Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny

Expression of endochitinase and exochitinase in lettuce chloroplasts increases plant biomass and kills fungal pathogen Candida albicans

Lettuce (Lactuca sativa) is a popular leafy vegetable with global production of ~28 million Mt, cultivated >1 million hectares, with a market value of US$ 4 billion in 2022. However, lettuce is highly susceptible to fungal pathogens that drastically reduce biomass and quality due to spoilage/rot. Therefore, in this study, we investigated the expression of chitinase genes via the lettuce chloroplast genome to enhance biomass and disease resistance. Site-specific integration of the expression cassette into chloroplast genomes was confirmed using two sets of PCR primers. Homoplasmy in transplastomic lines was confirmed in Southern blots by the absence of untransformed genomes. Maternal inheritance of transgenes was confirmed by the lack of segregation when seedlings were germinated in the selection medium. Chitinases expressed in chloroplasts are active in a broad range of pH (5-9) and temperatures (20-50 °C). Exochitinase expression significantly increased the number of leaves, root or shoot length and biomass throughout the growth cycle. Endochitinase expression reduced root/shoot biomass at early stages but recovered in older plants. Plant extracts expressing endochitinase/exochitinase showed activities as high as purified commercial enzymes. Antifungal activity in Candida albicans cultures inhibited growth up to 87%. A novel Carbotrace 680™ Optotracer binding to the ß-1,4 linkages of chitin, evaluated for the first time in plant systems, is highly sensitive to measure chitinase activity. To the best of our knowledge, this is the first report of chitinase expression via the chloroplast genomes of an edible plant, to confer desired agronomic traits or for biomedical applications.

Comparative plastome analyses and phylogenetic insights of Elatostema

BACKGROUND

Elatostema, one of the largest genera in Urticaceae, comprises approximately 570 species. The taxonomic delimitation of Elatostema and its closely related genera, Elatostematoides and Procris and the infrageneric classification of Elatostema, have historically been challenging. Previous studies have been limited by insufficient molecular data, hindering our understanding of species-level relationships and the evolution of plastid genomes in this group. To address these limitations, we assembled and analyzed a comprehensive plastome analysis of 42 species across Elatostema and its allied genera. Our study focused on plastome structure, sequence diversity, and phylogenetic relationships to elucidate the evolutionary history of these taxa.

RESULTS

Our findings reveal that Elatostema plastomes exhibit a typical quadripartite structure, with genome sizes ranging from 149,152 bp to 164,019 bp. Comparative analysis of plastome structures across Elatostema and its related genera indicates high conservation in genome size, structure, gene content, and inverted repeat boundary configuration. Our findings indicate a strong association between the length of small single-copy (SSC) regions and phylogenetic grouping within Elatostema and between Elatostema, Elatostematoides and Procris. The length variations in the ndhF-rpl32, rpl32-trnL, and rps15-SSC/IRa regions may account for this observed correlation, highlighting the utility of SSC sequences in resolving phylogenetic relationships within this genus. Furthermore, we identified seven highly variable regions with potential as DNA barcodes for species identification and phylogenetic analysis. Our phylogenomic analysis provides robust support for the taxonomic delimitation of Elatostema s.l. into three distinct genera: Elatostema, Procris, and Elatostematoides. We also reconfirm the infrageneric classification of Elatostema into four major clades.

CONCLUSIONS

The utilization of plastome sequences has enabled a highly resolved phylogenetic framework, shedding light on the evolutionary history and speciation mechanism within Elatostema, particularly its species-rich core Elatostema clade. These findings provide a valuable foundation for future taxonomic revisions and evolutionary studies within this challenging plant group.

Phylogeny and evolutionary dynamics of the Rubia genus based on the chloroplast genome of Rubia tibetica

Rubia tibetica, a well-known medicinal plant, holds significant medicinal value. In this study, we sequenced and assembled the complete chloroplast genome of R. tibetica and conducted comparative analyses with four other Rubia species to provide insights into genome structure, selective pressure, and phylogenetic relationships. The chloroplast genome of R. tibetica was 154,901 bp in length and exhibited a typical quadripartite circular structure. Comparative analysis revealed a highly conserved genome structure among Rubia species, with genome sizes ranging from 153,555 bp to 155,108 bp and a GC content of approximately 37%. Codon usage analysis indicated a preference for A/U-ending codons. Selective pressure analysis identified relaxed selection in genes such as rps15 and petA, suggesting species-specific adaptive strategies. Two hypervariable regions, rps16-trnQ and psaJ-rps18, were experimentally validated as potential molecular markers through PCR amplification and sequencing. However, sequencing results of the rps16-trnQ region differed from the reference chloroplast genome, requiring further investigation. Phylogenetic analysis was performed using maximum likelihood (ML) based on the complete chloroplast genome sequences of five Rubia species and confirmed the monophyly of the Rubia genus, with R. tibetica occupying a basal position. This suggesting the retention of ancestral traits and adaptation to the unique environment of the Qinghai-Tibet Plateau. Molecular dating analysis further revealed divergence times consistent with geological and climatic events in the region. These findings provide critical insights into the evolutionary dynamics of Rubia species and offer valuable resources for their classification, conservation, and medicinal application.

Synthetic and Biogenic Materials for Oral Delivery of Biologics: From Bench to Bedside

The development of nucleic acid and protein drugs for oral delivery has lagged behind their production for conventional nonoral routes. Over the past decade, the evolution of DNA- and RNA-based technologies combined with the innovation of state-of-the-art delivery vehicles for nucleic acids has brought rapid advancements to the biopharmaceutical field. Nucleic acid therapies have the potential to achieve long-lasting effects, or even cures, by inhibiting or editing genes, which is not possible with conventional small-molecule drugs. However, challenges and limitations must be addressed before these therapies can provide cures for chronic conditions and rare diseases, rather than only offering temporary relief. Nucleic acids and proteins face premature degradation in the acidic, enzyme-rich stomach environment and are rapidly cleared by the liver. To overcome these challenges, various delivery vehicles have been developed to transport therapeutic compounds to the intestines, where the active compounds are released and gut microbiota and mucosal immune system also play an important role. This review provides a comprehensive overview of the promises and pitfalls associated with the oral route of administration of biologics, current delivery systems, applications of orally delivered therapeutics, and the challenges and considerations for translation of nucleic acid and protein therapeutics into clinical practice.

The complete chloroplast genome sequences of three Cypripedium species and their phylogenetic analysis

Cypripedium macranthos Swartz, C. × ventricosum Swartz, and C. shanxiense S. C. Chen were highly promising ornamental plants. In this study, the latest complete chloroplast genome sequence of C. macranthos, C. × ventricosum, and C. shanxiense were reported using correct sample material from their native range, and their phylogenetic relationships with other related species were investigated preliminarily. The whole chloroplast genome lengths of C. macranthos, C. × ventricosum, and C. shanxiense were 181,030 bp, 175,385 bp, and 177,627 bp, respectively, with total GC contents of 34.56%, 34.48%, and 34.42%, respectively. Based on the maximum likelihood phylogenetic tree from the chloroplast genome sequences and internal transcribed spacer (ITS) sequences, it was confirmed that C. × ventricosum is most closely related to C. calceolus, and the idea that C. × ventricosum is an interspecific hybrid between C. calceolus and C. macranthos is supported. By integrating the results of phylogenetic analysis, genomic structural comparison, and considerations of sampling locations, it is evident that the former chloroplast genome of C. macranthos is inaccurate. This study provides crucial information for research on the phylogeny, genetics, and conservation of C. macranthos, C. × ventricosum, and C. shanxiense.

Clinical studies in Myxomatous Mitral Valve Disease dogs: most prescribed ACEI inhibits ACE2 enzyme activity and ARB increases AngII pool in plasma

The hypertension patient population has doubled since 1990, affecting 1.3 billion globally and >75% live in low-and middle-income countries. Angiotensin Converting Enzyme Inhibitors (ACEI) and Angiotensin Receptor Blockers (ARB) are the most prescribed drugs (>160 million times in the US), but mortality increased >30% since 1990s globally. Clinical relevance of Myxomatous Mitral Valve Disease (MMVD) is directly linked to WHO group 2 pulmonary hypertension, with no disease specific therapies. Therefore, MMVD pet dogs with elevated systolic blood pressure treated with ACEI/ARB, were supplemented with oral ACE2 enzyme and Angiotensin1-7 (Ang1-7) bioencapsulated in plant cells. The oral ACE2/Ang1-7 was well tolerated by healthy and MMVD dogs with no adverse events and increased sACE2 activity by 670-755% with ARB (Telmisartan) than with ACEI (Enalapril) background therapy. In vitro rhACE2 activity was inhibited >90% by ACEIs enalapril/benazeprilat at higher doses but lisinopril inhibited at much lower doses. Membrane ACE2 activity evaluated in exosomes was 43-fold higher than the sACE2 and this was also inhibited 211% by ACEI, when compared to ARB. Background ACEI treatment reduced the Ang-II pool by 11-20-fold and proportionately decreased the abundance of Ang1-7 + Ang1-5 peptides. In contrast, ARB treatment increased Ang-II pool 11-20-fold and Ang1-7 + Ang1-5 by 160-260%. Systolic blood pressure was regulated by ARB better than ACEI, despite very high Ang-II levels. This first report on evaluation of metabolic pools in the RAS pathway identifies surprising interactions between ACEI/ARB/ACE2 and significant changes in key molecular dynamics. Affordable biologics developed in plant cells may offer potential new treatment options for hypertension.

The complete chloroplast genome of Gerbera piloselloides (L.) Cass., 1820 (Carduoideae, Asteraceae) and its phylogenetic analysis

Gerbera piloselloides (L.) Cass., 1820 of the genus Gerbera is of importance in Chinese ethnic medicine. In this research, the whole genome DNA of G. piloselloides was extracted and sequenced using the Illumina NovaSeq platform, its chloroplast genome was assembled and annotated, and its sequence characteristics were analyzed using bioinformatic methods. The results showed that its chloroplast genome has a length of 151,871 bp and contains 133 annotated genes, consisting of 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. In total, 202 simple sequence repeat sites and 43 long repeats were detected in G. piloselloides, mainly consisting of mono-nucleotide and tri-nucleotide repeats, with A/T as the major base composition. The chloroplast genome of G. piloselloides contains 22,772 codons, with leucine-coding codons being the most abundant. Comparative genomics showed that the genome structure, composition and variation were basically the same in the Asteraceae family. The phylogenetic tree analysis indicated a close relationship between the genus Atractylodes and Gerbera, consistent with the morphological classification. The research of the G. piloselloides chloroplast genome will lay a foundation for species discrimination, genetic evolution analysis, and DNA barcode construction in Gerbera plants.

Chloroplast Functionality at the Interface of Growth, Defense, and Genetic Innovation: A Multi-Omics and Technological Perspective

Chloroplasts are important in plant growth, development, and defense mechanisms, making them central to addressing global agricultural challenges. This review explores the multi-faceted contributions of chloroplasts, including photosynthesis, hormone biosynthesis, and stress signaling, which orchestrate the trade-off between growth and defense. Advancements in chloroplast genomics, transcription, translation, and proteomics have deepened our understanding of their regulatory functions and interactions with nuclear-encoded proteins. Case studies have demonstrated the potential of chloroplast-targeted strategies, such as the expression of elongation factor EF-2 for heat tolerance and flavodiiron proteins for drought resilience, to enhance crop productivity and stress adaptation. Future research directions should focus on the need for integrating omics data with nanotechnology and synthetic biology to develop sustainable and resilient agricultural systems. This review uniquely integrates recent advancements in chloroplast genomics, transcriptional regulation, and synthetic biology to present a holistic perspective on optimizing plant growth and stress tolerance. We emphasize the role of chloroplast-driven trade-off in balancing growth and immunity, leveraging omics technologies and emerging biotechnological innovations. This comprehensive approach offers new insights into sustainable agricultural practices, making it a significant contribution to the field.

A phoenix in the greenhouse: characterization and phylogenomics of complete chloroplast genomes sheds light on the putatively extinct-in-the-wild Solanum ensifolium (Solanaceae)

BACKGROUND

The genus Solanum is a diverse group of flowering plants with significant economic importance. Within this genus, the subgenus Leptostemonum, comprising spiny solanums, is particularly noteworthy due to its high species diversity and endemism. Solanum ensifolium, a member of this subgenus, is a critically endangered species endemic to Puerto Rico and known locally as erubia. The species survives in greenhouses and botanical gardens and is thought to be extinct in the wild, but with reintroduction efforts in progress. Despite its conservation status, genomic data for S. ensifolium remains scarce, limiting our understanding of its evolutionary history and potential adaptations.

RESULTS

The S. ensifolium chloroplast genome (155,295 bp) exhibits a typical quadripartite structure and encodes 151 genes, including 95 protein-coding genes involved in photosynthesis, transcription, translation, and other essential cellular functions. Gene content and genome organization are similar to those observed in closely related Solanum species. Comparative genomic analysis of the annotated genome with that of closely related Solanum species revealed differences in nucleotide diversity between the large single-copy (LSC) and small single-copy regions (SSC), and the inverted repeat (IR) regions. Additionally, phylogenetic analyses confirmed placement of S. ensifolium within the Leptostemonum subgenus, affirming its suspected close relationship with S. crotonoides and S. aturense. Furthermore, of the three individuals of S. ensifolium for which chloroplast genomes were obtained, no genetic variation was observed.

CONCLUSIONS

The availability of the S. ensifolium chloroplast genome provides insights into its evolutionary history and conservation needs. Comparative genomics uncovered evolutionary differences in Solanum chloroplast genomes, including nucleotide diversity and structural variations. Phylogenetic analyses confirmed the close relationship between S. ensifolium and other Leptostemonum species. These findings enhance our understanding of this critically endangered species' evolution, guiding effective conservation strategies like using chloroplast variation to assess genetic diversity for ex situ conservation and reintroduction programs. The uniformity of the chloroplast genome in S. ensifolium may reveal that this species has undergone a genetic bottleneck. To prevent inbreeding depression and maintain evolutionary adaptability, efforts should be made to generate and preserve as much genetic diversity as possible.

OsPRDA1 Interacts With OsFSD2 To Promote Chloroplast Development by Regulating Chloroplast Gene Expression in Rice

Chloroplasts are vital for photosynthesis, and their development necessitates proper expression of chloroplast genes. However, the regulatory mechanisms underlying rice chloroplast gene expression have not been fully elucidated. In this study, we obtained an albino mutant of rice, white seedling and lethal 1 (wsl1), which displays significantly decreased chlorophyll contents and impaired chloroplast ultrastructure. The causal gene Oryza sativa PEP-RELATED DEVELOPMENT ARRESTED 1 (OsPRDA1) was isolated using Mutmap + and verified by gene editing and complementary assays. The expression of OsPRDA1 is induced by light, and OsPRDA1 is localized in chloroplasts. Transcription sequencing revealed that genes related to photosynthesis were differentially expressed in wsl1. The expression levels of the examined plastid-encoded RNA polymerase (PEP)-dependent chloroplast genes are downregulated due to the mutation of OsPRDA1. Moreover, OsPRDA1 interacts with OsFSD2, a member of PEP-associated proteins (PAPs). Knockout of OsFSD2 leads to the albino and seedling-lethal phenotype and downregulation of PEP-dependent chloroplast genes. Together, our results demonstrated that OsPRDA1 plays essential roles in rice chloroplast development, probably by facilitating the function of the PAP complex and chloroplast gene expression.

Analysis of the Codon Usage Bias Pattern in the Chloroplast Genomes of Chloranthus Species (Chloranthaceae)

BACKGROUND

The codon preference of chloroplast genomes not only reflects mutation patterns during the evolutionary processes of species but also significantly affects the efficiency of gene expression. This characteristic holds significant scientific importance in the application of chloroplast genetic engineering and the genetic improvement of species. Chloranthus, an ancestral angiosperm with significant economic, medicinal, and ornamental value, belongs to the basal angiosperms. However, the codon usage patterns among Chloranthus species have remained unclear.

METHODS

To investigate codon usage bias and its influencing factors in Chloranthus chloroplast genomes, we utilized CodonW, CUSP, and SPSS software to analyze the chloroplast genomes of seven Chloranthus species.

RESULTS

In this study, we reported and characterized the complete chloroplast genome of the Chinese endemic species Chloranthus angustifolius. The phylogenetic tree based on the whole chloroplast genomes showed that C. angustifolius is sister to Chloranthus fortunei, and the genus Chloranthus is divided into two major clades, consistent with previous studies. Our results revealed that the GC content at different codon positions across all seven Chloranthus species was less than 50%, with GC1 > GC2 > GC3. Additionally, the average effective number of codons (ENC) values exceeded 45. A total of 10 shared optimal codons were identified, nine of which end with A or U. PR2-plot, ENC-plot, and neutrality plot analyses indicated that natural selection primarily influenced codon usage bias in the chloroplast genomes of Chloranthus.

CONCLUSIONS

We newly obtained the chloroplast genome of C. angustifolius and proposed that natural selection played a key role in codon usage patterns in Chloranthus species. These findings contribute to our understanding of evolutionary history and genetic diversity within this genus.

Debulking influenza and herpes simplex virus strains by a wide-spectrum anti-viral protein formulated in clinical grade chewing gum

Lack of Herpes Simplex Virus (HSV) vaccine, low vaccination rates of Influenza viruses, waning immunity and viral transmission after vaccination underscore the need to reduce viral loads at their transmission sites. Oral virus transmission is several orders of magnitude higher than nasal transmission. Therefore, in this study, we evaluated neutralization of viruses using a natural viral trap protein (FRIL) formulated in clinical-grade chewing gum. FRIL is highly stable in the lablab bean powder (683 days) and in chewing gum (790 days), and fully functional (794 days) when stored at ambient temperature. They passed the bioburden test with no aerobic bacteria, yeasts/molds, with minimal moisture content (1.28-5.9%). Bean gum extracts trapped HSV-1/HSV-2 75-94% in a dose-dependent manner through virus self-aggregation. Mastication simulator released >50% release of FRIL within 15 min of chewing the bean gum. In plaque reduction assays, >95% neutralization of H1N1 and H3N2 required ∼40 mg/mL, HSV-1 160 mg/mL, and HSV-2 74 mg/mL of bean gum for 1,000 copies/mL virus particles. Therefore, a 2000 mg bean gum tablet has more than adequate potency for clinical evaluation and is safe with no detectable levels of glycosides. These observations augur well for evaluating bean gum in human clinical studies to minimize virus infection/transmission.

Multi-Omics on Traditional Medicinal Plant of the Genus Aconitum: Current Progress and Prospect

Aconitum stands out among the Ranunculaceae family for its notable use as an ornamental and medicinal plant. Diterpenoid alkaloids (DAs), the characteristic compounds of Aconitum, have been found to have effective analgesic and anti-inflammatory effects. Despite their medicinal potential, the toxicity of most DAs restricts the direct use of Aconitum in traditional medicine, necessitating complex processing before use. The use of high-throughput omics allows for the investigation of Aconitum plant genetics, gene regulation, metabolic pathways, and growth and development. We have collected comprehensive information on the omics studies of Aconitum medicinal plants, encompassing genomics, transcriptomics, metabolomics, proteomics, and microbiomics, from internationally recognized electronic scientific databases such as Web of Science, PubMed, and CNKI. In light of this, we identified research gaps and proposed potential areas and key objectives for Aconitum omics research, aiming to establish a framework for quality improvement, molecular breeding, and a deeper understanding of specialized metabolite production in Aconitum plants.

Plastome characterization and its phylogenetic implications on Lithocarpus (Fagaceae)

BACKGROUND

The genus Lithocarpus is a species-rich dominant woody lineage in East Asian evergreen broad-leaved forests. Despite its ecological and economic significance, the plastome structure and evolutionary history of the genus remain poorly understood. In this study, we comprehensively analyzed the 34 plastomes representing 33 Lithocarpus species. Of which, 21 were newly assembled. The plastome-based phylogenomic tree was reconstructed to reveal the maternal evolutionary patterns of the genus.

RESULTS

The Lithocarpus plastomes exhibit a typical quadripartite structure, ranging in length from 161,010 to 161,476 bp, and containing 131 genes, including 86 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Remarkably, the infA gene was identified as a pseudogene in 17 species. Significant variability was observed in simple sequence repeats (SSRs) as well as in the boundary regions between the two single-copy regions and the inverted repeat region (SC/IR) across the plastomes. Additionally, four genes (accD, atpF, rpl32, and rps8) were found to be under positive selection. The monophyletic status of Lithocarpus was strongly supported by plastome-based phylogeny; however, the phylogenetic tree topology showed a significant difference from that obtained by the nuclear genome-based phylogeny.

CONCLUSIONS

The plastome of Fagaceae is generally conserved. Nevertheless, genes related to metabolism, photosynthesis, and energy were under strong positive selection in Lithocarpus, likely driven by environmental pressures and local adaptation. The plastome-based phylogeny confirmed the monophyletic status of Lithocarpus and revealed a phylogeographic pattern indicating limited seed-mediated gene flow in the ancestral lineage. The prevalence of cytonuclear discordance in Lithocarpus and other Fagaceae genera suggests that ancient introgression, incomplete lineage sorting, and asymmetrical seed- and pollen-mediated geneflow might contribute to this discordance. Future studies are essential to test these hypotheses and further elucidate the divergence patterns of this unique Asian evergreen lineage.

Deciphering the complex organelle genomes of two Rhododendron species and insights into adaptive evolution patterns in high-altitude

BACKGROUND

The genomes within organelles are crucial for physiological functions such as respiration and photosynthesis and may also contribute to environmental adaptation. However, the limited availability of genetic resources, particularly mitochondrial genomes, poses significant challenges for in-depth investigations.

RESULTS

Here, we explored various assembly methodologies and successfully reconstructed the complex organelle genomes of two Rhododendron species: Rhododendron nivale subsp. boreale and Rhododendron vialii. The mitogenomes of these species exhibit various conformations, as evidenced by long-reads mapping. Notably, only the mitogenome of R. vialii can be depicted as a singular circular molecule. The plastomes of both species conform to the typical quadripartite structure but exhibit elongated inverted repeat (IR) regions. Compared to the high similarity between plastomes, the mitogenomes display more obvious differences in structure, repeat sequences, and codon usage. Based on the analysis of 58 organelle genomes from angiosperms inhabiting various altitudes, we inferred the genetic adaptations associated with high-altitude environments. Phylogenetic analysis revealed partial inconsistencies between plastome- and mitogenome-derived phylogenies. Additionally, evolutionary lineage was determined to exert a greater influence on codon usage than altitude. Importantly, genes such as atp4, atp9, mttB, and clpP exhibited signs of positive selection in several high-altitude species, suggesting a potential link to alpine adaptation.

CONCLUSIONS

We tested the effectiveness of different organelle assembly methods for dealing with complex genomes, while also providing and validating high-quality organelle genomes of two Rhododendron species. Additionally, we hypothesized potential strategies for high-altitude adaptation of organelles. These findings offer a reference for the assembly of complex organelle genomes, while also providing new insights and valuable resources for understanding their adaptive evolution patterns.

Comparative Analysis of the Codon Usage Pattern in the Chloroplast Genomes of Gnetales Species

Codon usage bias refers to the preferential use of synonymous codons, a widespread phenomenon found in bacteria, plants, and animals. Codon bias varies among species, families, and groups within kingdoms and between genes within an organism. Codon usage bias (CUB) analysis sheds light on the evolutionary dynamics of various species and optimizes targeted gene expression in heterologous host plants. As a significant order of gymnosperms, species within Gnetales possess extremely high ecological and pharmaceutical values. However, comprehensive analyses of CUB within the chloroplast genomes of Gnetales species remain unexplored. A systematic analysis was conducted to elucidate the codon usage patterns in 13 diverse Gnetales species based on the chloroplast genomes. Our results revealed that chloroplast coding sequences (cp CDSs) in 13 Gnetales species display a marked preference for AT bases and A/T-ending codons. A total of 20 predominantly high-frequency codons and between 2 and 7 optimal codons were identified across these species. The findings from the ENC-plot, PR2-plot, and neutrality analyses suggested that both mutation pressure and natural selection exert influence on the codon bias in these 13 Gnetales species, with natural selection emerging as the predominant influence. Correspondence analysis (COA) demonstrated variation in the codon usage patterns among the Gnetales species and indicated mutation pressure is another factor that could impact CUB. Additionally, our research identified a positive correlation between the measure of idiosyncratic codon usage level of conservatism (MILC) and synonymous codon usage order (SCUO) values, indicative of CUB's potential influence on gene expression. The comparative analysis concerning codon usage frequencies among the 13 Gnetales species and 4 model organisms revealed that Saccharomyces cerevisiae and Nicotiana tabacum were the optimal exogenous expression hosts. Furthermore, the cluster and phylogenetic analyses illustrated distinct patterns of differentiation, implying that codons, even with weak or neutral preferences, could affect the evolutionary trajectories of these species. Our results reveal the characteristics of codon usage patterns and contribute to an enhanced comprehension of evolutionary mechanisms in Gnetales species.

Exploring recent progress of molecular farming for therapeutic and recombinant molecules in plant systems

An excellent technique for producing pharmaceuticals called "molecular farming" enables the industrial mass production of useful recombinant proteins in genetically modified organisms. Protein-based pharmaceuticals are rising in significance because of a variety of factors, including their bioreactivity, precision, safety, and efficacy rate. Heterologous expression methods for the manufacturing of pharmaceutical products have been previously employed using yeast, bacteria, and animal cells. However, the high cost of mammalian cell system, and production, the chance for product complexity, and contamination, and the hurdles of scaling up to commercial production are the limitations of these traditional expression methods. Plants have been raised as a hopeful replacement system for the expression of biopharmaceutical products due to their potential benefits, which include low production costs, simplicity in scaling up to commercial manufacturing levels, and a lower threat of mammalian toxin contaminations and virus infections. Since plants are widely utilized as a source of therapeutic chemicals, molecular farming offers a unique way to produce molecular medicines such as recombinant antibodies, enzymes, growth factors, plasma proteins, and vaccines whose molecular basis for use in therapy is well established. Biopharming provides more economical and extensive pharmaceutical drug supplies, including vaccines for contagious diseases and pharmaceutical proteins for the treatment of conditions like heart disease and cancer. To assess its technical viability and the efficacy resulting from the adoption of molecular farming products, the following review explores the various methods and methodologies that are currently employed to create commercially valuable molecules in plant systems.

The complete chloroplast genome sequence of Lilium saccatum S. Yun Liang (Liliaceae, Lilieae) and its phylogenetic analysis

Lilium saccatum is a species of ornamental plant found in southeastern Xizang, China. In the present study, the complete chloroplast (cp) genome of L. saccatum was sequenced using next-generation sequencing (NGS). The de novo assembled cp genome was 151,839 bp in length, including a pair of inverted repeat regions (IRs; 26,421 bp), a small single-copy region (SSC; 17,528 bp), and a large single-copy region (LSC; 81,469 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the cp genome was 37.0%. Phylogenetic analysis of 24 cp genomes revealed that L. saccatum was closely related to L. souliei. This study could provide fundamental information for the phylogenomics and utilization of Lilium.

Comparative analysis of codon usage bias in the chloroplast genomes of eighteen Ampelopsideae species (Vitaceae)

BACKGROUND

The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family.

RESULTS

The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35-61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species.

CONCLUSION

The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies.

Deciphering the complete chloroplast genome sequence of Meconopsis torquata Prain: Insights into genome structure, comparative analysis and phylogenetic relationship

In the present study, we have characterized the complete chloroplast (Cp) genome of Meconopsis torquata Prain (family Papaveraceae), revealing the plastome size of 153,290 bp, and a GC content of 38.72 %. The cp genome features the typical circular quadripartite structure found in flowering plants, including a pair of inverted repeat regions (25,816 bp), isolated by a small single-copy region (17,740 bp) and a large single-copy (83,918 bp). Genome annotation revealed 132 genes: 87 protein-coding genes, 37 tRNAs and eight rRNAs. This comparative study demonstrated that the genome structure, gene number and GC ratio are consistent with several other cp genomes of Meconopsis and Papaver genera. A total of 120 SSRs were detected in the plastome, the majority (111) of which were mononucleotide repeats. Among the longer repeats, palindromic sequences were most common, followed by forward, reverse, and complement repeats. The whole genome alignment revealed the conserved nature of the inverted repeat region over single-copy zones. Nucleotide diversity unveiled hypervariable sites (ycf1, rps16, accD, atpB and psbD) in both the small and large single-copy regions, which could be useful for designing molecular markers for taxonomic identification. Phylogenetic analysis revealed a close alliance of M. torquata with other Meconopsis species, such as M. pinnatifolia and M. paniculata, with strong bootstrap support. Molecular dating suggests that M. torquata originated during the Tortonian age of the Miocene epoch of the Cenozoic era. These findings provide valuable insights for biological research, especially in understanding the genetic and evolutionary divergence within the Papaveraceae family.

The complete chloroplast genome of Pyankovia brachiata (amaranthaceae), an annual desert plant in China

Pyankovia brachiata (Pall.) Akhani & Roalson 2007, is an annual plant belonging to the genus Pyankovia, family Amaranthaceae, which is widely distributed in the inland deserts of Northwest China. P. brachiata was previously categorized under the genus Salsola in Salsoleae and has been a long-standing topic of debate. Therefore, the complete chloroplast genome of P. brachiata must be studied to provide a theoretical reference for species classification. In this study, we sequenced P. brachiata samples and determined the species' complete chloroplast genome. The complete chloroplast genome was 149,922 bp in length, with one large single copy (LSC: 83,565 bp), one small single copy (SSC: 18,535 bp), and two inverted repeat regions (IRa and IRb, 23,911 bp each). It contains 132 genes, including 87 protein-coding, eight rRNA, and 37 tRNA genes. The phylogenetic position showed that P. brachiata has the closest relationship with Caroxylon passerinum (accession number: NC057191.1). This study will provide genetic information and be beneficial to understanding the systematic position of P. brachiata within the Amaranthaceae.

Comparative Analysis and Phylogeny of the Complete Chloroplast Genomes of Nine Cynanchum (Apocynaceae) Species

Cynanchum belongs to the Apocynaceae family and is a morphologically diverse genus that includes around 200 shrub or perennial herb species. Despite the utilization of CPGs, few molecular phylogenetic studies have endeavored to elucidate infrafamilial relationships within Cynanchum through extensive taxon sampling. In this research, we constructed a phylogeny and estimated divergence time based on the chloroplast genomes (CPGs) of nine Cynanchum species. We sequenced and annotated nine chloroplast (CP) genomes in this study. The comparative analysis of these genomes from these Cynanchum species revealed a typical quadripartite structure, with a total sequence length ranging from 158,283 to 161,241 base pairs (bp). The CP genome (CPG) was highly conserved and moderately differentiated. Through annotation, we identified a total of 129-132 genes. Analysis of the boundaries of inverted repeat (IR) regions showed consistent positioning: the rps19 gene was located in the IRb region, varying from 46 to 50 bp. IRb/SSC junctions were located between the trnN and ndhF genes. We did not detect major expansions or contractions in the IR region or rearrangements or insertions in the CPGs of the nine Cynanchum species. The results of SSR analysis revealed a variation in the number of SSRs, ranging from 112 to 150. In five types of SSRs, the largest number was mononucleotide repeats, and the smallest number was hexanucleotide repeats. The number of long repeats in the cp genomes of nine Cynanchum species was from 35 to 80. In nine species of Cynanchum, the GC3s values ranged from 26.80% to 27.00%, indicating a strong bias towards A/U-ending codons. Comparative analyses revealed four hotspot regions in the CPG, ndhA-ndhH, trnI-GAU-rrn16, psbI-trnS-GCU, and rps7-ndhB, which could potentially serve as molecular markers. In addition, phylogenetic tree construction based on the CPG indicated that the nine Cynanchum species formed a monophyletic group. Molecular dating suggested that Cynanchum diverged from its sister genus approximately 18.87 million years ago (Mya) and species diversification within the Cynanchum species primarily occurred during the recent Miocene epoch. The divergence time estimation presented in this study will facilitate future research on Cynanchum, aid in species differentiation, and facilitate diverse investigations into this economically and ecologically important genus.

Plant organellar genomes: much done, much more to do

Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.

Genetic diversity of food-medicinal Lycium spp. in China: Insights from chloroplast genome

Objective

Goji (fruits of Lycium spp.) is commonly consumed as food and medicine. The increasing market demand for goji has led to its wide cultivation and broad breeding, which might cause loss of genetic diversity. This study aims to uncover the genetic diversity of the cultivated and wild Lycium.

Methods

The chloroplast genome (CPG) of 34 accessions of Chinese food-medicinal Lycium spp., including the popular cultivars and their wild relatives, was re-sequenced and assembled, based on which the genetic diversity was evaluated.

Results

Sequence structural comparison shows that CPG is comparatively conserved within species. Phylogenetic analysis indicates that CPG is sufficient for the discrimination of Lycium species; combined with nuclear ribosomal internal transcribed spacer (Nr ITS) sequences, materials with mixed genetic backgrounds can be identified. Nucleotide diversity analysis reveals that the modern cultivars are probably with a common maternal parent, while the wild accessions are with higher level of genetic diversity.

Conclusion

For the first time this study reveals the intraspecies genetic diversity of Lycium spp. using CPG, highlighting the urgent conservation demand of wild genetic resources of Lycium. Our study also demonstrates that CPG provides crucial evidence for identification of Lycium species with mixed genetic backgrounds and highlights the importance of the wild relatives in genetic diversity conservation. This CPG-based technology will contribute to the sustainable development of medicinal plants broadly.

Piece and parcel of gymnosperm organellar genomes

MAIN CONCLUSION

Significant past, present, and potential future research into the organellar (plastid and mitochondrial) genomes of gymnosperms that can provide insight into the unknown origin and evolution of plants is highlighted. Gymnosperms are vascular seed plants that predominated the ancient world before their sister clade, angiosperms, took over during the Late Cretaceous. The divergence of gymnosperms and angiosperms took place around 300 Mya, with the latter evolving into the diverse group of flowering plants that dominate the plant kingdom today. Although gymnosperms have reportedly made some evolutionary innovations, the literature on their genome advances, particularly their organellar (plastid and mitochondrial) genomes, is relatively scattered and fragmented. While organellar genomes can shed light on plant origin and evolution, they are frequently overlooked, due in part to their limited contribution to gene expression and lack of evolutionary dynamics when compared to nuclear genomes. A better understanding of gymnosperm organellar genomes is critical because they reveal genetic changes that have contributed to their unique adaptations and ecological success, potentially aiding in plant survival, enhancement, and biodiversity conservation in the face of climate change. This review reveals significant information and gaps in the existing knowledge base of organellar genomes in gymnosperms, as well as the challenges and research needed to unravel their complexity.

Comparative genomics and phylogenetic analysis of chloroplast genomes of Asian Caryodaphnopsis taxa (Lauraceae)

The genus Caryodaphnopsis, a member of the Lauraceae family, is characterized by seeds that are rich in oil, as well as highly exploitable fruits and wood. The Asian taxa within this genus exhibit complex morphological variations, posing challenges to their accurate classification and impeding their effective use and development as a resource. In this study, we sequenced the chloroplast genomes of 31 individuals representing nine Asian taxa within the Caryodaphnopsis genus. Our primary objectives were to reveal structural variations in these chloroplast genomes through comparative analyses and to infer the species' phylogenetic relationships. Our findings revealed that all chloroplast genomes had a tetrad structure, ranged in length from 148,828 to 154,946 bp, and harbored 128-131 genes. Notably, contraction of the IR region led to the absence of some genes in eight taxa. A comprehensive analysis identified 1267 long repetitive sequences and 2176 SSRs, 286 SNPs, and 135 indels across the 31 chloroplast genomes. The Ka/Ks ratio analysis indicated potential positive selection on the matK, rpl22, and rpoC2 genes. Furthermore, we identified six variable regions as promising barcode regions. Phylogenetic analysis grouped the nine Asian taxa into six branches, with C. henryi forming the basal group from which three distinct complexes emerged. This study contributes significantly to the current understanding of the evolutionary dynamics and phylogenetic relationships within the genus Caryodaphnopsis. Furthermore, the identified molecular markers hold potential for molecular barcoding applications in population genetics, providing valuable tools for future research and conservation efforts within this diverse genus.

Characterization of the Plastid Genomes of Four Caroxylon Thunb. Species from Kazakhstan

The family Chenopodiaceae Vent. (Amaranthaceae s.l.) is known for its taxonomic complexity, comprising species of significant economic and ecological importance. Despite its significance, the availability of plastid genome data for this family remains limited. This study involved assembling and characterizing the complete plastid genomes of four Caroxylon Thunb. species within the tribe Salsoleae s.l., utilizing next-generation sequencing technology. We compared genome features, nucleotide diversity, and repeat sequences and conducted a phylogenetic analysis of ten Salsoleae s.l. species. The size of the plastid genome varied among four Caroxylon species, ranging from 150,777 bp (C. nitrarium) to 151,307 bp (C. orientale). Each studied plastid genome encoded 133 genes, including 114 unique genes. This set of genes includes 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Eight divergent regions (accD, atpF, matK, ndhF-ndhG, petB, rpl20-rpl22, rpoC2, and ycf3) were identified in ten Salsoleae s.l. plastid genomes, which could be potential DNA-barcoding markers. Additionally, 1106 repeat elements were detected, consisting of 814 simple sequence repeats, 92 tandem repeats, 88 forward repeats, 111 palindromic repeats, and one reverse repeat. The phylogenetic analysis provided robust support for the relationships within Caroxylon species. These data represent a valuable resource for future phylogenetic studies within the genus.

Comparative chloroplast genomes of Argentina species: genome evolution and phylogenomic implications

The genus Argentina Hill belongs to the tribe Potentilleae Sweet and contains approximately 75 species predominantly distributed in the Sino-Himalayan region and the Malesian archipelago. So far we have less knowledge on the phylogenetic relationships within Argentina owing to limited sampling of Argentina taxa or gene fragments in previous studies. Moreover, to date there is no phylogenetic study on Argentina from the perspective of comparative chloroplast (cp) genomics. Here we performed comparative genomic analyses on the cp genomes of 39 accessions representing 18 taxa of Argentina. The Argentina cp genomes presented the typical quadripartite structure, with the sizes ranging from 155 096 bp to 157 166 bp. The 39 Argentina cp genomes contained a set of 112 unique genes, comprising four ribosomal RNA (rRNA) genes, 30 transfer RNA (tRNA) genes, as well as 78 protein-coding genes (PCGs). The cp genome organization, gene content and order in Argentina were highly conserved, but some visible divergences were present in IR/SC boundary regions. Ten regions (trnH-GUG-psbA, trnG-GCC-trnfM-CAU, trnD-GUC-trnY-GUA, rpl32-trnL-UAG, atpH-atpI, rps16-trnQ-UUG, trnS-GCU-trnG-UCC, ndhF-rpl32, trnR-UCU-atpA, and accD-psaI) were identified as excellent candidate DNA markers for future studies on species identification, population genetics and phylogeny of Argentina. Our results indicated that Argentina is monophyletic. In the current sampling, the A. smithiana - A. anserina clade was sister to the remainder of Argentina. Our results corroborated the previous taxonomic treatments to transfer A. phanerophlebia and A. micropetala from the genus Sibbaldia L. to Argentina. Our results showed close relationships among A. stenophylla, A. microphylla, A. taliensis, and A. tatsienluensis, congruent with previous studies based on the morphology of these species. Twenty-six genes (rps3, rps15, rps16, rps19, rpl16, rpl20, rpl22, rpoA, rpoB, rpoC1, rpoC2, atpA, atpF, psbB, psbF, ndhA, ndhB, ndhC, ndhD, ndhF, rbcL, accD, ccsA, matK, ycf1, ycf2) were with sites under positive selection, and adaptive evolution of these genes might have played crucial roles in Argentina species adaptation to the harsh mountain environment. This study will facilitate future work on taxonomy, phylogenetics, and adaptive evolution of Argentina.

Toward the Exploitation of Sustainable Green Factory: Biotechnology Use of Nannochloropsis spp

Securing food, energy, and raw materials for a growing population is one of the most significant challenges of our century. Algae play a central role as an alternative to plants. Wastewater and flue gas can secure nutrients and CO2 for carbon fixation. Unfortunately, algae domestication is necessary to enhance biomass production and reduce cultivation costs. Nannochloropsis spp. have increased in popularity among microalgae due to their ability to accumulate high amounts of lipids, including PUFAs. Recently, the interest in the use of Nannochloropsis spp. as a green bio-factory for producing high-value products increased proportionally to the advances of synthetic biology and genetic tools in these species. In this review, we summarized the state of the art of current nuclear genetic manipulation techniques and a few examples of their application. The industrial use of Nannochloropsis spp. has not been feasible yet, but genetic tools can finally lead to exploiting this full-of-potential microalga.

The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress

Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants.

Genetic Insights into the Extremely Dwarf Hibiscus syriacus var. micranthus: Complete Chloroplast Genome Analysis and Development of a Novel dCAPS Marker

This study explored the chloroplast (cp) genomes of three Hibiscus syriacus (HS) specimens endemic to Korea possessing unique ornamental and conservation values: the dwarf H. syriacus var. micranthus (HSVM), renowned for its small stature and breeding potential; HS 'Tamra', a cultivar from Korea's southernmost islands, noteworthy for its distinctive beauty; and HS Natural Monument no. 521 (N.M.521), a specimen of significant lifespan and height. Given the scarcity of evolutionary studies on these specimens, we assembled and analyzed their cp genomes. We successfully assembled genomes spanning 160,000 to 160,100 bp and identified intraspecific variants. Among these, a unique ATA 3-mer insertion in the trnL-UAA region was identified in HSVM, highlighting its value as a genetic resource. Leveraging this finding, we developed a novel InDel dCAPS marker, which was validated across 43 cultivars, enhancing our ability to distinguish HSVM and its derivatives from other HS cultivars. Phylogenetic analysis involving 23 Malvaceae species revealed that HSVM forms a clade with woody Hibiscus species, closely associating with N.M.520, which may suggest a shared ancestry or parallel evolutionary paths. This investigation advances our understanding of the genetic diversity in Korean HS and offers robust tools for accurate cultivar identification, aiding conservation and breeding efforts.

Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems, including the constituent elements within and among species. Through various efforts in genomic data archiving, integrative analysis and value-added curation, the National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), has successfully established and currently maintains a vast amount of database resources. This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts. Here, we present a comprehensive overview of central repositories dedicated to archiving, presenting, and sharing plant omics data, introduce knowledgebases focused on variants or gene-based functional insights, highlight species-specific multiple omics database resources, and briefly review the online application tools. We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-023-00134-4.

Codon usage bias and phylogenetic analysis of chloroplast genome in 36 gracilariaceae species

Gracilariaceae is a group of marine large red algae and main source of agar with important economic and ecological value. The codon usage patterns of chloroplast genomes in 36 species from Graciliaceae show that GC range from 0.284 to 0.335, the average GC3 range from 0.135 to 0.243 and the value of ENC range from 35.098 to 42.327, which indicates these genomes are rich in AT and prefer to use codons ending with AT in these species. Nc plot, PR2 plot, neutrality plot analyses and correlation analysis indicate that these biases may be caused by multiple factors, such as natural selection and mutation pressure, but prolonged natural selection is the main driving force influencing codon usage preference. The cluster analysis and phylogenetic analysis show that the differentiation relationship of them is different and indicate that codons with weak or unbiased preferences may also play an irreplaceable role in these species' evolution. In addition, we identified 26 common high-frequency codons and 8-18 optimal codons all ending in A/U in these 36 species. Our results will not only contribute to carrying out transgenic work in Gracilariaceae species to maximize the protein yield in the future, but also lay a theoretical foundation for further exploring systematic classification of them.

Cryo-EM structures of the plant plastid-encoded RNA polymerase

Chloroplasts are green plastids in the cytoplasm of eukaryotic algae and plants responsible for photosynthesis. The plastid-encoded RNA polymerase (PEP) plays an essential role during chloroplast biogenesis from proplastids and functions as the predominant RNA polymerase in mature chloroplasts. The PEP-centered transcription apparatus comprises a bacterial-origin PEP core and more than a dozen eukaryotic-origin PEP-associated proteins (PAPs) encoded in the nucleus. Here, we determined the cryo-EM structures of Nicotiana tabacum (tobacco) PEP-PAP apoenzyme and PEP-PAP transcription elongation complexes at near-atomic resolutions. Our data show the PEP core adopts a typical fold as bacterial RNAP. Fifteen PAPs bind at the periphery of the PEP core, facilitate assembling the PEP-PAP supercomplex, protect the complex from oxidation damage, and likely couple gene transcription with RNA processing. Our results report the high-resolution architecture of the chloroplast transcription apparatus and provide the structural basis for the mechanistic and functional study of transcription regulation in chloroplasts.

Comparative Phylogenetic Analysis of Ancient Korean Tea "Hadong Cheon-Nyeon Cha (Camellia sinensis var. sinensis)" Using Complete Chloroplast Genome Sequences

Wild teas are valuable genetic resources for studying evolution and breeding. Here, we report the complete chloroplast genome of the ancient Korean tea 'Hadong Cheon-nyeon Cha' (C. sinensis var. sinensis), which is known as the oldest tea tree in Korea. This study determined seven Camellia sinensis var. sinenesis, including Hadong Cheon-nyeon Cha (HCNC) chloroplast genome sequences, using Illumina sequencing technology via de novo assembly. The chloroplast genome sizes ranged from 157,019 to 157,114 bp and were organized into quadripartite regions with the typical chloroplast genomes. Further, differences in SNPs and InDels were detected across the seven chloroplast genomes through variance analysis. Principal component and phylogenetic analysis suggested that regional constraints, rather than functional constraints, strongly affected the sequence evolution of the cp genomes in this study. These genomic resources provide evolutionary insight into Korean tea plant cultivars and lay the foundation for a better understanding of the ancient Korean tea plant HCNC.

A new perspective on codon usage, selective pressure, and phylogenetic implications of the plastomes in the Telephium clade (Crassulaceae)

The Telephium clade of the Crassulaceae family contains many medicinal, ornamental, and ecologically restorative plants. However, the phylogenetic relationships within the clade remain debated, and comprehensive analyses of codon usage and selection pressure in Telephium plastomes are limited. In this study, we assembled and annotated four plastomes and performed extensive analyses. The plastomes exhibited a typical quadripartite structure and high conservation. The lengths ranged from 151,357 bp to 151,641 bp with 134 genes identified. The GC content was the highest within IR, followed by LSC, and lowest in the SSC region. Meanwhile, a unique inversion was observed within the LSC region of Meterostachys sikokianus. Polymorphisms analysis revealed minimum nucleotide diversity in the IR regions, with over ten highly polymorphic regions identified. Phylogenetically, two subclades formed within the monophyletic Telephium clade, with Umbilicus as the sister group to the remaining Hylotelephium subclade members. Notably, no significant positive selection was found among the 79 plastid genes, which showed varying evolutionary patterns. However, 19 genes contained codons under positive selection. The specific functions of these sites require further investigation. Synonymous codon usage was biased and conserved across the tested plastomes, shaped by natural selection, mutations and other factors of varying influence. We also identified 34 taxon-specific codon aversion motifs from 49 plastid genes. Our plastomic analyses elucidate phylogenetic relationships and evolutionary patterns in this medicinal clade, providing a foundation for further research on these ecologically and pharmaceutically important plants.

The complete chloroplast genome sequence of Rhododendron farrerae Tate ex Sweet (Ericaceae)

Rhododendron farrerae Tate ex Sweet 1831 is a species of ornamental plant found in southern China. In the present study, the complete chloroplast genome of R. farrerae was sequenced. The genome was 149,453 bp in length and lacked the typical quadripartite structure. The plastid genome contained 112 genes, including 74 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. The overall GC content of the genome was 35.65%. Phylogenetic analysis of 25 chloroplast genomes revealed that R. farrerae was closely related to Rhododendron huadingense. This study could provide fundamental information for the distribution, utilization, and phylogenomics of Rhododendron.

Green Biologics: Harnessing the Power of Plants to Produce Pharmaceuticals

Plants are increasingly used for the production of high-quality biological molecules for use as pharmaceuticals and biomaterials in industry. Plants have proved that they can produce life-saving therapeutic proteins (Elelyso™-Gaucher's disease treatment, ZMapp™-anti-Ebola monoclonal antibodies, seasonal flu vaccine, Covifenz™-SARS-CoV-2 virus-like particle vaccine); however, some of these therapeutic proteins are difficult to bring to market, which leads to serious difficulties for the manufacturing companies. The closure of one of the leading companies in the sector (the Canadian biotech company Medicago Inc., producer of Covifenz) as a result of the withdrawal of investments from the parent company has led to the serious question: What is hindering the exploitation of plant-made biologics to improve health outcomes? Exploring the vast potential of plants as biological factories, this review provides an updated perspective on plant-derived biologics (PDB). A key focus is placed on the advancements in plant-based expression systems and highlighting cutting-edge technologies that streamline the production of complex protein-based biologics. The versatility of plant-derived biologics across diverse fields, such as human and animal health, industry, and agriculture, is emphasized. This review also meticulously examines regulatory considerations specific to plant-derived biologics, shedding light on the disparities faced compared to biologics produced in other systems.

Engineering of insecticidal hybrid gene into potato chloroplast genome exhibits promising control of Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

The potato chloroplast was transformed with codon optimized synthetic hybrid cry gene (SN19) to mitigate crop losses by Colorado potato beetle (CPB). The bombarded explants (leaves and internode) were cultured on MS medium supplemented with BAP (2.0 mg/l), NAA (0.2 mg/l), TDZ (2.0 mg/l) and GA3 (0.1 mg/l); spectinomycin 50 mg/l was used as a selection agent in the medium. Leaf explants of cultivar Kuroda induced highest percentage (92%) of callus where cultivar Santae produced the highest percentage (85.7%) of transplastomic shoots. Sante and Challenger showed 9.6% shoot regeneration efficiency followed by cultivar Simply Red (8.8%). PCR amplification yielded 16 postive transplastomic plantlets out of 21 spectinomycin resistant ones. Target gene integration was confirmed by PCR and Southern blot, whereas RT-qPCR was used to assess the expression level of transgene. The localization of visual marker gene gfp was tracked by laser scanning confocal microscopy which confirmed its expression in chloroplasts of leaf cells. The transplastomic plants ensured high mortality to both larvae and adult CPB. Foliage consumption and weight gain of CPB fed on transplastomic leaves were lower compared to the control plants. Sucessful implementation of current research findings can lead to a viable solution to CPB mediated potato losses globally.

Delivery of biologics: Topical administration

Biologics are unaffordable to a large majority of the global population because of prohibitively expensive fermentation systems, purification and the requirement for cold chain for storage and transportation. Limitations of current production and delivery systems of biologics were evident during the recent pandemic when <2.5% of vaccines produced were available to low-income countries and ∼19 million doses were discarded in Africa due to lack of cold-chain infrastructure. Among FDA-approved biologics since 2015, >90% are delivered using invasive methods. While oral or topical drugs are highly preferred by patients because of their affordability and convenience, only two oral drugs have been approved by FDA since 2015. A newly launched oral biologic costs only ∼3% of the average cost of injectable biologics because of the simplified regulatory approval process by elimination of prohibitively expensive fermentation, purification, cold storage/transportation. In addition, the cost of developing a new biologic injectable product (∼$2.5 billion) has been dramatically reduced through oral or topical delivery. Topical delivery has the unique advantage of targeted delivery of high concentration protein drugs, without getting diluted in circulating blood. However, only very few topical drugs have been approved by the FDA. Therefore, this review highlights recent advances in oral or topical delivery of proteins at early or advanced stages of human clinical trials using chewing gums, patches or sprays, or nucleic acid drugs directly, or in combination with, nanoparticles and offers future directions.

Carotenoid Pathway Engineering in Tobacco Chloroplast Using a Synthetic Operon

The carotenoid pathway in plants has been altered through metabolic engineering to enhance their nutritional value and generate keto-carotenoids, which are widely sought after in the food, feed, and human health industries. In this study, the aim was to produce keto-carotenoids by manipulating the native carotenoid pathway in tobacco plants through chloroplast engineering. Transplastomic tobacco plants were generated that express a synthetic multigene operon composed of three heterologous genes, with Intercistronic Expression Elements (IEEs) for effective mRNA splicing. The metabolic changes observed in the transplastomic plants showed a significant shift towards the xanthophyll cycle, with only a minor production of keto-lutein. The use of a ketolase gene in combination with the lycopene cyclase and hydroxylase genes was a novel approach and demonstrated a successful redirection of the carotenoid pathway towards the xanthophyll cycle and the production of keto-lutein. This study presents a scalable molecular genetic platform for the development of novel keto-carotenoids in tobacco using the Design-Build-Test-Learn (DBTL) approach. This study corroborates chloroplast metabolic engineering using a synthetic biology approach for producing novel metabolites belonging to carotenoid class in industrially important tobacco plant. The synthetic multigene construct resulted in producing a novel metabolite, keto-lutein with high accumulation of xanthophyll metabolites. This figure was drawn using BioRender ( https://www.biorender.com ).

The complete chloroplast genome of Cicer reticulatum and comparative analysis against relative Cicer species

The chloroplast (cp) genome is an adequate genomic resource to investigate evolutionary relationships among plant species and it carries marker genes available for species identification. The Cicer reticulatum is one of perennial species as the progenitor of cultivated chickpeas. Although a large part of the land plants has a quadruple chloroplast genome organization, the cp genome of C. reticulatum consists of one LSC (Large Single Copy Region), one SSC (Small Single Copy Region), and one IR (Inverted Repeat) region, which indicates that it has an untypical and unique structure. This type of chloroplast genome belongs to the IR-lacking clade. Chloroplast DNA (cpDNA) was extracted from fresh leaves using a high salt-based protocol and sequencing was performed using DNA Nanoball Sequencing technology. The comparative analysis employed between the species to examine genomic differences and gene homology. The study also included codon usage frequency analysis, hotspot divergence analysis, and phylogenetic analysis using various bioinformatics tools. The cp genome of C. reticulatum was found 125,794 bp in length, with an overall GC content of 33.9%. With a total of 79 protein-coding genes, 34 tRNA genes, and 4 rRNA genes. Comparative genomic analysis revealed 99.93% similarity between C. reticulatum and C. arietinum. Phylogenetic analysis further indicated that the closest evolutionary relative to C. arietinum was C. reticulatum, whereas the previously sequenced wild Cicer species displayed slight distinctions across their entire coding regions. Several genomic regions, such as clpP and ycf1, were found to exhibit high nucleotide diversity, suggesting their potential utility as markers for investigating the evolutionary relationships within the Cicer genus. The first complete cp genome sequence of C. reticulatum will provide novel insights for future genetic research on Cicer crops.

Sequencing and Phylogenetic Analysis of the Chloroplast Genome of Three Apricot Species

The production and quality of apricots in China is currently limited by the availability of germplasm resource characterizations, including identification at the species and cultivar level. To help address this issue, the complete chloroplast genomes of Prunus armeniaca L., P. sibirica L. and kernel consumption apricot were sequenced, characterized, and phylogenetically analyzed. The three chloroplast (cp) genomes ranged from 157,951 to 158,224 bp, and 131 genes were identified, including 86 protein-coding genes, 37 rRNAs, and 8 tRNAs. The GC content ranged from 36.70% to 36.75%. Of the 170 repetitive sequences detected, 42 were shared by all three species, and 53-57 simple sequence repeats were detected with AT base preferences. Comparative genomic analysis revealed high similarity in overall structure and gene content as well as seven variation hotspot regions, including psbA-trnK-UUU, rpoC1-rpoB, rpl32-trnL-UAG, trnK-rps16, ndhG-ndhI, ccsA-ndhD, and ndhF-trnL. Phylogenetic analysis showed that the three apricot species clustered into one group, and the genetic relationship between P. armeniaca and kernel consumption apricot was the closest. The results of this study provide a theoretical basis for further research on the genetic diversity of apricots and the development and utilization of molecular markers for the genetic engineering and breeding of apricots.

Comparative Analyses of Chloroplast Genome Provide Effective Molecular Markers for Species and Cultivar Identification in Bougainvillea

Bougainvillea is popular in ornamental horticulture for its colorful bracts and excellent adaptability, but the complex genetic relationship among this genus is fuzzy due to limited genomic data. To reveal more genomic resources of Bougainvillea, we sequenced and assembled the complete chloroplast (cp) genome sequences of Bougainvillea spectabilis 'Splendens'. The cp genome size was 154,869 bp in length, containing 86 protein-coding genes, 38 tRNAs, and eight rRNAs. Cp genome comparison across 12 Bougainvillea species (B. spectabilis, B. glabra, B. peruviana, B. arborea, B. praecox, B. stipitata, B. campanulata, B. berberidifolia, B. infesta, B. modesta, B. spinosa, and B. pachyphylla) revealed five mutational hotspots. Phylogenetic analysis suggested that B. spectabilis published previously and B. glabra clustered into one subclade as two distinct groups, sister to the subclade of B. spectabilis 'Splendens'. We considered the phylogeny relationships between B. spectabilis and B. glabra to be controversial. Based on two hypervariable regions and three common plastid regions, we developed five molecular markers for species identification in Bougainvillea and applied them to classify 53 ornamental Bougainvillea cultivars. This study provides a valuable genetic resource for Bougainvillea breeding and offers effective molecular markers to distinguish the representative ornamental species of Bougainvillea.

Chloroplast Genome Engineering: A Plausible Approach to Combat Chili Thrips and Other Agronomic Insect Pests of Crops

The world population's growing demand for food is expected to increase dramatically by 2050. The agronomic productivity for food is severely affected due to biotic and abiotic constraints. At a global level, insect pests alone account for ~20% loss in crop yield every year. Deployment of noxious chemical pesticides to control insect pests always has a threatening effect on human health and environmental sustainability. Consequently, this necessitates for the establishment of innovative, environmentally friendly, cost-effective, and alternative means to mitigate insect pest management strategies. According to a recent study, using chloroplasts engineered with double-strand RNA (dsRNA) is novel successful combinatorial strategy deployed to effectively control the most vexing pest, the western flower thrips (WFT: Frankliniella occidentalis). Such biotechnological avenues allowed us to recapitulate the recent progress of research methods, such as RNAi, CRISPR/Cas, mini chromosomes, and RNA-binding proteins with plastid engineering for a plausible approach to effectively mitigate agronomic insect pests. We further discussed the significance of the maternal inheritance of the chloroplast, which is the major advantage of chloroplast genome engineering.

The complete chloroplast genome of Vaccinium oxycoccos (Ericaceae)

Vaccinium species have great significance as fruit crops due to their economic and food values. Here we report the chloroplast genome of V. oxycoccos. The chloroplast genome of V. oxycoccos was 177,088 bp in length with a GC content of 36.74%. LSC, SSC, and IR regions were 104,139 bp, 3031 bp, and 34,959 bp in length, respectively. The chloroplast genome contained 105 different genes, including 73 protein-coding genes, 4 rRNA genes, and 28 tRNA genes. The phylogenetic analysis indicated that V. oxycoccos was closely related to V. microcarpum in the family Ericaceae. This chloroplast genome not only enriches the genome information of Vaccinium, but also will be useful in the evolution study of the family Ericaceae.

The First Complete Chloroplast Genome of Campanula carpatica: Genome Characterization and Phylogenetic Diversity

Campanula carpatica is an ornamental flowering plant belonging to the family Campanulaceae. The complete chloroplast genome of C. carpatica was obtained using Illumina HiSeq X and Oxford Nanopore (Nanopore GridION) platforms. The chloroplast genome exhibited a typical circular structure with a total length of 169,341 bp, comprising a large single-copy region of 102,323 bp, a small single-copy region of 7744 bp, and a pair of inverted repeats (IRa/IRb) of 29,637 bp each. Out of a total 120 genes, 76 were protein-coding genes, 36 were transfer RNA genes, and eight were ribosomal RNA genes. The genomic characteristics of C. carpatica are similar to those of other Campanula species in terms of repetitive sequences, sequence divergence, and contraction/expansion events in the inverted repeat regions. A phylogenetic analysis of 63 shared genes in 16 plant species revealed that Campanula zangezura is the closest relative of C. carpatica. Phylogenetic analysis indicated that C. carpatica was within the Campanula clade, and C. pallida occupied the outermost position of that clade.

Affordable oral proinsulin bioencapsulated in plant cells regulates blood sugar levels similar to natural insulin

Diabetes Mellitus is a silent epidemic affecting >500 million, which claimed 6.7 million lives in 2021, a projected increase of >670% in <20 years old in the next two decades but insulin is unaffordable for the large majority of the globe. Therefore, we engineered proinsulin in plant cells to facilitate oral delivery. Stability of the proinsulin gene and expression in subsequent generations, after removal of the antibiotic-resistance gene, was confirmed using PCR, Southern and western blots. Proinsulin expression was high (up to 12 mg/g DW or 47.5% of total leaf protein), stable up to one year after storage of freeze-dried plant cells at ambient temperature and met FDA regulatory requirements of uniformity, moisture content and bioburden. GM1 receptor binding, required for uptake via gut epithelial cells was confirmed by pentameric assembly of CTB-Proinsulin. IP insulin injections (without C peptide) in STZ mice rapidly decreased blood glucose level leading to transient hypoglycemia, followed by hepatic glucose compensation. On the other hand, other than the 15-min lag period of oral proinsulin (transit time required to reach the gut), the kinetics of blood sugar regulation of oral CTB-Proinsulin in STZ mice was very similar to naturally secreted insulin in healthy mice (both contain C-peptide), without rapid decrease or hypoglycemia. Elimination of expensive fermentation, purification and cold storage/transportation should reduce cost and increase other health benefits of plant fibers. The recent approval of plant cell delivery of therapeutic proteins by FDA and approval of CTB-ACE2 for phase I/II human clinical studies augur well for advancing oral proinsulin to the clinic.

Progress, challenge and prospect of plant plastome annotation

The plastome (plastid genome) represents an indispensable molecular data source for studying phylogeny and evolution in plants. Although the plastome size is much smaller than that of nuclear genome, and multiple plastome annotation tools have been specifically developed, accurate annotation of plastomes is still a challenging task. Different plastome annotation tools apply different principles and workflows, and annotation errors frequently occur in published plastomes and those issued in GenBank. It is therefore timely to compare available annotation tools and establish standards for plastome annotation. In this review, we review the basic characteristics of plastomes, trends in the publication of new plastomes, the annotation principles and application of major plastome annotation tools, and common errors in plastome annotation. We propose possible methods to judge pseudogenes and RNA-editing genes, jointly consider sequence similarity, customed algorithms, conserved domain or protein structure. We also propose the necessity of establishing a database of reference plastomes with standardized annotations, and put forward a set of quantitative standards for evaluating plastome annotation quality for the scientific community. In addition, we discuss how to generate standardized GenBank annotation flatfiles for submission and downstream analysis. Finally, we prospect future technologies for plastome annotation integrating plastome annotation approaches with diverse evidences and algorithms of nuclear genome annotation tools. This review will help researchers more efficiently use available tools to achieve high-quality plastome annotation, and promote the process of standardized annotation of the plastome.