The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression

Comparative and evolutionary analysis of chloroplast genomes from five rare Styrax species

BACKGROUND

Styrax, a vital raw material for shipbuilding, construction, perfumes, and drugs, represents the largest and most diverse genus in the Styracaceae. However, there is a relative scarcity of research on Styrax, particularly in evolution and genetics. Therefore, this study conducted comparative and evolutionary analyses of the chloroplast genomes of five rare Styrax species (S. argentifolius, S. buchananii, S. chrysocarpus, S. finlaysonianus, and S. rhytidocarpus).

RESULTS

The results indicated that, despite high levels of conservation in chloroplast genome structure among these species, specific mutation hotspot regions exist, particularly involving the expansion and contraction of the IR region. Additionally, evidence of positive selection was detected in eight genes (atpB, ccsA, ndhD, petA, rbcL, rpoC1, ycf1, and ycf2), which may be associated with adaptive evolution in response to environmental changes. Phylogenetic analysis revealed conflicts between trees constructed based on coding sequences and complete chloroplast genomes for several species, which were similar to previous phylogenetic studies.

CONCLUSION

This study underscores the importance of increasing sample sizes to enhance the accuracy of phylogenetic analyses and provides a new perspective on understanding the adaptive evolution of Styrax species. These findings are not only important for the conservation and sustainable use of Styrax, but also provide valuable insights for research in plant evolution and ecology within the genus.

Complete Chloroplast Genome Analysis of Casearia kurzii: Gene Loss at the IR Boundary and Monophyletic Evolution Within Casearia

Genomic analysis is crucial for understanding the evolutionary history, phylogenetic relationships, and effective conservation of plant species. Casearia kurzii is an important medicinal plant of the genus Casearia, but its complete chloroplast genome has not previously been reported, limiting genetic studies and conservation efforts. In this study, we assembled and annotated the complete chloroplast genome of C. kurzii using Illumina sequencing technology and conducted a comparative genomics analysis with 14 closely related species to clarify its phylogenetic position within Casearia. The chloroplast genome was 157,998 bp, showing a typical quadripartite structure. Key findings included: (1) the loss of the rpl22 gene at the IR boundary; (2) the identification of 60 simple sequence repeats (SSRs) and (3) the discovery of five candidate molecular markers for species-level identification. Phylogenetic analysis revealed that C. kurzii formed a strongly supported monophyletic clade (100% bootstrap support) with C. velutina, C. decandra, and C. glomerata, this clade originated approximately 15.8 million years ago. This study provides molecular tools for accurate identification and conservation of C. kurzii and related species, laying the foundation for exploring adaptive evolution within Casearia and advancing comparative genomics research.

Comprehensive analysis of complete chloroplast genome sequence of Morina L

In order to understand the structure characteristics of the chloroplast genome of Morina and explore the phylogenetic relationships within Morina, the whole chloroplast genomes of Morina chinensis and Morina kokonorica were sequenced in this study. Together with other two species of Morina which have been sequenced, the chloroplast genome structure of Morina was compared. Analysis of codon usage preference, analysis of the contraction and expansion of IR region, and comparison of the whole sequence were done. A total of 129 functional genes were annotated in M. chinensis and M. kokonorica chloroplast genome, with one more rpl23 gene than other 2 species. Tetranucleotide and pentanucleotide were only detected in M. chinensis. The ycf1 gene distributed in the SSC region in Morina longifolia, but on the IRa/SSC boundary of M. chinensis, M. kokonorica and Morina chlorantha genome. And the sequence of M. longifolia is the longest due to the extension of LSC and SSC. Phylogenetic analysis showed that the Morinoideae was an independent subfamily separated from Dipsacoideae and the relationship between Linnaeoideae and Morinoideae was closer. The divergence time between Morinoideae and Linnaeoideae was about 67.28 Ma and the divergence time of Morinoideae and Dipsacoideae was about 72.58 Ma. This study is conducive to the development and utilization of the resources of Morina, and provides a theoretical basis for the further study of this species.

Chloroplast-nuclear genome interaction drives asymmetric inverted repeats in chloroplast genome of Huperzia

Huperzia plants are important natural medicine species that have attracted increased amounts of attention due to the presence of huperzine A (Hup A), which efficiently, selectively, and reversibly inhibits acetylcholinesterase activity. However, due to the complexity of the genome structure and lack of genetic information, the phylogenetic and evolutionary relationships of Huperzia species are still unclear. In this study, seven chloroplast genome structures of Huperzia were verified and comparatively analyzed, and the phylogenetic relationships between Huperzia and other related ferns were evaluated. The results showed that a 58 kb insertion in the middle of the IRb region in the seven chloroplast genomes led to large differences in sequence size, GC content and tRNA number between IRa and IRb. All seven chloroplast genomes exhibited asymmetric structural conformations in the IR regions. We used sequence alignment and screening of the organelle and nuclear genomes to identify the source of the gene. The inserted sequence had no homologous region with the mitochondrial genome, and the same sequence as another segment was found in the nuclear genome. Then, the chloroplast genomes of Huperzia were comparatively analyzed. Phylogenetic tree showed that Phlegmariurus and Huperzia were closely related and belonged to the same branch. H. javanica and Huperzia serrata are closely related. From the perspective of phylogenetic tree, their phylogenetic relationship is closely related to geographical distribution. In conclusion, this study provides insights into the interaction mechanism between chloroplast genome and nuclear genome and the phylogeny of Huperzia. In addition, by comparing the chloroplast genomes of Huperzia, we analyzed its genetic diversity and provided important molecular information for the protection of these endangered species.

Comparative analysis of chloroplast genomes in three Araceae species: genomic difference, genetic distance and species morphology association

Many species in the Araceae have extremely high medicinal value, while the chloroplast genome is relatively conserved, and the encoded and expressed bioactive substances are also abundant. Therefore, chloroplast genomes can serve as one of the basis for species evolution and are extremely important for individual material accumulation. To study the relationship between the chloroplast genome and morphology of target species, this study selected three Araceae species for chloroplast genome sequencing assembly, downloaded the complete chloroplast genomes sequences of another 11 Araceae species. Grouping based on genetic distance, we analyze the association between chloroplast genome structure and morphology. The results showed that there were significant differences in genome size among the three species, but Relative Synonymous Codon Usage (RSCU) exhibited high similarity; Based on the phylogenetic tree, these 14 species can be divided into three branches, with differences in genes such as rrn4, rrn5, rrn23, and trnN among species within each branch; Morphologically, the length of the male inflorescence in BranchⅢ is significantly greater than that in BranchⅡ; There is a strong positive correlation between the length of the plant stem and the three parameters (Length of LSC, Length of SSC and Length of chloroplast genome) of the genome. This study conducted correlation research from the perspective of chloroplast genome and species morphology. On the one hand, the genetic distance and chloroplast genome structure differences between the target species were determined, and on the other hand, explored the correlation between chloroplast genome and species morphology, providing a theoretical basis for the study of phylogenetic relationships and morphology of Araceae species.

Comparative chloroplast genomes of Incarvillea species (Bignoniaceae) unveiled genomic diversity and shed light on phylogenetic relationships

BACKGROUND INCARVILLEA

Juss. is a small herbaceous genus within the Bignoniaceae family. It comprises 16 species, which are subdivided into five subgenera. The species are distributed mainly in the Himalaya-Hengduan Mountains, although there are exceptions, including I. sinensis, I. algae, I. semiretschenskia, and I. potaninii. Phylogenetic analyses based on trnL-F and nr ITS sequences provided support for the monophyly of the genus and its subgenera. However, the interspecific relationships among subgenera remain unresolved, and further investigation is necessary to elucidate these relationships. In this study, we sequenced and assembled 34 chloroplast genomes from 12 Incarvillea species, representing all five subgenera, and explored the phylogeny of the genus based on the cp. genome data.

RESULTS

The results demonstrated that 34 newly assembled chloroplast genomes exhibited lengths between 159,132 and 169,244 bp, and encoded a total of 129-141 genes. These included 84-95 protein-coding genes, 37 or 38 tRNA genes, and eight rRNA genes. A comparative analysis of the chloroplast genomes revealed the structural rearrangements and the expansions/contractions of the IR regions among the Incarvillea species. A total of 12 mutation hotspot regions were identified in the cp. genomes of the genus Incarvillea, encompassing six genes (atpI, psaI, rps18, trnQ-UUG, infA and ycf1) and six intergenic spacer regions (psbT-psbf1, rps11-rpl36, infA-rps8, trnN-GUU-ycf1, ndhE-ndhG and ndhI-ndhA). The Pi values of all highly variable regions exceeded 0.06. The phylogenetic analysis corroborated the monophyly of the genus and elucidated the relationships between five subgenere, namely ((Niedzwedzkia, Incarvillea), ((Amphicome, Olgaea),Pteroscleris)).

CONCLUSION

A comprehensive comparison of cp. genomic sequences revealed the diversity of the genus Incarvillea in terms of size, gene content and gene order of cp. genomes. Based on the cp. genome data, a robust phylogenetic tree of the genus Incarvillea was generated through phylogenetic analysis, with interspecific relationships well resolved. The results of this study enhance the understanding of the evolutionary history of the genus, and will facilitate further studies on the diversity and resource protection of the genus.

The Complete Chloroplast Genome and the Phylogenetic Analysis of Fimbristylis littoralis (Cyperaceae) Collected in Cherry Blossom Nursery

Fimbristylis littoralis, also known as globe fringerush, is one of the most troublesome annual Cyperaceae weeds in dryland fields and nurseries in the Yangtze Plain, Middle and Lower in China. The chloroplast (cp) genome of F. littoralis, and even this genus, has not been studied yet. In this study, the feature of the cp genome of F. littoralis and its phylogenetic relationships has been reported for the first time. It exhibited a typical circular tetramerous structure, with 86 protein-encoding genes. There were 149 simple sequence repeats (SSRs) and 1932 long repeats (LRs) detected. The IR expansion and contraction revealed the uniqueness of F. littoralis because there is a special cross-boundary gene, rps3, located at the LSC/IRb junction. Phylogenetic and divergence time dating analysis showed the close relationship between F. littoralis and the genus Cyperus, as well as many evolutionary directions of Cyperaceae family plants. The most recommended chemical method for removing this weed from nurseries is to spray 13 g ai ha-1 (the amount of active ingredient applied per hectare) of saflufenacil before emergence or 7.5 g ai ha-1 of halosulfuron-methyl after emergence. In conclusion, this study was the first to report the complete cp genome of a plant in the genus Fimbristylis. Our findings also provided valuable biological information for studying the phylogenetic relationships and evolution among the family Cyperaceae.

Elucidating the evolutionary dynamics of parasitism in Cuscuta: in-depth phylogenetic reconstruction and extensive plastomes reduction

BACKGROUND

The genus Cuscuta L. (Convolvulaceae), commonly known as dodder, is a holoparasite plant that relies on host plants for nutrition, leading to significant genomic changes, particularly in plastomes. This dependency has led to significant reductions and modifications in their plastomes compared to autotrophic plants. In contrast to the well-conserved plastomes of photosynthetic plants, Cuscuta exhibits substantial genomic reductions reflecting the loss of photosynthetic functions and associated genes.

RESULT

This study examines eight plastomes within Cuscuta and reconstructs the phylogenetic relationships among 40 Cuscuta taxa using five other genera as an outgroup. The size of plastid genome varies significantly, with the smallest being 60 kb and the largest 121 kb, highlighting extensive genomic reduction. In special cases, the subgenera Cuscuta exhibit the loss of inverted repeats, distinguishing from them other subge within the Cuscuta genus. This reduction is most pronounced in genes related to photosynthesis, such as atp, pet, psa, psb, and ycf genes, particularly in the subg. Grammica (Lour.) Peter. The study also notes the frequent and independent loss of the plastid genes infA, rpl23, rpl32, rps15, and rps16 across various angiosperm lineages, often involving transfer to the nuclear genome. In parasitic plants like Cuscuta, the ndh genes, crucial for photosynthesis, are often lost. The study also highlights that in the subg. Grammica, the matK and rpo genes, along with trnR-ACG genes, are lost in parallel, indicating that these parasitic plants do not need matK and rpo genes after the loss of ndh genes for survival. Analysis of selective relaxation pressure on plastid genes shows a reductive trend, with genes such as atp, pet, psa, psb, rpo, and ycf progressively becoming pseudogenes over time, with housekeeping genes like rpl and rps expected to follow. However, the pseudogenization process is specific to the subg. Grammica, Pachystigma (Engelm.) Baker & C.H.Wright, and Cuscuta, rather than in the subg. Monogynella (Des Moul.) Peter, Engl. & Prantl (ancient clade species).

CONCLUSION

The study of Cuscuta plastomes reveals the profound impact of parasitism on genome evolution, highlighting the complex interplay of gene retention and loss through phylogenomic approaches. This research enriches our understanding of plant genome evolution and the intricate host-parasite relationships. It also sheds light on the evolutionary history and genomic adaptations of Cuscuta, illustrating the diverse strategies enabling subg. Grammica, Pachystigma, Cuscuta, and Monogynella thrive as parasitic species. These findings provide valuable insights into the molecular mechanisms underlying parasitism and its impact on plastid genome organization.

Codon usage patterns and genomic variation analysis of chloroplast genomes provides new insights into the evolution of Aroideae

Aroideae is an important subfamily of the Araceae family and contains many plants with medicinal and edible value. It is difficult to identify and classify Aroideae species accurately on the basis of morphology alone because of their polymorphic phenotypic traits. The chloroplast genome (CPG) is useful for studying on plant taxonomy and phylogeny, and the analysis of codon usage bias (CUB) in CPGs provides further insights into the intricate phylogenetic relationships among Aroideae. The results showed that the codon third position of the chloroplast genome coding sequence in Aroideae was rich in A and T, with a GC content of 37.91%. The ENC-plot and PR2-plot revealed that the codon usage bias of Aroideae was influenced by multiple factors, with natural selection as the dominant factor. Thirteen to twenty optimal codons ending in A/T were identified in 61 Aroideae species. Additionally, the comparative analysis of CPGs revealed that two single copy regions and non-coding regions were variable in Aroideae. Eight highly divergent regions (Pi > 0.064) were identified (ndhF, rpl32, ccsA, ndhE, ndhG, ndhF-rpl32, ccsA-ndhD, and ndhE-ndhG) , in which ndhE have the potential to serve as a reliable DNA marker to discriminate chloroplasts in Aroideae subfamily. Furthermore, the maximum likelihood-based phylogenetic trees constructed from complete chloroplast genomes and protein-coding sequences presented similar topologies. Principal component clustering analysis based on relative synonymous codon usage values (RSCUs) revealed that Calla was clearly deviated from Montrichardia and Anubias, and that Alocasia was closer to Colocasieae than to Arisaemateae. These findings suggest that the use of RSCU for clustering analysis could offer new theoretical support for species classification and evolution. Our research could provide a theoretical foundation for the chloroplast genetic engineering, taxonomy, and phylogenetic relationships of Aroideae chloroplasts.

Comparative analysis of the complete chloroplast genome of seven Wikstroemia taxa (Thymelaeaceae) provides insights into the genome structure and phylogenetic relationships

MAIN CONCLUSION

New insights into the phylogeny of species in the family Thymelaeaceae and support of the recognition of D. genkwa and D. aurantiaca as species in the genus Wikstroemia are provided. Wikstroemia (Thymelaeaceae) is an economically important genus because some of its species are used in traditional medicine and also contribute to pulp production. The morphological characteristics of Wikstroemia species exhibit continuous natural variation, posing a challenge in accurately distinguishing this genus from its sister genera solely based on morphological traits. Consequently, the classification of, and phylogenetic relationships between, Wikstroemia and its sister genera, as inferred from morphological characteristics, remain contentious. Chloroplast genome information has proven to be a valuable tool in plant phylogeny. Here, we performed a comparative analysis of the chloroplast genomes of 15 species in the genus Wikstroemia, all of which exhibited typical quadripartite structures, with sizes ranging from 150,054 bp to 175,898bp. These genomes encoded 122-143 genes, including 79-95 protein-coding genes, 36-40 tRNA genes, and 8 rRNA genes. The overall GC content displayed minimal variation, ranging from 36.6% to 37.47%. The distributions of SSRs and codon bias exhibited similarities among Wikstroemia species. High variability hotspots were found in 15 intergenic spacers and 5 genes. Phylogenetic analyses consistently grouped all Wikstroemia species into a single clade. Notably, Daphne genkwa and D. aurantiaca were found to be nested within Wikstroemia, rather than being closely related to other Daphne species. Furthermore, phylogenetic analyses suggested that Wikstroemia is paraphyletic relative to Stellera chamaejasme. These findings provide new insights into the phylogeny of Wikstroemia and Daphne within the Thymelaeaceae, contributing to improved species identification and increasing the taxonomic and phylogenetic resolution of Wikstroemia.

Intracellular gene transfer (IGT) events from the mitochondrial genome to the plastid genome of the subtribe ferulinae drude (Apiaceae) and their implications

BACKGROUND

Intracellular gene transfer (IGT) is a phenomenon in genome evolution that occurs between the nuclear and organellar genomes of plants or between the genomes of different organelles. The majority of the plastid genomes (plastomes) in angiosperms have a conserved structure, but some species exhibit unexpected structural variations.

RESULTS

In this study, we focused on the Ferulinae, which includes Ferula, one of the largest genera in the Apiaceae family. We discovered IGTs in the rps12-trnV IGS region of the plastome's inverted repeat (IR). We found that partial mitochondrial genome (mitogenome) sequences, ranging in length from about 2.8 to 5.8 kb, were imported into the plastome. In addition to these, that are known from other Scandiceae subtribes, the Ferulinae plastomes contained two unique mitogenome sequences. We have named these sequences Ferula Mitochondrial Plastid sequences (FeMP). FeMP1 varies in length from 336 bp to 1,100 bp, while FeMP2 ranges from 50 bp to 740 bp in length, with the exception of F. conocaula and F. kingdon-wardii, which do not possess FeMP2. Notably, FeMP2 includes a complete rps7 gene of mitogenome origin. In the maximum likelihood (ML) tree constructed from 79 protein-coding genes, Ferulinae appears as a monophyletic group, while Ferula shows paraphyly. Dorema and Fergania are nested within the Ferula clade, sharing the unusual characteristics of the Ferula plastome. Based on these findings, a reclassification of Dorema and Fergania is warranted.

CONCLUSIONS

Our results shed light on the mechanism of plastome evolution in the Scandiceae with a focus on the unique plastome structure found in the Apiaceae. These findings enhance our understanding of the evolution of plant organellar genomes.

Cyclic electron flow compensates loss of PGDH3 and concomitant stromal NADH reduction

In nature plants constantly experience changes in light intensities. Low illumination limits photosynthesis and growth. However, also high light intensities are a threat to plants as the photosynthetic machinery gets damaged when the incoming energy surpasses the capacity of photochemistry. One limitation of photochemistry is the constant resupply of stromal electron (e-) acceptors, mainly NADP. NADP is reduced at the acceptor-side of photosystem I. The resulting NADPH is utilized by the Calvin-Benson-Bassham cycle (CBBC) and the malate valve to ensure sufficient oxidized NADP ready to accept e- from PSI. Lately, additional pathways, which function as stromal e- sinks under abiotic stress conditions, were discovered. One such reaction in Arabidopsis thaliana is catalyzed by PHOSPHOGLYCERATE DEHYDROGENASE 3 (PGDH3), which diverts e- from the CBBC into NADH. pgdh3 loss-of-function mutants exhibit elevated non-photochemical quenching (NPQ) and fluctuating light susceptibility. To optimize plant photosynthesis in challenging environments knowledge on PGDH3's metabolic integration is needed. We used the source of high NPQ in pgdh3 as a starting point. Our study reveals that increased NPQ originates from high cyclic electron flow (CEF). Interestingly, PGDH3 function seems very important when the CEF-generator PROTON GRADIENT REGULATION5 (PGR5) is lost. Consequently, pgr5pgdh3 double mutants are more sensitive to fluctuating light.

Complete chloroplast genome sequence of Solanum mochiquense, one of the tuber-bearing potato relatives

Solanum mochiquense is one of the wild tuber-bearing Solanum species belonging to the Solanaceae family. In this study, the chloroplast genome sequence of the species was completed with Illumina sequencing technology. The total length of the chloroplast genome is 155,547 bp with a GC content of 37.87%. It comprises a large single copy (LSC) region of 85,941 bp, a small single copy (SSC) region of 18,382 bp, and two inverted repeat regions (IRa and IRb) of 25,612 bp. Additionally, 158 functional genes in the genome were identified, including 105 protein-coding genes, eight ribosomal RNA genes, and 45 transfer RNA genes. Phylogenetic analysis revealed that S. mochiquense is grouped into a large clade with other Solanum species including cultivated potatoes (S. tuberosum). This study provides useful genomic information for future breeding and evolutionary studies of S. mochiquense and other Solanum species.

Climatic factors, but not geographic distance, promote genetic structure and differentiation of Cleistogenes squarrosa (Trin.) Keng populations

Climate can shape plant genetic diversity and genetic structure, and genetic diversity and genetic structure can reflect the adaptation of plants to climate change. We used rbcl and trnL-trnF sequences to analyze the genetic diversity and genetic structure of C. squarrosa under the influence of different environmental factors in Inner Mongolia grassland. The results showed that the genetic diversity of this species was low. (The trnL-trnF sequences have higher genetic diversity than rbcl sequences.) C. squarrosa had low genetic diversity compared to other prairie plants, but had a more pronounced genetic structure. The haplotype network diagram of the combined sequences could be divided into two categories, and the results of the NJ, MP, and ML trees also showed that the haplotypes were divided into two branches. The results of genetic structure analysis showed that that the populations located in the desert steppe fall into exactly one cluster, and the populations located in the typical steppe fall into exactly another cluster. The neutrality tests were all negative and the mismatch distribution also showed a single peak across the population, suggesting that C. squarrosa had undergone population expansion and was well adapted to the local environment. The results of the mantel test showed that climate had a greater influence on the genetic distance of C. squarrosa, with annual precipitation having a higher influence than mean annual temperature. This study provided basic genetic information on the genetic structure of C. squarrosa and contributes to the study of genetic adaptation mechanisms in grassland plants.

Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus Tulipa L

Species of Tulipa are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features of the complete chloroplast genome sequence of four local and endangered species including T. alberti, T. kaufmanniana, T. greigii, and T. dubia from Kazakhstan using Illumina sequencing technology. The comparative analyses revealed that the complete genomes of four species were highly conserved in terms of total genome size (152. 006 bp - 152. 382 bp), including a pair of inverted repeat regions (26. 330 bp - 26. 371 bp), separated by a large single copy region (82.169 bp - 82,378 bp) and a small copy region (17.172 bp -17.260 bp). Total GC content (36.58-36.62 %), gene number (131), and intron length (540 bp - 2620 bp) of 28 genes. The complete genomes of four species showed nucleotide diversity (π =0,003257). The total number of SSR loci was 159 in T. alberti, 158 in T. kaufmanniana, 174 in T. greigii, and 163 in T. dubia. The result indicated that ten CDS genes, namely rpoC2, cemA, rbcL, rpl36, psbH, rps3, rpl22, ndhF, ycf1, and matK, with effective polymorphic simple sequence repeats (SSRs), high sequence variability (SV) ranging from 2.581 to 6.102, and high nucleotide diversity (Pi) of these loci ranging from 0,004 to 0,010. For all intergenic regions longer than 150 bp, twenty one most variable regions were found with high sequence variability (SV) ranging from 4,848 to 11,862 and high nucleotide diversity (Pi) ranging from 0,01599 to 0,01839. Relative synonymous codon usage (RSCU) analysis was used to identify overrepresented and underrepresented codons for each amino acid. Based on the phylogenic analysis, the sequences clustered into four major groups, reflecting distinct evolutionary lineages corresponding to the subgenera Eriostemons, Tulipa, and Orithyia. Notably, T. greigii was distinctively grouped with species from Orithyia and Eriostemons rather than with other Tulipa species, suggesting a unique evolutionary history potentially shaped by geographical isolation or specific ecological pressures. The complete chloroplast genome of the four Tulipa species provides fundamental information for future research studies, even for designing the high number of available molecular markers.

Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae)

BACKGROUND

Capsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear.

RESULTS

The cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281-306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another.

CONCLUSIONS

This study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

Structure, function, and assembly of PSI in thylakoid membranes of vascular plants

The photosynthetic apparatus is formed by thylakoid membrane-embedded multiprotein complexes that carry out linear electron transport in oxygenic photosynthesis. The machinery is largely conserved from cyanobacteria to land plants, and structure and function of the protein complexes involved are relatively well studied. By contrast, how the machinery is assembled in thylakoid membranes remains poorly understood. The complexes participating in photosynthetic electron transfer are composed of many proteins, pigments, and redox-active cofactors, whose temporally and spatially highly coordinated incorporation is essential to build functional mature complexes. Several proteins, jointly referred to as assembly factors, engage in the biogenesis of these complexes to bring the components together in a step-wise manner, in the right order and time. In this review, we focus on the biogenesis of the terminal protein supercomplex of the photosynthetic electron transport chain, PSI, in vascular plants. We summarize our current knowledge of the assembly process and the factors involved and describe the challenges associated with resolving the assembly pathway in molecular detail.

Phylogenomics analysis of Scutellaria (Lamiaceae) of the world

BACKGROUND

Scutellaria, a sub-cosmopolitan genus, stands as one of the Lamiaceae family's largest genera, encompassing approximately 500 species found in both temperate and tropical montane regions. Recognized for its significant medicinal properties, this genus has garnered attention as a research focus, showcasing anti-cancer, anti-inflammatory, antioxidant, and hepatoprotective qualities. Additionally, it finds application in agriculture and horticulture. Comprehending Scutellaria's taxonomy is pivotal for its effective utilization and conservation. However, the current taxonomic frameworks, primarily based on morphological characteristics, are inadequate. Despite several phylogenetic studies, the species relationships and delimitations remain ambiguous, leaving the genus without a stable and reliable classification system.

RESULTS

This study analyzed 234 complete chloroplast genomes, comprising 220 new and 14 previously published sequences across 206 species, subspecies, and varieties worldwide. Phylogenetic analysis was conducted using six data matrices through Maximum Likelihood and Bayesian Inference, resulting in a robustly supported phylogenetic framework for Scutellaria. We propose three subgenera, recommending the elevation of Section Anaspis to subgeneric rank and the merging of Sections Lupulinaria and Apeltanthus. The circumscription of Subgenus Apeltanthus and Section Perilomia needs to be reconsidered. Comparative analysis of chloroplast genomes highlighted the IR/SC boundary feature as a significant taxonomic indicator. We identified a total of 758 SSRs, 558 longer repetitive sequences, and ten highly variable regions, including trnK-rps16, trnC-petN, petN-psbM, accD-psaI, petA-psbJ, rpl32-trnL, ccsA-ndhD, rps15-ycf1, ndhF, and ycf1. These findings serve as valuable references for future research on species identification, phylogeny, and population genetics.

CONCLUSIONS

The phylogeny of Scutellaria, based on the most comprehensive sample collection to date and complete chloroplast genome analysis, has significantly enhanced our understanding of its infrageneric relationships. The extensive examination of chloroplast genome characteristics establishes a solid foundation for the future development and utilization of Scutellaria, an important medicinal plant globally.

Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle

BACKGROUND

The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed.

RESULTS

Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species.

CONCLUSIONS

Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.

Intraspecific Differentiation of Styrax japonicus (Styracaceae) as Revealed by Comparative Chloroplast and Evolutionary Analyses

Styrax japonicus is a medicinal and ornamental shrub belonging to the Styracaceae family. To explore the diversity and characteristics of the chloroplast genome of S. japonicus, we conducted sequencing and comparison of the chloroplast genomes of four naturally distributed S. japonicus. The results demonstrated that the four chloroplast genomes (157,914-157,962 bp) exhibited a typical quadripartite structure consisting of a large single copy (LSC) region, a small single copy (SSC) region, and a pair of reverse repeats (IRa and IRb), and the structure was highly conserved. DNA polymorphism analysis revealed that three coding genes (infA, psbK, and rpl33) and five intergene regions (petA-psbJ, trnC-petN, trnD-trnY, trnE-trnT, and trnY-trnE) were identified as mutation hotspots. These genetic fragments have the potential to be utilized as DNA barcodes for future identification purposes. When comparing the boundary genes, a small contraction was observed in the IR region of four S. japonicus. Selection pressure analysis indicated positive selection for ycf1 and ndhD. These findings collectively suggest the adaptive evolution of S. japonicus. The phylogenetic structure revealed conflicting relationships among several S. japonicus, indicating divergent evolutionary paths within this species. Our study concludes by uncovering the genetic traits of the chloroplast genome in the differentiation of S. japonicus variety, offering fresh perspectives on the evolutionary lineage of this species.

Comparative chloroplast genomes of Dactylicapnos species: insights into phylogenetic relationships

BACKGROUND

Dactylicapnos is a climbing herbaceous vine, distributed from the Himalayas to southwestern China, and some of the species have important medicinal values. However, the chloroplast genomes of Dactylicapnos have never been investigated. In this study, chloroplast genomes of seven Dactylicapnos species covering all three sections and one informal group of Dactylicapnos were sequenced and assembled, and the detailed comparative analyses of the chloroplast genome structure were provided for the first time.

RESULTS

The results showed that the chloroplast genomes of Dactylicapnos have a typical quadripartite structure with lengths from 172,344 bp to 176,370 bp, encoding a total of 133-140 genes, containing 88-94 protein-coding genes, 8 rRNAs and 37-39 tRNAs. 31 codons were identified as relative synonymous codon usage values greater than one in the chloroplast genome of Dactylicapnos genus based on 80 protein-coding genes. The results of the phylogenetic analysis showed that seven Dactylicapnos species can be divided into three main categories. Phylogenetic analysis revealed that seven species form three major clades which should be treated as three sections.

CONCLUSIONS

This study provides the initial report of the chloroplast genomes of Dactylicapnos, their structural variation, comparative genomic and phylogenetic analysis for the first time. The results provide important genetic information for development of medical resources, species identification, infrageneric classification and diversification of Dactylicapnos.

Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome

BACKGROUND

Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear.

RESULTS

We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species.

CONCLUSIONS

These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.

Intraspecific and Intrageneric Genomic Variation across Three Sedum Species (Crassulaceae): A Plastomic Perspective

Sedum is the largest succulent genus in Crassulaceae. Because of predominant maternal inheritance, little recombination, and slow evolution, plastomes can serve as powerful super barcodes for inter- or intra-species phylogenetic analyses. While previous research has focused on plastomes between Sedum species, intra-species studies are scarce. Here, we sequenced plastomes from three Sedum species (Sedum alfredii, Sedum plumbizincicola, and Sedum japonicum) to understand their evolutionary relationships and plastome structural evolution. Our analyses revealed minimal size and GC content variation across species. However, gene distribution at IR boundaries, repeat structures, and codon usage patterns showed diversity at both inter-specific and intra-specific levels. Notably, an rps19 gene expansion and a bias toward A/T-ending codons were observed. Codon aversion motifs also varied, potentially serving as markers for future studies. Phylogenetic analyses confirmed the non-monophyly of Sedum and divided the Acre clade into two groups. Individuals from the same species clustered together, with strong support for the relationships between S. alfredii, S. tricarpum, and S. plumbizincicola. Additionally, S. japonicum clearly affiliates with the Acre clade. This study provides valuable insights into both intra-specific and intra-generic plastome variation in Sedum, as well as overall plastome evolution within the genus.

Comparative Analysis of Chloroplast Genomes for the Genus Manglietia Blume (Magnoliaceae): Molecular Structure and Phylogenetic Evolution

Manglietia Blume, belonging to the Magnoliaceae family and mainly distributed in tropical and subtropical regions of Asia, has great scientific and economic value. In this study, we employed next-generation sequencing followed by de novo assembly to investigate the adaptive evolution of Manglietia using plastid genetic information. We newly sequenced the complete or nearly complete plastomes of four Manglietia species (Manglietia aromatica, Manglietia calcarea, Manglietia kwangtungensis, and Manglietia glauca) and conducted comparative analysis with seventeen published plastomes to examine the evolutionary pattern within this genus. The plastomes of these five newly sequenced Manglietia species range from 157,093 bp (M. calcarea2) to 160,493 bp (M. kwangtungensis), all exhibiting circular structures when mapped. Nucleotide diversity was observed across the plastomes, leading us to identify 13 mutational hotspot regions, comprising eight intergenic spacer regions and five gene regions. Our phylogenetic analyses based on 77 protein-coding genes generated phylogenetic relationships with high support and resolution for Manglietia. This genus can be divided into three clades, and the previously proposed infrageneric classifications are not supported by our studies. Furthermore, the close affinity between M. aromatica and M. calcarea is supported by the present work, and further studies are necessary to conclude the taxonomic treatment for the latter. These results provide resources for the comparative plastome, breeding, and plastid genetic engineering of Magnoliaceae and flowering plants.

The newly assembled chloroplast genome of Aeluropus littoralis: molecular feature characterization and phylogenetic analysis with related species

Aeluropus littoralis, a halophyte grass, is widely distributed from the Mediterranean to the Indian subcontinent through the Mongolian Gobi. This model halophyte has garnered increasing attention owing to its use as forage and its high tolerance to environmental stressors. The chloroplast genomes of many plants have been extensively examined for molecular, phylogenetic and transplastomic applications. However, no published research on the A. littoralis chloroplast (cp) genome was discovered. Here, the entire chloroplast genome of A. littoralis was assembled implementing accurate long-read sequences. The entire chloroplast genome, with an estimated length of 135,532 bp (GC content: 38.2%), has a quadripartite architecture and includes a pair of inverted repeat (IR) regions, IRa and IRb (21,012 bp each), separated by a large and a small single-copy regions (80,823 and 12,685 bp, respectively). The features of A. littoralis consist of 133 genes that synthesize 87 peptides, 38 transfer RNAs, and 8 ribosomal RNAs. Of these genes, 86 were unique, whereas 19 were duplicated in IR regions. Additionally, a total of forty-six simple sequence repeats, categorized into 32-mono, four-di, two-tri, and eight-tetranucleotides, were discovered. Furthermore, ten sets of repeats greater than 20 bp were located primarily in the LSC region. Evolutionary analysis based on chloroplast sequence data revealed that A. littoralis with A. lagopoides and A. sinensis belong to the Aeluropodinae subtribe, which is a sister to the Eleusininae in the tribe Cynodonteae and the subfamily Chloridoideae. This subfamily belongs to the PACMAD clade, which contains the majority of the C4 photosynthetic plants in the Poaceae. The newly constructed A. littoralis cp genome offers valuable knowledge for DNA barcoding, phylogenetic, transplastomic research, and other biological studies.

Complete chloroplast genome and comparison of herbicides toxicity on Aeschynomene indica (Leguminosae) in upland direct-seeding paddy field

BACKGROUND

Indian jointvetch (Aeschynomene indica) is a common and pernicious weed found in the upland direct-seeding rice fields in the lower reaches of the Yangtze River in China. However, there are few reports on the degree of harm, genetic characteristics, and management methods of this weed. The purpose of this study is to clarify the harm of Indian jointvetch to upland direct-seeding rice, analyze the genetic characteristics of this weed based on chloroplast genomics and identify its related species, and screen herbicides that are effective in managing this weed in upland direct-seeding rice fields.

RESULTS

In a field investigation in upland direct-seeding rice paddies in Shanghai and Jiangsu, we determined that the plant height and maximum lateral distance of Indian jointvetch reached approximately 134.2 cm and 57.9 cm, respectively. With Indian jointvetch present at a density of 4/m2 and 8/m2, the yield of rice decreased by approximately 50% and 70%, respectively. We further obtained the first assembly of the complete chloroplast (cp.) genome sequence of Indian jointvetch (163,613 bp). There were 161 simple sequence repeats, 166 long repeats, and 83 protein-encoding genes. The phylogenetic tree and inverted repeat region expansion and contraction analysis based on cp. genomes demonstrated that species with closer affinity to A. indica included Glycine soja, Glycine max, and Sesbania cannabina. Moreover, a total of 3281, 3840, and 3838 single nucleotide polymorphisms were detected in the coding sequence regions of the cp. genomes of S. cannabina voucher IBSC, G. soja, and G. max compared with the A. indica sequence, respectively. A greenhouse pot experiment indicated that two pre-emergence herbicides, saflufenacil and oxyfluorfen, and two post-emergence herbicides, florpyrauxifen-benzyl and penoxsulam, can more effectively manage Indian jointvetch than other common herbicides in paddy fields. The combination of these two types of herbicides is recommended for managing Indian jointvetch throughout the entire growth period of upland direct-seeding rice.

CONCLUSIONS

This study provides molecular resources for future research focusing on the identification of the infrageneric taxa, phylogenetic resolution, and biodiversity of Leguminosae plants, along with recommendations for reliable management methods to control Indian jointvetch.

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.

Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus

Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.

Plastid genome of Passiflora tripartita var. mollissima (poro-poro) from Huánuco, Peru

Passiflora tripartita var. mollissima, known locally as poro-poro, is an important native fruit used in traditional Peruvian medicine with relevant agro-industrial and pharmaceutical potential for its antioxidant capacity for human health. However, to date, only a few genetic data are available, which limits exploring its genetic diversity and developing new genetic studies for its improvement. We report the poro-poro plastid genome to expand the knowledge of its molecular markers, evolutionary studies, molecular pathways, and conservation genetics. The complete chloroplast (cp) genome is 163,451 bp in length with a typical quadripartite structure, containing a large single-copy region of 85,525 bp and a small single-copy region of 13,518 bp, separated by a pair of inverted repeat regions (IR) of 32,204 bp, and the overall GC content was 36.87%. This cp genome contains 128 genes (110 genes were unique and 18 genes were found duplicated in each IR region), including 84 protein-coding genes, 36 transfer RNA-coding genes, eight ribosomal RNA-coding genes, and 13 genes with introns (11 genes with one intron and two genes with two introns). The inverted repeat region boundaries among species were similar in organization, gene order, and content, with a few revisions. The phylogenetic tree reconstructed based on single-copy orthologous genes and maximum likelihood analysis demonstrates poro-poro is most closely related to Passiflora menispermifolia and Passiflora oerstedii. In summary, our study constitutes a valuable resource for studying molecular evolution, phylogenetics, and domestication. It also provides a powerful foundation for conservation genetics research and plant breeding programs. To our knowledge, this is the first report on the plastid genome of Passiflora tripartita var. mollissima from Peru.

Characteristics of chloroplast and mitochondrial genomes and intracellular gene transfer in the Korean endemic shrub, Sophora koreensis Nakai (Fabaceae)

Sophora koreensis Nakai, an endemic species distributed only in the Korean Peninsula, is of great geographical, economic, and taxonomic importance. Although its complete chloroplast (cp) genome sequence has been reported, its mitochondrial (mt) genome sequence has not yet been studied. Therefore, in this study, we aimed to investigate its mt genome sequence and compare it with those reported for other Fabaceae species. Total genomic DNA was extracted from fresh S. koreensis leaves collected from natural habitats in Gangwon-do Province, South Korea. This was followed by polymerase chain reaction (PCR) amplification of cpDNA insertions in the mt genome and the detection of microsatellites and dispersed repeats in the cp and mt genomes. Finally, the cp and mt genomes of S. koreensis were compared with those reported for other Fabaceae species. The cp sequence of S. koreensis showed identical gene orders and contents as those previously reported. Only six substitutions and one deletion were detected with 99 % homology. Conversely, the complete mt genome sequence, which was 517,845 bp in length and encoded 61 genes, including 43 protein-coding, 15 transfer RNAs, and 3 ribosomal RNA genes, was considerably different from that of S. japonica in terms of gene order and composition. Further, the mt genome of S. koreensis included ca. 7 and 3 kb insertions, representing an intracellular gene transfer (IGT) event, and the regions with these insertions were determined to be originally present in the cp genome. This IGT event was also confirmed via PCR amplification. IGT events can be induced via biological gene expression control or the use of repetitive sequences, and they provide important insights into the evolutionary lineage of S. koreensis. However, further studies are needed to clarify the gene transfer mechanisms between the two organelles.

Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa

Alfalfa (Medicago sativa) is a perennial forage legume that is widely distributed all over the world; therefore, it has an extremely complex genetic background. Though population structure and phylogenetic studies have been conducted on a large group of alfalfa nuclear genomes, information about the chloroplast genomes is still lacking. Chloroplast genomes are generally considered to be conservative and play an important role in population diversity analysis and species adaptation in plants. Here, 231 complete alfalfa chloroplast genomes were successfully assembled from 359 alfalfa resequencing data, on the basis of which the alfalfa chloroplast pan-genome was constructed. We investigated the genetic variations of the alfalfa chloroplast genome through comparative genomic, genetic diversity, phylogenetic, population genetic structure, and haplotype analysis. Meanwhile, the expression of alfalfa chloroplast genes under cold stress was explored through transcriptome analysis. As a result, chloroplast genomes of 231 alfalfa lack an IR region, and the size of the chloroplast genome ranges from 125,192 bp to 126,105 bp. Using population structure, haplotypes, and construction of a phylogenetic tree, it was found that alfalfa populations could be divided into four groups, and multiple highly variable regions were found in the alfalfa chloroplast genome. Transcriptome analysis showed that tRNA genes were significantly up-regulated in the cold-sensitive varieties, while rps7, rpl32, and ndhB were down-regulated, and the editing efficiency of ycf1, ycf2, and ndhF was decreased in the cold-tolerant varieties, which may be due to the fact that chloroplasts store nutrients through photosynthesis to resist cold. The huge number of genetic variants in this study provide powerful resources for molecular markers.

PEP-ASSOCIATED PROTEIN 3 regulates rice tiller formation and grain yield by controlling chloroplast biogenesis

Plastid-encoded RNA polymerase (PEP) plays a pivotal role in chloroplast development by governing the transcription of chloroplast genes, and PEP-associated proteins (PAPs) modulate PEP transcriptional activity. Therefore, PAPs provide an intriguing target for those efforts to improve yield, by enhancing chloroplast development. In this study, we identified the rice (Oryza sativa) OsPAP3 gene and characterized its function in chloroplast development. OsPAP3 expression was light-dependent and leaf-specific, similar to the PEP-dependent chloroplast gene RUBISCO LARGE SUBUNIT (OsRbcL), and OsPAP3 protein localized to chloroplast nucleoids where PEP functions. Analysis of loss-of-function and gain-of-function mutants showed that the expression of OsPAP3 is tightly linked to chloroplast gene expression and chloroplast biogenesis in rice. Homozygous knockout mutants of OsPAP3 had fewer chloroplasts than wild type, whereas plants overexpressing OsPAP3 had more chloroplasts. Also, OsPAP3 knockout suppressed the PEP-dependent expression of chloroplast genes, but OsPAP3 overexpression increased their expression. These findings indicate that OsPAP3 regulates chloroplast biogenesis in rice by controlling the PEP-dependent expression of chloroplast genes. More importantly, data from 3 seasons of field cultivation revealed that the overexpression of OsPAP3 improves rice grain yield by approximately 25%, largely due to increased tiller formation. Collectively, these observations suggest that OsPAP3 regulates rice growth and productivity by promoting chloroplast development.

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.

An insight on the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina, Asclepiadoideae (Apocynaceae)

Abstract We studied the complete chloroplast genome of Gomphocarpus siniacus and Duvalia velutina from Asclepiadoideae subfamily; due to their medicinal importance and distribution worldwide their interest became high. In this study we analyzed the complete chloroplast genomes of G. siniacus and D. velutina using Illumina sequencing technology. The sequences were compared with the other species from Apocynaceae family. The complete genome of G. siniacus is 162,570 bp while D. velutina has154, 478 bp in length. Both genomes consist of 119 genes; encode 31 tRNA genes, and eight rRNA genes. Comparative studies of the two genomes showed variations in SSR markers in which G. siniacus possesses 223 while D. velutina has 186. This could be used for barcoding in order to aid in easy identification of the species. Phylogenetic analysis on the other hand reaffirms the tribal position of G. siniacus in Asclepiadeae and D. velutina in Ceropegieae. These findings could be used in subsequent research studies of angiosperms identification, genetic engineering, herb genomics and phylogenomic studies of Apocynaceae family.

Comprehensive analysis of complete chloroplast genome sequence of Plantago asiatica L. (Plantaginaceae)

Plantago asiatica L. is a representative individual species of Plantaginaceae, whose high reputation is owed to its edible and medicinal values. However, the phylogeny and genes of the P. asiatica chloroplast have not yet been well described. Here we report the findings of a comprehensive analysis of the P. asiatica chloroplast genome. The P. asiatica chloroplast genome is 164,992 bp, circular, and has a GC content of 37.98%. The circular genome contains 141 genes, including 8 rRNAs, 38 tRNAs, and 95 protein-coding genes. Seventy-two simple sequence repeats are detected. Comparative chloroplast genome analysis of six related species suggests that a higher similarity exists in the coding region than the non-coding region, and differences in the degree of preservation is smaller between P. asiatica and Plantago depressa than among others. Our phylogenetic analysis illustrates P. asiatica has a relatively close relationship with P. depressa, which was also divided into different clades with Plantago ovata and Plantago lagopus in the genus Plantago. This analysis of the P. asiatica chloroplast genome contributes to an improved deeply understanding of the evolutionary relationships among Plantaginaceae.

A multiple shoot induction system for peptide-mediated gene delivery into plastids in Arabidopsis thaliana, Nicotiana benthamiana, and Fragaria×ananassa

The plastid is a promising target for the production of valuable biomolecules via genetic engineering. We recently developed a plastid-specific gene delivery system for leaves or seedlings using KH-AtOEP34, a functional peptide composed of the polycationic DNA-binding peptide KH and the Arabidopsis thaliana plastid-targeting peptide OEP34. Here, we established a liquid culture system for inducing multiple shoots in the model plants A. thaliana and Nicotiana benthamiana and the crop plant strawberry (Fragaria×ananassa) and tested the use of these plant materials for peptide-mediated gene delivery to plastids. Our liquid culture system efficiently induced multiple shoots that were enriched in meristems. Using these meristems, we performed KH-AtOEP34-mediated gene delivery to plastids and tested the delivery and integration of a cassette composed of the spectinomycin resistance gene aadA, the GFP reporter gene, and sequences homologous to plastid DNA. Genotyping PCR revealed the integration of the cassette DNA into plastid DNA several days after delivery in all three plants. Confocal laser scanning microscopy and immunoblotting confirmed the presence of plasmid-derived GFP in the plastids of meristems, indicating that the plasmid DNA was successfully integrated into plastid DNA and that the cassette was expressed. These results suggest the meristems developed in our liquid culture system are applicable to peptide-mediated delivery of exogeneous DNA into plastids. The multiple shoots generated in our liquid novel culture system represent promising materials for in planta peptide-mediated plastid transformation in combination with spectinomycin selection.

Genomic exploration of Sesuvium sesuvioides: comparative study and phylogenetic analysis within the order Caryophyllales from Cholistan desert, Pakistan

BACKGROUND

The Aizoaceae family's Sesuvium sesuvioides (Fenzl) Verdc is a medicinal species of the Cholistan desert, Pakistan. The purpose of this study was to determine the genomic features and phylogenetic position of the Sesuvium genus in the Aizoaceae family. We used the Illumina HiSeq2500 and paired-end sequencing to publish the complete chloroplast sequence of S. sesuvioides.

RESULTS

The 155,849 bp length cp genome sequence of S. sesuvioides has a 36.8% GC content. The Leucine codon has the greatest codon use (10.6%), 81 simple sequence repetitions of 19 kinds, and 79 oligonucleotide repeats. We investigated the phylogeny of the order Caryophyllales' 27 species from 23 families and 25 distinct genera. The maximum likelihood tree indicated Sesuvium as a monophyletic genus, and sister to Tetragonia. A comparison of S. sesuvioides, with Sesuvium portulacastrum, Mesembryanthemum crystallinum, Mesembryanthemum cordifolium, and Tetragonia tetragonoides was performed using the NCBI platform. In the comparative investigation of genomes, all five genera revealed comparable cp genome structure, gene number and composition. All five species lacked the rps15 gene and the rpl2 intron. In most comparisons with S. sesuvioides, transition substitutions (Ts) were more frequent than transversion substitutions (Tv), producing Ts/Tv ratios larger than one, and the Ka/Ks ratio was lower than one. We determined ten highly polymorphic regions, comprising rpl22, rpl32-trnL-UAG, trnD-GUC-trnY-GUA, trnE-UUC-trnT-GGU, trnK-UUU-rps16, trnM-CAU-atpE, trnH-GUG-psbA, psaJ-rpl33, rps4-trnT-UGU, and trnF-GAA-ndhJ.

CONCLUSION

The whole S. sesuvioides chloroplast will be examined as a resource for in-depth taxonomic research of the genus when more Sesuvium and Aizoaceae species are sequenced in the future. The chloroplast genomes of the Aizoaceae family are well preserved, with little alterations, indicating the family's monophyletic origin. This study's highly polymorphic regions could be utilized to build realistic and low-cost molecular markers for resolving taxonomic discrepancies, new species identification, and finding evolutionary links among Aizoaceae species. To properly comprehend the evolution of the Aizoaceae family, further species need to be sequenced.

Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, codon usage bias, and phylogenetic relationships

The phylogeny of the species from Phrymaceae and Mazaceae has undergone many adjustments and changes in recent years. Moreover, there is little plastome information on the Phrymaceae. In this study, we compared the plastomes of six species from the Phrymaceae and 10 species from the Mazaceae. The gene order, contents, and orientation of the 16 plastomes were found to be highly similar. A total of 13 highly variable regions were identified among the 16 species. An accelerated rate of substitution was found in the protein-coding genes, particularly cemA and matK. The combination of effective number of codons, parity rule 2, and neutrality plots revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported {Mazaceae [(Phrymaceae + Wightiaceae) + (Paulowniaceae + Orobanchaceae)]} relationships in the Lamiales. Our findings can provide useful information to analyze the phylogeny and molecular evolution within the Phrymaceae and Mazaceae.

Comparison of chloroplast genomes and phylogenetic analysis of four species in Quercus section Cyclobalanopsis

The identification in Quercus L. species was considered to be difficult all the time. The fundamental phylogenies of Quercus have already been discussed by morphological and molecular means. However, the morphological characteristics of some Quercus groups may not be consistent with the molecular results (such as the group Helferiana), which may lead to blurring of species relationships and prevent further evolutionary researches. To understand the interspecific relationships and phylogenetic positions, we sequenced and assembled the CPGs (160,715 bp-160842 bp) of four Quercus section Cyclobalanopsis species by Illumina pair-end sequencing. The genomic structure, GC content, and IR/SC boundaries exhibited significant conservatism. Six highly variable hotspots were detected in comparison analysis, among which rpoC1, clpP and ycf1 could be used as molecular markers. Besides, two genes (petA, ycf2) were detected to be under positive selection pressure. The phylogenetic analysis showed: Trigonobalanus genus and Fagus genus located at the base of the phylogeny tree; The Quercus genus species were distincted to two clades, including five sections. All Compound Trichome Base species clustered into a single branch, which was in accordance with the results of the morphological studies. But neither of group Gilva nor group Helferiana had formed a monophyly. Six Compound Trichome Base species gathered together in pairs to form three branch respectively (Quercus kerrii and Quercus chungii; Quercus austrocochinchinensis with Quercus gilva; Quercus helferiana and Quercus rex). Due to a low support rate (0.338) in the phylogeny tree, the interspecies relationship between the two branches differentiated by this node remained unclear. We believe that Q. helferiana and Q. kerrii can exist as independent species due to their distance in the phylogeny tree. Our study provided genetic information in Quercus genus, which could be applied to further studies in taxonomy and phylogenetics.

Complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens: genome structures, comparative and phylogenetic analysis

The genus Cerastium includes about 200 species that are mostly found in the temperate climates of the Northern Hemisphere. Here we report the complete chloroplast genomes of Cerastium alpinum, C. arcticum and C. nigrescens. The length of cp genomes ranged from 147,940 to 148,722 bp. Their quadripartite circular structure had the same gene organization and content, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Repeat sequences varied from 16 to 23 per species, with palindromic repeats being the most frequent. The number of identified SSRs ranged from 20 to 23 per species and they were mainly composed of mononucleotide repeats containing A/T units. Based on Ka/Ks ratio values, most genes were subjected to purifying selection. The newly sequenced chloroplast genomes were characterized by a high frequency of RNA editing, including both C to U and U to C conversion. The phylogenetic relationships within the genus Cerastium and family Caryophyllaceae were reconstructed based on the sequences of 71 protein-coding genes. The topology of the phylogenetic tree was consistent with the systematic position of the studied species. All representatives of the genus Cerastium were gathered in a single clade with C. glomeratum sharing the least similarity with the others.

The complete chloroplast genome of Phyla nodiflora (Linnaeus) Greene (1899) from the Verbenaceae family and its phylogenetic analysis

Phyla nodiflora (Linnaeus) Greene (1899) is a perennial creeping herb belonging to the family Verbenaceae. It has numerous pharmacological properties, including anti-dandruff, anti-inflammatory, anti-oxidant, anti-melanogenesis, anti-hypertensive, and anti-hyperuricemic properties. We generated the complete chloroplast genome sequence of P. nodiflora using Illumina paired-end sequencing data. The P. nodiflora chloroplast genome is 154,341 bp in length, containing a large single copy (LSC) region of 85,185 bp and a small single copy (SSC) region of 17,222 bp, separated by a pair of inverted repeats (IRs) of 25,967 bp. The genome contained 128 genes, including 86 protein-coding, 34 tRNA, and eight rRNA genes. Six genes had one intron, one gene had two introns, and the others did not have an intron. Overall GC content of the chloroplast genome was 39%, while those of LSC, SSC, and IR regions were 38.2%, 33.7%, and 44%, respectively. Phylogenetic analysis of the chloroplast genome revealed that P. nodiflora is closely related to the other species from Verbenaceae.

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.

The complete chloroplast genome of Ocimum americanum Linnaeus 1755 and phylogenetic analysis among the Lamiaceae family

Ocimum americanum Linnaeus 1755 (Lemon basil) is an essential medicinal species in the Ocimum genus. Its leaf decoction is traditionally used to treat diabetes, constipation, diarrhea, piles, and dysentery. The essential oils from this species have intense fungicidal activity. The complete chloroplast genome sequence of O. americanum was assembled from Illumina paired-end sequencing data. The O. americanum chloroplast genome was 152,460 bp in length, containing a large single copy (LSC) region of 83,459 bp and a small single copy (SSC) region of 17,607 bp, separated by a pair of inverted repeats (IRs) of 25,697 bp. The genome contained 134 unique genes, including 89 protein-coding, 37 tRNA, and eight rRNA genes. Among them, nine genes had a single intron, and two genes contained two introns. The overall GC content of the chloroplast genome was 38%, while the corresponding values of LSC, SSC, and IR regions were 35.8%, 31.7%, and 43.1%, respectively. In the phylogenetic analysis, all the Ocimum species formed a group closely related to Plectranthus barbatus. O. americanum was more closely related to O. gratissimum and O. basilicum than the other species of Ocimum included in this study.

Dig up tall fescue plastid genomes for the identification of morphotype-specific DNA variants

BACKGROUND

Tall fescue (Festuca arundinacea Schreb.) is an important cool-season perennial grass species. Hexaploid tall fescue has three distinct morphotypes used either as forage or turf purposes. Its chloroplast genome is conserved due to it being maternally inherited to the next generation progenies. To identify morphotype-specific DNA markers and the genetic variations, plastid genomes of all three tall fescue morphotypes, i.e., Continental cv. Texoma MaxQ II, Rhizomatous cv. Torpedo, and Mediterranean cv. Resolute, have been sequenced using Illumina MiSeq sequencing platform.

RESULTS

The plastid genomes of Continental-, Rhizomatous-, and Mediterranean tall fescue were assembled into circular master molecules of 135,283 bp, 135,336 bp, and 135,324 bp, respectively. The tall fescue plastid genome of all morphotypes contained 77 protein-coding, 20 tRNAs, four rRNAs, two pseudo protein-coding, and three hypothetical protein-coding genes. We identified 630 SNPs and 124 InDels between Continental and Mediterranean, 62 SNPs and 20 InDels between Continental and Rhizomatous, and 635 SNPs and 123 InDels between Rhizomatous and Mediterranean tall fescue. Only four InDels in four genes (ccsA, rps18, accD, and ndhH-p) were identified, which discriminated Continental and Rhizomatous plastid genomes from the Mediterranean plastid genome. Here, we identified and reported eight InDel markers (NRITCHL18, NRITCHL35, NRITCHL43, NRITCHL65, NRITCHL72, NRITCHL101, NRITCHL104, and NRITCHL110) from the intergenic regions that can successfully discriminate tall fescue morphotypes. Divergence time estimation revealed that Mediterranean tall fescue evolved approximately 7.09 Mya, whereas the divergence between Continental- and Rhizomatous tall fescue occurred about 0.6 Mya.

CONCLUSIONS

To our knowledge, this is the first report of the assembled plastid genomes of Rhizomatous and Mediterranean tall fescue. Our results will help to identify tall fescue morphotypes at the time of pre-breeding and will contribute to the development of lawn and forage types of commercial varieties.

Deciphering the complex cotton genome for improving fiber traits and abiotic stress resilience in sustainable agriculture

BACKGROUND

Understanding the complex cotton genome is of paramount importance in devising a strategy for sustainable agriculture. Cotton is probably the most economically important cash crop known for its cellulose-rich fiber content. The cotton genome has become an ideal model for deciphering polyploidization due to its polyploidy, setting it apart from other major crops. However, the main challenge in understanding the functional and regulatory functions of many genes in cotton is still the complex cotton polyploidy genome, which is not limited to a single role. Cotton production is vulnerable to the sensitive effects of climate change, which can alter or aggravate soil, pests, and diseases. Thus, conventional plant breeding coupled with advanced technologies has led to substantial progress being made in cotton production.

GENOMICS APPROACHES IN COTTON

In the frontier areas of genomics research, cotton genomics has gained momentum accomplished by robust high-throughput sequencing platforms combined with novel computational tools to make the cotton genome more tractable. Advances in long-read sequencing have allowed for the generation of the complete set of cotton gene transcripts giving incisive scientific knowledge in cotton improvement. In contrast, the integration of the latest sequencing platforms has been used to generate multiple high-quality reference genomes in diploid and tetraploid cotton. While pan-genome and 3D genomic studies are still in the early stages in cotton, it is anticipated that rapid advances in sequencing, assembly algorithms, and analysis pipelines will have a greater impact on advanced cotton research.

CONCLUSIONS

This review article briefly compiles substantial contributions in different areas of the cotton genome, which include genome sequencing, genes, and their molecular regulatory networks in fiber development and stress tolerance mechanism. This will greatly help us in understanding the robust genomic organization which in turn will help unearth candidate genes for functionally important agronomic traits.

Comparison of Biological and Genetic Characteristics between Two Most Common Broad-Leaved Weeds in Paddy Fields: Ammannia arenaria and A. multiflora (Lythraceae)

Ammannia arenaria and A. multifloras, morphologically similar at the seedling stage, are the most common broad-leaved weeds in paddy fields. Our study showed that A. arenaria occupied more space than A. multifloras when competing with rice. However, A. multifloras germination has lower temperature adaptability. No difference in sensitivity to common herbicides between two Ammannia species was observed. Chloroplast (cp) genomes could be conducive to clarify their genetic relationship. The complete cp genome sequences of A. arenaria (158,401 bp) and A. multiflora (157,900 bp) were assembled for the first time. In A. arenaria, there were 91 simple sequence repeats, 115 long repeats, and 86 protein-encoding genes, one, sixteen, and thirty more than those in A. multiflora. Inverted repeats regions expansion and contraction and the phylogenetic tree based on cp genomes demonstrated the closely relationship between the two species. However, in A. arenaria, 20 single nucleotide polymorphisms in the CDS region were detected compared to A. multiflora, which can be used to distinguish the two species. Moreover, there was one unique gene, infA, only in A. arenaria. This study provides reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure, and biodiversity of Ammannia species.

The complete chloroplast genome of Ulmus mianzhuensis with insights into structural variations, adaptive evolution, and phylogenetic relationships of Ulmus (Ulmaceae)

BACKGROUND

Ulmus mianzhuensis is an endemic tree species in China with high ornamental and economic value. Currently, little is known regarding its genomic architecture, phylogenetic position, or adaptive evolution. Here, we sequenced the complete chloroplast genome (cp genome) of U. mianzhuensis and further compared the variations in gene organization and structure within Ulmus species to define their genomic evolution, then reconstructed the phylogenomic relationship of 31 related Ulmus species to explore the systematic position of U. mianzhuensis and the utility of cp genome for resolving phylogenetics among Ulmus species.

RESULTS

Our results revealed that all the Ulmus species exhibited a typical quadripartite structure, with a large single copy (LSC) region of 87,170 - 88,408 bp, a small single copy (SSC) region of 18,650 - 19,038 bp and an inverted repeat (IR) region of 26,288 - 26,546 bp. Within Ulmus species, gene structure and content of cp genomes were highly conserved, although slight variations were found in the boundary of SC/IR regions. Moreover, genome-wide sliding window analysis uncovered the variability of ndhC-trnV-UAC, ndhF-rpl32, and psbI-trnS-GCU were higher among 31 Ulmus that may be useful for the population genetics and potential DNA barcodes. Two genes (rps15 and atpF) were further detected under a positive selection of Ulmus species. Comparative phylogenetic analysis based on the cp genome and protein-coding genes revealed consistent topology that U. mianzhuensis is a sister group to U. parvifolia (sect. Microptelea) with a relatively low-level nucleotide variation of the cp genome. Additionally, our analyses also found that the traditional taxonomic system of five sections in Ulmus is not supported by the current phylogenomic topology with a nested evolutionary relationship between sections.

CONCLUSIONS

Features of the cp genome length, GC content, organization, and gene order were highly conserved within Ulmus. Furthermore, molecular evidence from the low variation of the cp genome suggested that U. mianzhuensis should be merged into U. parvifolia and regarded as a subspecies of U. parvifolia. Overall, we demonstrated that the cp genome provides valuable information for understanding the genetic variation and phylogenetic relationship in Ulmus.

Insights into phylogenetic relationships in Pinus inferred from a comparative analysis of complete chloroplast genomes

BACKGROUND

Pinus is the largest genus of Pinaceae and the most primitive group of modern genera. Pines have become the focus of many molecular evolution studies because of their wide use and ecological significance. However, due to the lack of complete chloroplast genome data, the evolutionary relationship and classification of pines are still controversial. With the development of new generation sequencing technology, sequence data of pines are becoming abundant. Here, we systematically analyzed and summarized the chloroplast genomes of 33 published pine species.

RESULTS

Generally, pines chloroplast genome structure showed strong conservation and high similarity. The chloroplast genome length ranged from 114,082 to 121,530 bp with similar positions and arrangements of all genes, while the GC content ranged from 38.45 to 39.00%. Reverse repeats showed a shrinking evolutionary trend, with IRa/IRb length ranging from 267 to 495 bp. A total of 3,205 microsatellite sequences and 5,436 repeats were detected in the studied species chloroplasts. Additionally, two hypervariable regions were assessed, providing potential molecular markers for future phylogenetic studies and population genetics. Through the phylogenetic analysis of complete chloroplast genomes, we offered novel opinions on the genus traditional evolutionary theory and classification.

CONCLUSION

We compared and analyzed the chloroplast genomes of 33 pine species, verified the traditional evolutionary theory and classification, and reclassified some controversial species classification. This study is helpful in analyzing the evolution, genetic structure, and the development of chloroplast DNA markers in Pinus.

Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis

Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.