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Oceanic islands offer excellent opportunities to study the ecology, evolutionary biology, and biogeography of plants. To uncover the genetic basis of various evolutionary trends commonly observed on these islands, the origins and phylogenetic relationships of the species being studied should be understood. Callicarpa glabra, Callicarpa parvifolia, and Callicarpa subpubescens are evergreen woody plants endemic to the Ogasawara Islands, which are remote oceanic islands located off of the Japanese Archipelago. These species are ideal for studying evolutionary changes on oceanic islands because of their adaptive radiation and shift toward dioecious sex expression. We used a phylogenomic perspective to determine the evolutionary relationship of the three species within the genus and infer their colonization time. Based on the analysis of both chloroplast genomes and 86 nuclear single-copy genes, we found that these three species were monophyletic and embedded in a backbone clade that included multiple East Asian species. The phylogenetic tree based on over 10,000 nuclear genes placed the insular species in the East Asian clade, although the topology did not entirely correspond to the chloroplast tree, probably because of incomplete lineage sorting and interspecific hybridization. The three endemic species were estimated to have diverged from continental species approximately three million years ago (Mya). The results of this study suggested that the ancestor of the Ogasawara endemic species originated from long-distance dispersal from East Asia mainland in the late Pliocene, and then progressively speciated within the islands., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)

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., Competing Interests: Declarations. Conflict of interest: The authors declare that they have no competing interests. Ethics approval and consent to participate: The collected Wikstroemia species are widely distributed in China. Experimental researches with Wikstroemia species comply with Hexi University guidelines ( https://labmc.hxu.edu.cn/index.htm ), and do not include the genetic transformation of the same, preserving the genetic background of the species used. It does not require ethical approval. Consent for publication: Not applicable., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of plants of the Berberis genus and is used to treat various ailments. These species have similar morphologies, potentially leading to misidentifications that can impact medicine efficacy. Therefore, developing suitable molecular markers to identify medicinal species is imperative. Furthermore, discrepancies exist in the taxonomy of the Berberis genus. In the present study, we de novo assembled the chloroplast genomes of six Berberis species (Berberis woomungensis C. Y. Wu, Berberis pruinosa Franch., Berberis thunbergii DC., Berberis chinensis Poir., Berberis wilsoniae Hemsl., and Berberis sp.) that commonly constitute Berberidis Radix and compared them with previously reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Higher synonymous substitutions, indicative of predominant purifying selection on protein-coding genes, were observed compared to non-synonymous substitutions. However, positive selection was identified in six genes across 29 Berberis species-accD, matK, ndhD, rbcL, ycf1, and ycf2-highlighting their potential roles in adaptive responses to specific environmental conditions within the genus. Inverted repeats expansion and contraction affected the rate of mutations and were associated with the phylogenetic classification of Berberis. Our phylogenetic analysis supported the division of the Berberis complex into four genera, which corroborates previous studies involving extensive sampling. We identified the ndhD-ccsA region as the most polymorphic region and applied this region to Chinese patent medicines containing Berberidis Radix through metabarcoding. The metabarcoding analysis confirmed that five Berberis species commonly constitute Berberidis Radix in Chinese patent medicines. In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, metabarcoding provides insight into the species composition of Berberidis Radix in Chinese patent medicines., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Phaius Lour. (Collabieae, Orchidaceae) is a small genus consisting of about 45 species, with highly ornamental and medicinal values. However, the phylogenetic relationship of Phaius among Calanthe s. l. has been highly debated based on morphological and molecular data. The complete chloroplast (cp) genome has been widely used as a useful molecular marker for resolving phylogenetic problems, while few genomic data on Phaius was available. Therefore, complete cp genomes of eight Phaius species were sequenced and characterized in detail to provide a better understanding of its phylogenetics in Calanthe s. l., Results: The cp genomes of eight species investigated exhibited conserved quadripartite structures with varied lengths ranging between 157,997 bp to 158,735 bp. The overall GC content of these genomes ranged between 36.82 and 36.97%. Gene annotation revealed 136 genes in all eight genomes, of which 21 were duplicated in inverted regions and 15 with introns. Comparative analysis of eight cp genomes revealed stable sequence identity with greater variation in the single-copy regions, alongside notable differences in the genes at the LSC/IRb and IRb/SSC junctions, as well as in the number of SSRs. The phylogenetic analysis based on CDS from 49 complete cp genomes of Collabieae indicated that the eight Phaius species, together with other two species P. philippinensis and P. hainanensis, were clustered into a monophyletic clade among Calanthe s. l. and divided into two subclades with strong supports. Additionally, it was also supported that Calanthe s. l. should be divided into five genera with strong supports, including Calanthe s. s., Cephalantheropsis, Styloglossum, Phaius, and Preptanthe., Conclusions: It was the first report on the complete cp genome of six Phaius species (P. columnaris, P. mishmensis, P. takeoi, P. tonkinensis, P. wallichii and P. wenshanensis) and has been comparatively analyzed in detail with P. flavus and P. tancarvilleae. It provided a comprehensive investigation of various cp genomic features for phylogenetic implications, including overall genome structure, codon usage, repeat sequences, IR boundaries, DNA polymorphisms, and phylogenetic reconstruction. It was suggested that Phaius and Calanthe s. s. should be treated as two independent genera. The concept of new genus Paraphaius was not confirmed by complete cp genomic data here. The intergeneric relationship of Phaius and its alliance in Calanthe group could be understood better by more cp genomic data., Competing Interests: Declarations. Ethics approval and consent to participate: The study was conducted the plant material that complies with relevant institutional, national, and international guidelines and legislation. The eight Phaius species were cultivated in Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences. Consent for publication: Not applicable. Clinical trial number: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Impatiens is a genus of functional herbaceous plants in the Balsaminaceae, which are not only of great ornamental value and one of the world's top three flower bedding plants but also have a wide range of medicinal and edible uses. Currently, the taxonomy and phylogenetic relationships of Impatiens species are still controversial. In order to better understand their chloroplast properties and phylogenetic evolution, nine Impatiens plants ( Impatiens repens , Impatiens rectirostrata , Impatiens baishaensis , Impatiens rostellata , Impatiens faberi , Impatiens oxyanthera , Impatiens tienchuanensis , Impatiens blepharosepala , Impatiens distracta ) were sequenced, and their complete chloroplast genomes were analysed. Nine species of Impatiens chloroplast genomes ranged in length from 150,810 bp ( I. rectirostrata ) to 152,345 bp ( I. blepharosepala ). The chloroplast genomes were all typical circular DNA molecules, and the GC content in each region was consistent with the published chloroplast genomes of Impatiens plants. The results showed that the seven mutational hotspots ( trnL-UAG , ndhG , ycf1 , ccsA , rrn23 , trnA-UGC , and ycf2 ) could be used as supporting data for further analyses of the phylogenetic tree and species identification. In addition, the results of the phylogenetic tree support that Balsaminaceae is a monophyletic taxon, and that Hydrocera triflora is at the base of the branch, is the original species of Balsaminaceae, and is in a sister group relationship with Impatiens species. The results of this paper enrich the data of Impatiens chloroplast genomes, and the availability of these chloroplast genomes will provide rich genetic information for species identification, thus enhancing the taxonomic accuracy and phylogenetic resolution of Impatiens , and further promoting the investigation and rational use of Impatiens plant resources.

Bauhinia s.s. belongs to the Cercidoideae subfamily, located at the base of the Leguminosae family. It displays a variety of growth habits and morphologies, and is widely utilized as both ornamental and medicinal plants globally. The objective of this research is to uncover chloroplast genomes of species from Eastern Asia and Southern Africa, thereby advancing our understanding of the diversity within this genus. This study sequenced Bauhinia purpurea , Bauhinia brachycarpa var. microphylla , Bauhinia variegata var. candida , Bauhinia galpinii , and Bauhinia monandra using the Illumina platform and conducted the construction of phylogenetic trees as well as the estimation of divergence times. Compared to Asian species, the IR regions of African species underwent a contraction of approximately 100-400 bp. The phylogenetic analysis indicated that Asian and African species clustered into two distinct clades, with high support. The divergence of Bauhinia s.s. species occurred in the late Paleocene, and the rps18 and cemA genes were under positive selection. Six hypervariable regions were screened for evolutionary studies and the super-barcode data were used for species delimitation. The results revealed certain differences between African and Asian species in their chloroplast genomes of Bauhinia species.

Background : Section Camellia is the most diverse group in the genus Camellia L., and this group of plants has a long history of cultivation in China as popular ornamental flowers and oil plants. Sect. Camellia plants present diverse morphological variations and complexity among species, resulting in uncertainty in the classification of species, which has resulted in a degree of inconvenience and confusion in the use of plant resources and research. Methods : Here, We sequenced and assembled the chloroplast genomes of 6 sect. Camelli a and performed comparative chloroplast genome analysis and phylogenetic studies combined with 15 existing sect. Camellia plants. Results : The chloroplast genome of 21 species in sect. Camellia species were quadripartite with length of 156,587-157,068 bp base pairs (bp), and a highly conserved and moderately differentiated chloroplast genome arrangement. The 21 sect. Camellia chloroplast genomes were similar to those of angiosperms, with high consistency in gene number, gene content and gene structure. After the annotation process, we identified a total of 132 genes, specifically 87 sequences coding for proteins (CDS), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The ycf 1 gene in 21 species of the sect. Camellia was present only in the small single-copy/inverted repeat of a (SSC/IRa) region. Sequence variation was greater in the large single-copy (LSC) region than in the IR region, and the majority of the protein-coding genes presented high codon preferences. The chloroplast genomes of 21 plant species exhibit relatively conserved SC (single copy region)/IR (inverted repeat region) boundaries. We detected a total of 2975 single sequence repeats (SSRs) as well as 833 dispersed nuclear elements (INEs). Among these SSRs, A/T repeats and AT/AT repeats dominated, while among INEs, forward repeats and palindromic repeats predominated. Codon usage frequencies were largely similar, with 30 high-frequency codons detected. Comparative analysis revealed five hotspot regions ( rps 16, psa J, rpl 33, rps 8, and rpl 16) and two gene intervals ( atp H- atp I and pet D- rpo A) in the cp genome, which can be used as potential molecular markers. In addition, the phylogenetic tree constructed from the chloroplast genome revealed that these 21 species and Camellia oleifera aggregated into a single branch, which was further subdivided into two evolutionarily independent sub-branches. Conclusions : It was confirmed that sect. Camellia and C. oleifera Abel are closely related in Camellia genus. These findings will enhance our knowledge of the sect. Camellia of plants, deepen our understanding of their genetic characteristics and phylogenetic pathways, and provide strong support for the scientific development and rational utilization of the plant resources of the sect. Camellia .

The Hypericaceae family, comprising nine genera and over seven hundred species, includes Hypericum plants traditionally used for medicinal purposes. In this study, we performed high-throughput sequencing on three Hypericum species: Hypericum acmosepalum , Hypericum addingtonii , and Hypericum beanii , and conducted comparative genomic analyses with related species. The chloroplast genome sizes were 152,654 bp, 122,570 bp, and 137,652 bp, respectively, with an average GC content of 37.9%. All genomes showed a quadripartite structure, with significant variations in IR regions (3231-26,846 bp). The total number of genes ranged from 91 to 129. SSRs were predominantly located in the LSC region, with mononucleotide repeats being dominant. Comparative analysis identified several hotspot regions, including accD , rpoC2 , rpoB , and rpl22 in the LSC region and matK , rpl32 , rpl33 , and rps4 in the SSC region. Nucleotide polymorphism analysis revealed eight highly variable regions and eleven gene loci, providing potential molecular markers for species identification. Phylogenetic analysis indicated that Triadenum and Cratoxylum are closely related to Hypericum , with H. acmosepalum and H. beanii being closest relatives and Hypericum hookerianum as their sister species. These findings provide molecular tools for species identification and insights for conservation strategies of medicinal Hypericum species.

The chloroplast genome has considerable potential to enhance crop productivity, but it remains underutilized in breeding because it is difficult to modify. This study elucidates the potential of recently developed chloroplast-targeted C-to-T base editors in facilitating the use of the chloroplast genome for crop breeding. The herbicide metribuzin interferes with photosynthesis by binding to the D1 protein of photosystem II, encoded by the chloroplast genome. Naturally occurring D1 mutants with V219I or A251V substitutions are known to have resistance to some herbicides including metribuzin. Here, using the base editors, we introduced these substitutions and showed that the A251V single mutation and the V219 & A251V double mutations conferred significant metribuzin resistance to Arabidopsis thaliana. The V219I & A251V double mutants exhibited increased metribuzin resistance and grew better than the A251V single mutants. Furthermore, the double mutants grew as well as wild-type plants in the absence of metribuzin. The single and double mutants, which are a challenge to obtain through traditional mutagenesis and crossbreeding methods, can be relatively easily generated using C-to-T base editors. In view of the conservation of V219 and A251 across numerous species, C-to-T base editing can potentially confer metribuzin resistance to a wide range of crops. Compared to nuclear genes, chloroplast genes are also less likely to spread into wild populations. Our findings suggest that chloroplast-targeting C-to-T base editors will find many roles in future crop breeding efforts., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Background: Arnebiae Radix has long been used in traditional medicine for its pleiotropic properties. However, distinguishing Arnebiae Radix from its substitutes or closely related species has been challenging due to limited phenotypic characteristics., Purpose: We aimed to identify the molecular markers for distinguishing Arnebiae Radix from its confusion species., Study Design: Chloroplast genome sequences were used to identify the markers., Methods: Chloroplast genomes from 15 species across five genera, including all historically used source plants, were sequenced and assembled., Results: The results revealed significant similarities across all chloroplast genomes in terms of structure, size, gene content, repeat sequences pattens, and codon usage patterns. Phylogenetic analysis showed that the genera Lithospermum, Buglossoides, and Aegonychon formed one clade, while Arnebia guttata, Ar. decumbens, and Ar. euchroma form another. Despite most regions of the chloroplast genomes are highly conserved, three regions-petA-psbJ, ndhF-rpl32, and ycf1-exhibited high variability among difference species, providing high-resolution markers for species identification. Specifically, 376 and 325 species-specific sites were identified in Ar. euchroma and Ar. guttata, respectively. Additionally, four species-specific sites were identified as novel molecular markers, potentially aiding in distinguishing Arnebiae Radix and its confusion or substitute species., Conclusion: This study provided new genetic insights for differentiating Arnebiae Radix and its confusion species, paving the way for further exploration of these medicinal plants., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Euphorbia fauriei, a perennial plant endemic to South Korea, exhibits both morphological characteristics and intricate genetic identities akin to E. pekinensis. This study aimed to provide clarity on the taxonomic status of E. faurirei and E. pekinensis through a comprehensive chloroplast genome analysis. Additionally, we sequenced the Acalypha australis chloroplast genome as an outgroup for the construction of a phylogenetic tree with other Euphorbia species. The three chloroplast genomes, ranging from 162,834 bp to 168,832 bp, displayed typical quadripartite structures. The Euphorbia genomes contained 111 unique genes, whereas the A. australis genome contained two additional protein-coding genes (PCGs), rpl32 and rps16. Comparative analysis unveiled the loss of rpl32 and rps16 as synapomorphic characteristics in Euphorbia, whereas the loss of infA occurred across Euphorbiaceae. High collinearity and sequence similarity were observed among Euphorbia species, accompanied by significant inversion regions in the E. pekinensis chloroplast genomes from China and Japan, indicating regional genetic variability. Nucleotide substitution analysis revealed that the ndh group exhibited the highest K A /K S values (0.224), whereas the atp, psa, psb and rps groups had the lowest. Phylogenomic analysis utilizing whole genomes, PCGs, and intron and intergenic regions consistently demonstrated that E. pekinensis from South Korea clusters closely with E. fauriei. These findings challenge the current taxonomic distinction between E. pekinensis and E. fauriei in Korea, suggesting that while they exhibit distinct characteristics, E. fauriei should be considered a closely related subspecies rather than the same species as E. pekinensis. This study emphasizes the need for population studies to clarify the taxonomic relationships between E. pekinensis and E. fauriei., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: The confused taxonomic classification of Crucigenia is mainly inferred through morphological evidence and few nuclear genes and chloroplast genomic fragments. The phylogenetic status of C. quadrata, as the type species of Crucigenia, remains considerably controversial. Additionally, there are currently no reports on the chloroplast genome of Crucigenia., Results: In this study, we utilize molecular phylogenetics and comparative genomics to show that C. quadrata belongs to Chlorophyceae rather than Trebouxiophyceae. The Bayesian and maximum likelihood (ML) phylogenetic trees support a monophyletic group of C. quadrata and Scenedesmaceae (Chlorophyceae) species. Our study presents the first complete chloroplast genome of C. quadrata, which is 197,184 bp in length and has a GC content of 31%. It has a typical quadripartite structure, and the chloroplast genome codons exhibit usage bias. Nucleotide diversity analysis highlights six genes (ccsA, psbF, chlN, cemA, rps3, rps18) as hotspots for genetic variation. Coding gene sequence divergence analyses indicate that four genes (cemA, clpP, psaA, rps3) are subject to positive selection., Conclusions: The determination of the phylogenetic status and the comparative chloroplast genomic analyses of C. quadrata will not only be useful in enhancing our understanding of the intricacy of Crucigenia taxonomy but also provide the important basis for studying the evolution of the incertae sedis taxa within Trebouxiophyceae., Competing Interests: Declarations. Ethics approval and consent to participate: The plant materials used in the study were purchased from the Freshwater Algae Culture Collection at the Institute of Hydrobiology. The collection and use of plant materials comply with relevant institutions, national and international guidelines and legislation. This article does not involve any endangered or protected species. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

Paspalum vaginatum, valued for its salt tolerance, is a vital species in the turfgrass and agricultural industries. Despite its significance, there are still gaps in its genetic composition, particularly in the mitochondrial (mtDNA) and chloroplast (cpDNA) genomes. Our study aimed to fill these knowledge gaps by investigating the evolutionary relationships within the paspalum family and examining the functions of organelle-encoded genes as well as the critical role of reactive oxygen species (ROS) in organelle-nucleus communication. By genome sequencing, assembly, and annotation, we determined 504,515 bp of P. vaginatum mtDNA and 140,483 bp of its cpDNA. Comparative analyses with other Paspalum species and major crops highlight the intricate evolutionary dynamics and varying levels of genetic relatedness observed across different organelle genomes. The complex response of organelle gene expression to salt stress in this study will aid in understanding the molecular mechanisms and evolutionary trajectories of P. vaginatum organelle genomes., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests. Ling Pan reports financial support was provided by National Natural Science Foundation of China. Xiaoshan Wang reports financial support was provided by National Key Research and Development Program of China. Junming Zhao reports financial support was provided by Sichuan Science and Technology Program. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Persicaria jucunda is a plant distributed at meadow or wetland. Our study reports the complete chloroplast genome. The chloroplast genome of P. jucunda is a typical tetrameric structure with a total length of 159,843 bp, containing a large single-copy (LSC) region of 84,350 bp, a small single-copy (SSC) region of 13,151 bp, and two inverted repeat regions (IRs) of 31,171 bp. The total GC content was 38.2%, 36.5% for the LSC region, 33.2% for the SSC region, and 41.5% for the IR region. The P. jucunda chloroplast genome contains 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 36 chloroplast genomes showed similarity to P. foliosa and P. kawagoeana among the species analyzed. The chloroplast genome provides a valuable genetic resource for phylogenetic studies.

Cryptocoryne is a popular ornamental aquatic plant for aquarists, although only six species are found in China. Destruction of the natural habitats of Cryptocoryne for human activities has led to a decline in its numbers. In this report, we sequenced and annotated the Cryptocoryne crispatula var. balansae chloroplast genome for the first time. Results showed that the length of the chloroplast genome was 182,935 bp and the GC content was 34%. The chloroplast genome encoded 137 genes, including 92 encoded protein genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis supported the the monophyletic nature of the genus and indicated that it was the first species to be differentiated in the chloroplast genome of Cryptocoryne and formed a separate branch. These findings offer valuable genomic resources for comparative studies in Cryptocoryne and Araceae, thereby aiding genetic diversity and phylogenetic analyses.

Cathetus clarkei, a significant folk medicinal plant, is utilized to treat a variety of ailments. In this study, we reported the complete chloroplast genome sequence of this species. The length of the complete chloroplast genome was 155,810 bp, included a pair of inverted repeat (IR) regions (26,340 bp), a large single-copy region (LSC, 84,853 bp), and a small single-copy region (SSC, 18,277 bp). It comprised 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The total GC content was 36.8%. The phylogenetic tree revealed that C. clarkei had a close relationship with P. cochinchinensis, followed by P. reticulatus. This study provides a reference for important medicinal plants within the Phyllanthaceae, and we can gain a deeper understanding of how the species adapts to changes in the environment, helping us to identify and protect it.

Rubus swinhoei Hance is an important plant owing to its medicinal root and edible fruit, and extensively distributed in China. In this study, we reported the complete chloroplast genome of R. swinhoei. The chloroplast genome was 156,335 bp in size with the overall GC content of 37.15%, having a circular and quadripartite structure, which contained a large single-copy (LSC) and a small single-copy (SSC) regions of 85,897 bp and 18,858 bp separated by a pair of 25,790 bp inverted repeat (IR) regions. The complete chloroplast genome comprised 131 unique genes of which 86 and 37 were protein-coding genes and tRNA genes, respectively, and also eight rRNA genes. The phylogenetic analysis revealed that R. swinhoei was closely related to R. kawakamii. The genome information reported in this paper will be beneficial for further investigation on the evolution of this species.

Heracleum hemsleyanum Diels is a traditional medicinal herb in China. We reported its first complete chloroplast genome. The chloroplast genome was 146,775 bp in length with 37.53% GC content, containing a large single copy region (LSC, 93,309 bp), a small single copy region (SSC, 17,502 bp), and a pair of inverted repeat regions (IRs, 17,982 bp). Moreover, the chloroplast genome encoded 130 genes, including 86 protein-coding genes (PCGs), 36 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Phylogenetic analysis indicated that H. hemsleyanum was closely related to Heracleum moellendorffii and Heracleum yungningense. This assembled chloroplast genome will provide vital information on the genetic resources, phylogenetic relationships, and the species identification of the genus Heracleum.

Solanum melongena ‘Yunqie 9’ was selected by the Horticultural Research Institute of Yunnan Academy of Agricultural Sciences based on the local environment of Yunnan Province. It is excellent in fruit quality and yield, but it is relatively weak in disease resistance. No information on complete chloroplast genome and position in the phylogeny of Solanum to restrict its genetic improvement. In this study, the chloroplast genome of ‘Yunqie 9’ was sequenced using Illumina high-throughput sequencing technology. The size of the complete chloroplast genome was 155,579 bp in length with an GC content of 37.70%, composed of a large single-copy region (86,189 bp), a small single-copy region (18,504 bp), and a pair of inverted repeat regions (25,443 bp). A total of 134 coding genes were annotated in the entire chloroplast genome, including 89 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis based on chloroplast genome sequences of 20 species in the Solanaceae family indicated that except for the cultivated Solanum, ’Yunqie 9’ was closely related to Solanum melongena×Solanum torvum and Solanum insanum.

The essential photoprotective role of proton gradient regulation 5 (PGR5)-dependent cyclic electron flow (CEF) has been reported in Arabidopsis, rice, and algae. However, its functional assessment has not been performed in tomato yet. In this study, we focused on elucidate the function of SlPGR5 and SlPGR5-like photosynthetic phenotype 1 (PGRL1) in tomato. We performed RNA interference and found that SlPGR5/SlPGRL1-suppressed transformants exhibited extremely low CO2 assimilation capacity, their photosystem I (PSI) and PSII were severely photoinhibited and chloroplasts were obviously damaged. The SlPGR5/SlPGRL1-suppressed plants almost completely inhibited CEF and Y(ND), and PSII photoinhibition may be directly related to the inability to produce sufficient proton motive force to induce NPQ. The transgenic plants overexpressing SlPGR5 and SlPGRL1 driven by 35S promoter capable alleviate photoinhibition of plants under low night temperature. The transcriptomic and proteomic analyses suggested that the nuclear gene transcription and turnover of chloroplast proteins, including the plastoglobule-related proteins, were closely related to SlPGR5/SlPGRL1 pathway dependent CEF. The bridge relationship between CEF and chloroplast quality maintenance was a novel report to our knowledge. In conclusion, these results revealed the regulatory mechanism of the SlPGR5/SlPGRL1 pathway in photoprotection and maintenance of chloroplast function in tomato, which is crucial for reduce yield loss, especially under adverse environmental conditions.

Karelinia caspia (Compositae) is a perennial herbaceous plant owning high economic, feeding and medicinal values. It is widely distributed in desertification and saline alkali areas. The complete chloroplast genome was firstly reported in this study. The chloroplast genome of K. caspia with a total size of 151,239 bp consists of two inverted repeats separated by a large single-copy region and a small single-copy region. Its chloroplast genome contains 129 genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Also, a total of 62 simple sequence repeats were identified. These results will be useful for study on the evolution and genetic diversity of K. caspia in the future.

Vaccinium henryi Hemsl. 1889 is an endemic deciduous shrub in China, belonging to the family Ericaceae. In this study, the first complete chloroplast genome of V. henryi was assembled and annotated. The genome was 176,339 bp in size containing a large single-copy region of length 106,115 bp, a small single-copy region of length 3022 bp, and a pair of inverted repeat regions of 33,601 bp each. It contained 139 genes, including 91 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis exhibited that V. henryi and V. oldhamii were phylogenetic closely related. The chloroplast genome of V. henryi would provide valuable information for phylogenetic and evolutionary research on genus Vaccinium.

Abstract Background The St-genome-sharing taxa are highly complex group of the species with the St nuclear genome and monophyletic origin in maternal lineages within the Triticeae, which contains more than half of polyploid species that distributed in a wide range of ecological habitats. While high level of genetic heterogeneity in plastome DNA due to a reticulate evolutionary event has been considered to link with the richness of the St-genome-sharing taxa, the relationship between the dynamics of diversification and molecular evolution is lack of understanding. Results Here, integrating 106 previously and 12 newly sequenced plastomes representing almost all previously recognized genomic types and genus of the Triticeae, this study applies phylogenetic reconstruction methods in combination with lineage diversification analyses, estimate of sequence evolution, and gene expression to investigate the dynamics of diversification in the tribe. Phylogenomic analysis confirmed previous phylogenetic relationships, with the St/E/V lineages (Pseudoroegneria/Lophopyrum + Thinopyrum/Dasypyrum) being suffered from a chloroplast capture event prior to polyploidization events. Analyses of diversification rates detected a significant acceleration approximately five million years ago in the St-genome-sharing taxa. Molecular tests of evolution and gene expression further indicated that radiation within the accelerated group has been accompanied by adaptive genetic changes in a few chloroplast-encoded genes directly or indirectly related to photosynthesis. Conclusions Our results support an important role for adaptive evolution in plastomes during accelerated diversification. In combination with plastome data, further investigations using other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of the St-genome-sharing taxa, especially to determine whether adaptive changes in the nuclear genome are accelerated as well because plastome represents the maternal inheritation in angiosperms.

Background: Paeonia lactiflora Pall., a member of Paeoniaceae family, is a medicinal herb widely used in traditional Chinese medicine. Chloroplasts are multifunctional organelles containing distinct genetic material. This study provides a foundation for identifying P. lactiflora, protecting and utilizing germplasm resources, and supporting molecular breeding efforts., Results and Conclusion: In this study, five complete chloroplast genome sequences of P. lactiflora samples originating from different regions in China were sequenced using the Illumina NovaSeq 4000 platform. All five P. lactiflora chloroplasts had a typical cyclic tetrameric structure with 130 genes annotated. Comparative genomic analysis indicated that rpoB and psbK-psbI function as the potential specific DNA barcodes for intraspecific identification of P. lactiflora. PCR amplification of rpoB and psbK-psbI was performed on 246 samples from 7 production areas, achieving 100% amplification efficiency. Sequence analysis revealed that 5 and 10 haplotypes were identified based on rpoB and psbK-psbI, respectively. The joint analysis of two sequences identified 15 haplotypes named Hap1 ~ Hap15. Hap5 emerged as the most prevalent and geographically widespread haplotype across China. Haplotypic diversity (Hd) was 0.786, and nucleotide diversity was 0.00281, suggesting that P. lactiflora had high genetic diversity at the species level. The Neighbor-Joining tree showed that the 15 haplotypes were clustered into two branches, indicating extensive genetic exchange between clusters. The introduction of new individuals or rare genes into different clusters through gene flow increased genetic variation within clusters, enriching P. lactiflora genetic diversity., Competing Interests: Declarations. Competing interests:  The authors declare that the research was conducted in absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Ethical approval: Not applicable. Consent to participate: Not applicable. Consent for publication: Not applicable., (© 2025. The Author(s), under exclusive licence to Springer Nature B.V.)

Abstract The chloroplast (cp) genome is a widely used tool for exploring plant evolutionary relationships, yet its effectiveness in fully resolving these relationships remains uncertain. Integrating cp genome data with nuclear DNA information offers a more comprehensive view but often requires separate datasets. In response, we employed the same raw read sequencing data to construct cp genome-based trees and nuclear DNA phylogenetic trees using Read2Tree, a cost-efficient method for extracting conserved nuclear gene sequences from raw read data, focusing on the Aurantioideae subfamily, which includes Citrus and its relatives. The resulting nuclear DNA trees were consistent with existing nuclear evolutionary relationships derived from high-throughput sequencing, but diverged from cp genome-based trees. To elucidate the underlying complex evolutionary processes causing these discordances, we implemented an integrative workflow that utilized multiple alignments of each gene generated by Read2Tree, in conjunction with other phylogenomic methods. Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.

Hemisteptia lyrata, widely distributed in China, has a 152,467 bp chloroplast genome with a large single-copy (LSC) region of 83,473 bp, a small single-copy (SSC) region of 18,594 bp, a pair of inverted repeat regions (IRs) of 25,194 bp in length. The GC content is 36.46%. A total of 133 genes were encoded, of which 88 were protein coding genes, eight were rRNA genes, and 37 were tRNAs. The phylogenetic analysis using the maximum-likelihood method showed that H. lyrata is closely related to the species in Saussurea. This study provides genomic resources for phylogenetic genetics and resource exploitation of H. lyrata.

Lycium barbarum var. implicatum (2010), is a new variety of L. barbarum in Solanaceae. Here, we sequenced, assembled, and annotated the complete chloroplast (cp) genome of L. barbarum var. implicatum. Results showed that the complete cp genome of L. barbarum var. implicatum was 154,888 bp in length, containing a large single copy (LSC) region of 85,894 bp, a pair of inverted repeats (IR) region of 25,393 bp, and a small single copy (SSC) region of 18,208 bp. Maximum-likelihood (ML) phylogenetic tree elucidated that L. barbarum var. implicatum was sister to L. ruthenicum. Our results provide useful information for future phylogenetic studies in the family of Solanaceae.

We determined the complete chloroplast genome sequence of Sedum lushanense S. S. Lai 2004. The genome was 148,691 bp in length, including a large single copy (LSC; 80,497 bp), a small single copy (SSC; 16,620 bp), and two inverted repeats (IR; 25,787 bp) regions. It contained 84 coding gene sequences (CDS), 34 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. A maximum likelihood phylogenetic analysis revealed a close relationship between S. lushanense and S. lineare. Therefore, our study provided new genetic information on S. lushanense, contributing to a better understanding of its relationship with other related species and the evolutionary history of Crassulaceae.

Viola vaginata, a perennial herb in subsection Stolonosae, is endemic to the snowy mountainous regions on the Sea of Japan side of Japan. Its complete chloroplast genome was 156,056 bp in length, comprising one large single-copy region (86,407 bp), one small single-copy region (17,301 bp), and two inverted repeat regions (27,174 bp each). It contained 111 unique genes, including 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. Phylogenetic analysis placed V. vaginata in a clade with subsection Biobatae species and some Patellares species, while other Patellares species formed a distinct clade, contrasting with previous nuclear ITS results. These findings highlight the phylogenetic complexity within Viola.

Aster scaber Thunb. (1784) is primarily distributed in eastern Asia, has a total length of 152,778 bp and consists of a large single copy (LSC) region of 84,517 bp, a small single copy (SSC) region of 18,277 bp, and two inverted repeat (IRs) regions of 24,992 bp . The GC content is 37.31%. A total of 133 genes were annotated, including 88 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis using the maximum likelihood method showed that A. scaber is closely related to Aster species. This study provides chloroplast genome resource for further research on the phylogenetics and resource development of A. scaber.

Paeonia suffruticosa Andr. is an endemic shrub flower in China with 2n = 10. This study used 228 cultivars from four populations, i.e., Jiangnan, Japan, Northwest, and Zhongyuan, as materials to explore the genetic diversity levels among different populations of tree peony varieties. The results showed that 34 bands were amplified using five pairs of cpSSR primers, with an average of 6.8 bands per primer pair. The average number of different alleles (Na), effective alleles (Ne), Shannon's information index (I), diversity (H), and polymorphic information content (PIC) were 3.600, 2.053, 0.708, 0.433, and 0.388, respectively. The PIC value was between 0.250 and 0.500, indicating a moderate level of polymorphism for the five cpSSR primer pairs. The genetic diversity levels of peony cultivars varied among different populations, with the Northwest population showing relatively lower levels (I = 0.590, H = 0.289, and PIC = 0.263). A total of 52 haplotypes were identified in the four examined populations, and the number of haplotypes per population ranged from 11 to 22. Forty-four private haplotypes were detected across populations, and the Northwest population exhibiting the highest count of private haplotypes with 17. The mean number of effective number of haplotypes (Neh), haplotypic richness (Rh), and diversity (H) were 8.351, 6.824, and 0.893, respectively. Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources, and the main variation was found within individuals of peony germplasm. Cluster analysis, principal coordinate analysis, and genetic structure analysis classified tree peonies from different origins into two groups, indicating a certain degree of genetic differentiation among these four tree peony cultivation groups. This study provides a theoretical basis for the exploration, utilization, and conservation of peony germplasm resources, as well as for research on the breeding of excellent varieties.

ABSTRACT Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the deleterious effects of abscission on chloroplast ultrastructure in the cells of the tomato flower pedicel abscission zone, revealing spatiotemporal differential gene expression and key transcriptional networks involved in chloroplast vesiculation during abscission. Significant changes in chloroplast structure and vesicle formation were observed 8 and 14 h after abscission induction, coinciding with the differential expression of vesiculation‐related genes, particularly with upregulation of Senescence‐Associated Gene 12 (SAG12) and Chloroplast Vesiculation (CV). This suggests a possible vesicle transport of chloroplast degrading material for recycling by autophagy‐independent senescence‐associated vacuoles (SAVs) and CV‐containing vesicles (CCVs). Ethylene signaling appears to be involved in the regulation of these processes, as treatment with a competitive inhibitor of ethylene action, 1‐methylcyclopropene, delayed vesiculation, reduced the expression of SAG12, and increased expression of Curvature Thylakoid 1A (CURT1A). In addition, chloroplast vesiculation during abscission was associated with differential expression of photosynthesis‐related genes, particularly those involved in light reactions, underscoring the possible functional impact of the observed structural changes. This work provides new insights into the molecular and ultrastructural mechanisms underlying abscission and offers potential new targets for agricultural or biotechnological applications.

IntroductionHeliconia, a genus within the Zingiberales order, is renowned for its diverse morphology, suggesting a rich genetic reservoir. However, genetic research on plants within the Heliconiaceae family has primarily focused on taxonomy and phylogenetics, with limited exploration into other genetic aspects, particularly the chloroplast genome. Given the significance of chloroplast genomes in evolutionary studies, a deeper understanding of their structure and diversity within Heliconia is essential.MethodsIn this study, we sequenced and assembled the complete chloroplast genomes of four representative Heliconia species: Heliconia bihai, Heliconia caribaea, Heliconia orthotricha, and Heliconia tortuosa. The chloroplast genomes were analyzed for structure, gene content, and nucleotide diversity. We also performed comparative analysis with other species within the Zingiberales order to investigate structural and functional differences.ResultsThe assembled chloroplast genomes of the four Heliconia species exhibited a typical quadripartite structure and ranged in length from 161,680 bp to 161,913 bp. All genomes contained 86 protein-coding genes. Comparative analysis revealed that the chloroplast genome structures of the different Heliconia species were highly conserved, with minor variations. Notably, the chloroplast genome of Heliconia was slightly shorter than those of other Zingiberales species, primarily due to the reduced length of the inverted repeat region. In terms of nucleotide diversity, Heliconia species exhibited lower diversity in their chloroplast genomes compared to other families within the Zingiberales order.DiscussionThis study provides valuable insights into the conserved nature of the chloroplast genome in Heliconia. The reduced chloroplast genome size, particularly the shortened inverted repeat region, marks a distinct feature of Heliconia within the Zingiberales family. Our findings also underscore the low nucleotide diversity within the chloroplast genomes of Heliconia species, which could be indicative of their evolutionary history and limited genetic differentiation. These results contribute to a broader understanding of chloroplast genome evolution in the Zingiberales and offer important genetic resources for future research on Heliconia and related species.

The succulent shrubs Desmidorchis penicillata and D. retrospiciens, part of the taxonomically challenging genus Desmidorchis, are well‐known for their ecological resilience and medicinal significance. This study sequences the first complete chloroplast genomes of these species, shedding light on their genomic characteristics and evolutionary relationships. The circular genomes of D. penicillata (161 776 bp) and D. retrospiciens (162 277 bp) display a quadripartite structure typical of Angiosperms. Gene content, order, and GC content are consistent, featuring 114 unique genes, including 80 protein‐coding, 30 transfer RNAs, and four ribosomal RNAs genes. Codon usage analysis underscores A/U‐rich preferences, while RNA editing sites, predominantly in ndhB and ndhD genes, suggest post‐transcriptional modifications. Analysis of long repeated sequences reveals a predominance of forward and palindromic repeats. Simple sequence repeats (SSRs), particularly A/T motifs, are abundant, with high presence of mononucleotide, offering potential molecular markers. Comparative analysis with their relatives in subtribe Stapeliinae identifies mutational hotspots such as ycf1, ndhF, trnG(GCC)‐trnfM(CGA) and ndhG‐ndhI that could be potential DNA barcoding markers. The inverted repeat (IR) boundaries analysis revealed an expansion of IR on the small single copy region, leading to the formation of a pseudogene. Overall, substitution rate analysis indicated purifying selection, with a few genes (rpl22, clpP and rps11) showing signatures of positive selection. Additionally, the phylogenetic analysis positioned Desmidorchis within the Stapeliinae clade and strongly supported the sister relationship between D. penicillata and D. retrospiciens. This study provides comprehensive molecular data for future research in Desmidorchis. [ABSTRACT FROM AUTHOR]

ABSTRACT The genus Polygonatum boasts abundant germplasm resources and comprises numerous species. Among these, medicinal plants of this genus, which have a long history, have garnered attention of scholars. This study sequenced and analyzed the chloroplast genomes of six species of Polygonatum medicinal plants (P. zanlanscianense, P. kingianum, P. sibiricum, P. cyrtonema, P. filipes, and P. odoratum, respectively) to explore their interspecific relationships. The sequence length (154, 578–155, 807 bp) and genome structure were conserved among the six Polygonatum species, with a typical tetrad structure. Among the 127–131 genes contained in the genomes, 84–85 are protein‐coding genes, 37–38 are transfer RNA genes, and 6–8 are ribosomal RNA genes. The genomes contained 64–76 simple sequence repeats (SSRs) and 36–62 long repetitive sequences. Codon bias patterns tended to use codons ending in A/T. In 30 types of codons with RSCU > 1, 93.3% ended in A/T of the six species. Twenty‐one highly variable plastid regions were identified in the chloroplast genomes of the six medicinal plants. Furthermore, a phylogenetic analysis encompassing these and 53 other chloroplast genomes of Polygonatum species revealed that P. cyrtonema, P. odoratum, and P. filipes clustered together on one clade, whereas P. kingianum and P. zanlanscianense formed separate clades. Notably, P. sibiricum emerged as a standalone clade, and our phylogenetic tree reinforces the classification of P. sibiricum as forming a monophyly. This study provides a novel basis for intragenus taxonomy and DNA barcoding molecular identification within the genus Polygonatum medicinal plants.