identified as caused by Alternaria alternata, was widely spread and led to serious damage for the exportation sector of this crop. Therefore, a study was conducted to better understand what can be conducted to minimize the problem in the future. Isolates were gathered and evaluated on five chrysanthemum cultivars (i.e., 'Feeling Green Dark', 'Talitha', 'Chrystal Regan', 'Arctic queen', and 'Podolsk Purple') grown in a greenhouse. The objectives were to isolate and identify the phytopathogen and detect the resistant degree of these cultivars with emphasis on the early growth stages of the crop. The results showed that 'Podolsk Purple' was the most resistant cultivar against the different isolates during the rooting and seedling growth stages. 'Chrystal Regan' was very susceptible to the different isolates. In addition, the isolate from 'Feeling Green Dark' was the strongest, which negatively affected the chlorophyll content and its fluorescence parameters besides other measured vegetative and anatomical features. The findings indicated that the best anatomical characters of the stem and leaf, like the thickness of cuticle and cortex, stem diameter, xylem vessel diameter, and thickness of epidermis as well as lamina thickness were recorded in the 'Podolsk Purple' cultivar. This study highlighted that by using the right cultivars, chrysanthemum can be cultivated during the winter season under Egyptian conditions. These results can be a part of solution to overcome the leaf blight caused by A. alternata on chrysanthemum during the early growing stages.

Pueraria montana Population Structure and Genetic Diversity Based on Chloroplast Genome Data

Despite having a generally conserved structure, chloroplast genome data have been helpful for plant population genetics and evolution research. To mine Pueraria montana chloroplast genome variation architecture and phylogeny, we investigated the chloroplast variation architecture of 104 P. montana accessions from across China. P. montana's chloroplast genome showed high diversity levels, with 1674 variations, including 1118 single nucleotide polymorphisms and 556 indels. The intergenic spacers, psbZ-trnS and ccsA-ndhD, are the two mutation hotspot regions in the P. montana chloroplast genome. Phylogenetic analysis based on the chloroplast genome dataset supported four P. montana clades. P. montana variations were conserved among and within clades, which showed high gene flow levels. Most P. montana clades were estimated to have diverged at 3.82-5.17 million years ago. Moreover, the East Asian summer monsoon and South Asian summer monsoon may have accelerated population divergence. Our results show that chloroplast genome sequences were highly variable and can be used as molecular markers to assess genetic variation and relationships in P. montana.

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

Lagerstroemia indica L. is a well-known ornamental plant with large pyramidal racemes, long flower duration, and diverse colors and cultivars. It has been cultivated for nearly 1600 years and is essential for investigating the germplasm and assessing genetic variation to support international cultivar identification and breeding programs. In this study, 20 common Lagerstroemia indica cultivars from different varietal groups and flower morphologies, as well as multiple wild relative species, were analyzed to investigate the maternal donor of Lagerstroemia indica cultivars and to discover the genetic variation and relationships among cultivars based on plastome and nuclear ribosomal DNA (nrDNA) sequences. A total of 47 single nucleotide polymorphisms (SNPs) and 24 insertion/deletions (indels) were identified in the 20 L. indica cultivars' plastome and 25 SNPs were identified in the nrDNA. Phylogenetic analysis based on the plastome sequences showed that all the cultivars formed a clade with the species of L. indica, indicating that L. indica was the maternal donor of the cultivars. Population structure and PCA analyses supported two clades of cultivars, which exhibited significant genetic differences according to the plastome dataset. The results of the nrDNA supported that all 20 cultivars were divided into three clades and most of the cultivars had at least two genetic backgrounds and higher gene flow. Our results suggest that the plastome and nrDNA sequences can be used as molecular markers for assessing the genetic variation and relationships of L. indica cultivars.

Complete Chloroplast Genome Sequence of the Long Blooming Cultivar Camellia 'Xiari Qixin': Genome Features, Comparative and Phylogenetic Analysis

The camellia flower is a famous woody plant with a long-cultivated history and high ornamental value. It is extensively planted and utilized around the world and owns a massive germplasm resource. Camellia 'Xiari Qixin' belongs to one of the typical cultivars in the four seasons camellia hybrids series. Due to its long flowering period, this kind of cultivar is identified as a precious resource of camellia flowers. In this study, the complete chloroplast genome sequence of C. 'Xiari Qixin' was first reported. Its whole chloroplast genome is 157,039 bp in length with an overall GC content of 37.30%, composed of a large single copy region (LSC, 86,674 bp), a small single copy region (SSC, 18,281 bp), and a pair of inverted repeat regions (IRs, 26,042 bp each). A total of 134 genes were predicted in this genome, including 8 ribosomal RNA genes, 37 transfer RNA genes, and 89 protein-coding genes. In addition, 50 simple sequence repeats (SSRs) and 36 long repeat sequences were detected. By comparing C. 'Xiari Qixin' and seven Camellia species on the chloroplast genome, seven mutation hotspot regions were identified, including psbK, trnS (GCU)-trnG(GCC), trnG(GCC), petN-psbM, trnF(GAA)-ndhJ, trnP(UGG)-psaJ, and ycf1. Phylogenetic analysis of 30 chloroplast genomes showed that the genetic relationship between C. 'Xiari Qixin' and Camellia azalea is quite close in evolution. These results could not only provide a valuable database for determining the maternal origin of Camellia cultivars, but also contribute to the exploration of the phylogenetic relationship and utilization of germplasm resources for Camellia.

Evaluation of Chrysanthemi Indici Flos germplasms based on nine bioactive constituents and color parameters

Chrysanthemi Indici Flos (CIF) is the inflorescence of Chrysanthemum indicum L., which exists in various shades of yellow and has pharmacologically active constituents. It is widely used for medicinal purposes in China, Japan, and South Korea to treat inflammatory diseases. Its external color is usually used to judge its internal quality in trade; however, the correlation between its color and chemical constituents is unknown. Here, we simultaneously determined five phenylpropanoids (neochlorogenic acid, chlorogenic acid, and isochlorogenic acids A, B, and C) and four flavonoids (linarin, luteolin, apigenin, and acacetin) of 70 CIF germplasms using a newly established UPLC method; furthermore, we measured their color parameters (L*, a*, and b*) using a spectrophotometer. Our results showed considerable variations in the bioactive constituent contents and color parameters of CIF. The content of the five phenylpropanoids and the relative correlation degree γi of the nine constituents were positively correlated with color parameters, which could be rapidly predicted based on L* and/or b*. Moreover, we screened out a high-quality germplasm with a high linarin content and bright colors using the hierarchical clustering method. Our results provide comprehensive insight into CIF's quality evaluation process, particularly the methods for procuring high-quality medicinal materials and breeding by color.

Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae

Argyranthemum frutescens, which belongs to the Anthemideae (Asteraceae), is widely cultivated as an ornamental plant. In this study, the complete chloroplast genome of A. frutescens was obtained based on the sequences generated by Illumina HiSeq. The chloroplast genome of A. frutescens was 149,626 base pairs (bp) in length, containing a pair of inverted repeats (IR, 24,510 bp) regions separated by a small single-copy (SSC, 18,352 bp) sequence and a large single-copy (LSC, 82,254 bp) sequence. The genome contained 132 genes, consisting of 85 coding DNA sequences, 37 tRNA genes, and 8 rRNA genes, with nineteen genes duplicated in the IR region. A comparison chloroplast genome analysis among ten species from the tribe of Anthemideae revealed that the chloroplast genome size varied, but the genome structure, gene content, and oligonucleotide repeats were highly conserved. Highly divergent regions, e.g., ycf1, trnK-psbK, petN-psbM intronic, were detected. Phylogenetic analysis supported Argyranthemum as a separate genus. The findings of this study will be helpful in the exploration of the phylogenetic relationships of the tribe of Anthemideae and contribute to the breeding improvement of A. frutescens.