Search Results (275)

This study presents an integrative investigation of four rare and threatened plant species—Taraxacum kok-saghyz L.E. Rodin, Astragalus rubtzovii Boriss., Schmalhausenia nidulans (Regel) Petr., and Rheum wittrockii Lundstr.—native to the Ile Alatau and Ketmen ridges of the Northern Tian Shan in Kazakhstan. Combining chloroplast genome sequencing, geobotanical surveys, and anatomical and population structure analyses, we aimed to assess the ecological adaptation, genetic distinctiveness, and conservation status of these species. Field surveys revealed that population structures varied across species, with T. kok-saghyz and S. nidulans dominated by mature vegetative and generative individuals, while A. rubtzovii and R. wittrockii exhibited stable age spectra marked by reproductive maturity and ongoing recruitment. Chloroplast genome assemblies revealed characteristic patterns of plastid evolution, including structural conservation in S. nidulans and R. wittrockii, and a reduced inverted repeat region in A. rubtzovii, consistent with its placement in the IR-lacking clade of Fabaceae. Morphological and anatomical traits reflected habitat-specific adaptations such as tomentose surfaces, thickened epidermis, and efficient vascular systems. Despite these adaptations, anthropogenic pressures including overgrazing and habitat degradation pose significant risks to population viability. Our findings underscore the need for targeted conservation measures, continuous monitoring, and habitat management to ensure the long-term survival of these ecologically and genetically valuable endemic species. Full article

Tripterygium wilfordii has extremely important pharmaceutical value in both traditional and modern medicine. The mitogenome of T. wilfordii was subjected to assembly and annotation with Nanopore long reads and Illumina short reads in this study. The mitogenome is 720,306 bp in length and is responsible for encoding 55 specific genes, including 35 protein-coding genes (PCGs), 17 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Upon repetitive sequence analysis, 223 simple sequence repeats (SSRs), 24 long tandem repeats (LTRs), and 47 dispersed repetitive sequences (DRSs) were identified. The 24 common PCGs were used for phylogenetic analysis, which revealed that T. wilfordii is more closely related to Euonymus alatus. Moreover, mitochondrial plastid DNA (MTPT) analysis revealed eight MTPTs in the mitochondrial genome. Furthermore, 600 RNA-editing sites were detected in the protein-coding genes according to RNA-seq results. Among these genes, the ccmB gene contained the greatest number of sites, followed by the nad4 gene. This is the first study to report the T. wilfordii mitogenome and illustrate its linear structure. The findings of this study will help elucidate the evolution of the T. wilfordii mitogenome and facilitate its potential application in genetic breeding. Full article

This study describes the first complete chloroplast genome of Ranunculus cf. penicillatus and provides new insights into the genetic composition and evolutionary relationships of the Ranunculus genus. The genome was assembled and characterized using high-throughput sequencing technologies, revealing a circular structure encompassing 158,313 base pairs. Comparative analysis with the chloroplast genomes of related species within the Ranunculus genus highlights notable variations in structural organization, which can elucidate potential adaptive evolutionary mechanisms. Phylogenetic analyses conducted using the maximum likelihood approach resulted in the placement of Ranunculus cf. penicillatus within a well-defined clade, revealing its relationship with other taxa. This study not only enriches the existing plastid genomic data of the genus Ranunculus but also serves as an additional resource for future studies on the phylogenetics, systematics, and conservation biology of this diverse group of aquatic plants. The findings highlight the importance of complete chloroplast genomes in the Ranunculus section Batrachium, an evolutionarily young group of aquatic plants, for understanding plant diversity and evolution. The genome can be accessed on GenBank with the accession number PV690257. Full article

Phylogenetic relationships within the subtribe Arethusinae (Arethuseae: Epidendroideae: Orchidaceae) remain unresolved, with particular uncertainty surrounding the phylogenetic positions of Anthogonium gracile and Eleorchis japonica. The monophyly of this subtribe remains contentious, making it one of the challenging taxa in Orchidaceae phylogenetics. In this study, we sequenced and analyzed the complete plastome sequences of A. gracile and E. japonica for the first time, aiming to elucidate their plastome characteristics and phylogenetic relationships. Both plastomes exhibited a conserved quadripartite structure, with 158,358 bp in A. gracile and 152,432 bp in E. japonica, and GC contents of 37.1% and 37.3%, respectively. Comparative analyses revealed strong structural conservation, but notable gene losses: E. japonica lacked seven ndh genes (ndhC/D/F/G/H/I/K), whereas A. gracile retained a complete ndh gene set. Repetitive sequence analysis identified an abundance of simple sequence repeats (68 and 77), tandem repeats (43 and 30), and long repeats (35 and 40). Codon usage displayed a bias toward the A/U termination, with leucine and isoleucine being the most frequent. Selection pressure analysis indicated that 68 protein-coding genes underwent purifying selection (Ka/Ks < 1), suggesting evolutionary conservation of plastome protein-coding genes. Nucleotide diversity analysis highlighted six hypervariable regions (rps8-rpl14, rps16-trnQ^UUG, psbB-psbT, trnT^UGU-trnL^UAA, trnF^GAA-ndhJ, and ycf1), suggesting their potential as molecular markers. Phylogenomic reconstruction, using complete plastome sequences, (ML, MP, and BI) indicated that Arethusinae was non-monophyletic. A. gracile formed a sister relationship with Mengzia foliosa and E. japonica, whereas Arundina graminifolia exhibited a sister relationship with Coelogyninae members. These results shed new light on the plastome characteristics and phylogenetic relationships of Arethusinae. Full article

The chloroplast signal recognition particle (cpSRP) components cpSRP43 and cpSRP54 not only form a complex with light-harvesting chlorophyll (Chl)-binding proteins to direct them to the thylakoid membrane, but also serve other functions. cpSRP43 independently acts as a chaperone for some tetrapyrrole biosynthesis (TBS) enzymes, while cpSRP54 participates in the co-translational targeting of plastid-encoded proteins. However, it remains unclear to what extent the two cpSRP components are coregulated—despite their distinct functions—and whether both participate in genomes-uncoupled (GUN)-mediated retrograde signaling. Here, we demonstrate that cpSRP43 and cpSRP54 accumulation is strongly interdependently controlled: overexpression of one protein increases the level of the other, while a deficiency in one of the two proteins leads to a simultaneous decrease in the other component. Disruption of this balance, e.g., by combining the overexpression of one component with a knockout of the other, results in severe chlorosis, stunted growth, and reduced levels of Chl and tetrapyrrole intermediates. Moreover, cpSRP43 deficiency exacerbates the pale-green phenotype of gun4 and gun5 mutants, highlighting a synergistic impact on TBS; however, cpSRP43 overexpression fails to rescue these defects. Remarkably, loss of cpSRP43 does not affect the expression of nuclear-encoded photosynthetic genes under intrinsic plastid stress, clearly demonstrating that cpSRP43 is not involved in plastid-to-nucleus retrograde signaling. Overall, our findings underscore that the fine-tuned expression of cpSRP43 and cpSRP54 is crucial for proper chloroplast function and pigment biosynthesis, while cpSRP43 alone does not participate in the retrograde signaling pathway. Full article

Tropidia, a type genus of Tropidieae (Orchidaceae, Epidendroideae), represents an important lineage for investigating plastome evolution and phylogenetic relationships within Epidendroideae. Despite its importance, the lack of available plastid genomic data has hindered comprehensive analyses of its genome structure and phylogenetic relationships. In this study, we assembled and characterized the complete plastid genomes of Tropidia angulosa and T. nipponica, providing valuable insights into plastome evolution and phylogenetic placement of Tropidieae. The plastomes of T. angulosa and T. nipponica exhibited a highly conserved quadripartite structure, sharing similar genomic size (161,395 bp and 160,801 bp) and GC content (36.87% and 36.90%). Both plastomes contained identical gene content and gene order, with 79 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. A total of 169 simple-sequence repeats (SSRs) and 92 long-sequence repeats (LSRs) were identified, most of which were distributed in large single-copy (63.91% and 66.30%) and non-coding regions (83.43% and 65.22%). Comparative plastomes analyses revealed the overall structural stability among photosynthetic lineages, whereas structural variation was primarily detected in mycoheterotrophic lineages. Phylogenomic reconstruction based on plastid-coding sequences revealed that Tropidieae occupies a relatively isolated phylogenetic position within Epidendroideae. These findings contribute to a more comprehensive understanding of plastome evolution and the phylogenetic framework of Epidendroideae. Full article

Rubus is a genus of small berry-producing shrubs, valued for their medicinal properties and as a food source. This genus is a large, globally distributed group that includes over 700 species. Despite numerous plastid and nuclear genomes having been reported for Rubus, there is a notable lack of research on its mitogenomes. We utilized PMAT to assemble the mitogenomes of six Rubus species according to long-read HiFi reads and annotated them through homologous alignment. Subsequently, we compared their characteristic differences within Rubus mitogenomes. The complete mitogenomes of R. parviflorus, R. spectabilis, R. idaeus, R. armeniacus, and R. caesius all exhibit master circle structures, with lengths ranging from 360,869 bp to 447,754 bp. However, R. chamaemorus displays a double-circle structure composed of two small circular molecules, spanning 392,134 bp. These mitogenomes encode a total of 54–61 genes, including 33–34 PCGs, 17–24 tRNAs, and 3 rRNA genes. Compared to the other five Rubus species, R. chamaemorus has fewer sequence repeats. These six species exhibit similar codon usage patterns. A large number of gene transfers were detected between organellar genomes of six Rubus species. Additionally, two phylogenetic trees were constructed using 31 mitogenomes and 94 chloroplast genomes, revealing a minor conflict within Rubus. Overall, this study clarifies the mitogenome characteristics of Rubus and provides valuable insights into the evolution of the genus. Full article

The living gymnosperms include about 1200 species in five major groups: cycads, ginkgo, gnetophytes, Pinaceae (conifers I), and cupressophytes (conifers II). Molecular phylogenetic studies have yet to reach a unanimously agreed-upon relationship among them. Moreover, cytonuclear phylogenetic incongruence has been repeatedly observed in gymnosperms. We collated a comprehensive dataset from available genomes of 17 gymnosperms across the five major groups and added our own high-quality assembly of a species from Podocarpaceae (the second largest conifer family) to increase sampling width. We used these data to infer reconciled nuclear species phylogenies using two separate methods to ensure the robustness of our conclusions. We also reconstructed organelle phylogenomic trees from 42 mitochondrial and 82 plastid genes from 38 and 289 gymnosperm species across the five major groups, respectively. Our nuclear phylogeny consistently recovers the Ginkgo–cycads clade as the first lineage split from other gymnosperm clades and the Pinaceae as sister to gnetophytes (the Gnepines hypothesis). In contrast, the mitochondrial tree places cycads as the earliest lineage in gymnosperms and gnetophytes as sister to cupressophytes (the Gnecup hypothesis) while the plastomic tree supports the Ginkgo–cycads clade and gnetophytes as the sister to cupressophytes. We also examined the effect of mitochondrial RNA editing sites on the gymnosperm phylogeny by manipulating the nucleotide and amino acid sequences at these sites. Only complete removal of editing sites has an effect on phylogenetic inference, leading to a closer congruence between mitogenomic and nuclear phylogenies. This suggests that RNA editing sites carry a phylogenetic signal with distinct evolutionary traits. Full article

Background/Objectives: Polygonatum grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Asparagaceae Juss.), a Korean endemic species, has been described based on its erect stem, tubular perianth shape, and pedicel length. However, its taxonomic status remains unclear due to limited molecular data. Methods: This study presents the complete plastid genomes (plastomes) of two P. grandicaule individuals and its close relative, P. odoratum (Mill.) Druce var. thunbergii (C.Morren & Decne.) H.Hara. Results: The plastomes, ranging from 154,578 to 154,579 base pairs (bp), are identical to those of P. falcatum A.Gray, P. odoratum var. odoratum, and another Korean endemic species, P. infundiflorum Y.S.Kim, B.U.Oh & C.G.Jang. All contain 78 plastid protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, except for the pseudogene infA. Phylogenetic analyses using 78 plastid PCGs and whole intergenic spacer (IGS) regions strongly support the three sections within Polygonatum Mill. and show that P. odoratum and its variety are nested within P. falcatum, P. grandicaule, and P. infundiflorum. Conclusions: Given the limited genomic variation and phylogenetic relationships, we propose treating P. falcatum, P. grandicaule, and P. infundiflorum as part of the P. odoratum complex, despite their morphological differences. This study offers valuable putative molecular markers for species identification and supports the application of plastome-based super-barcoding in the morphologically diverse genus Polygonatum. Full article

Prunus cerasoides D.-Don is a rare winter-blooming species and a distinctive and potential germplasm resource for cherry blossoms. We have characterized the mitochondrial genome (mitogenome) of P. cerasoides and acquired a monocyclic molecule measuring 421,258 bp. A total of 58 unique genes were annotated, comprising 36 protein-coding genes, 19 tRNAs, and three rRNAs. In the mitochondrial genome of P. cerasoides, we detected 86 simple sequence repeats, 727 dispersed repeats, and 21 tandem repeats. We detected 456 RNA editing sites from 34 unique protein-coding genes, leading to the cytosine to uracil transitions. Collinear analysis revealed that the mitogenome of P. cerasoides is quite conservative among species of the subgenus Cerasus. Moreover, our study detected 26 segments of plastid genomic DNA that had transferred from the plastome to the mitogenome. Six genes were found to be completely transferred from these fragments. The maximum likelihood phylogenetic analysis utilizing the mitogenomes of 29 distinct Rosaceae species supports the classification of P. cerasoides into separate branches. Comprehending the mitochondrial genomic characterization of P. cerasoides is crucial for elucidating its genetic foundation and offers insights into evolutionary relationships within the Prunus species. Full article

The tribe Loteae (Papilioniodeae-Leguminosae), according to plastid data, belongs to the Robinioid clade, which also includes the tribes Robinieae and Sesbanieae. The tribe Loteae contains 16 genera and about two hundred seventy-five species, of which the plastid genomes of five species have been studied to date. The main objectives of our study were to obtain new information on the plastid genome structure of the Loteae representatives in order to assess plastid genome variability and reconstruct phylogenetic relationships within the tribe Loteae. We performed sequencing, assembly, structural and phylogenetic analyses of the Loteae plastid genomes. All assembled Loteae plastomes showed a quadripartite structure with an overall length ranging from 150,069 to 152,206 bp and showed relative stability of inverted repeat borders. The Loteae plastomes demonstrated full collinearity; the most variable sites of the studied plastomes were found in petN-trnC and rps16-accD spacers from the LSC region and in the ycf1 gene within the SSC. All inferred relationships attained maximal support with the Hippocrepis lineage separated first, followed by Coronilla and Anthyllis; Lotus is a sister group to the clade Acmispon + Ornithopus. In this study, completely resolved relationships representing a backbone of plastid phylogeny were produced. The obtained results demonstrated that plastid genomes in the tribe Loteae are structurally conservative in contrast to the closely related tribes Robinieae and Sesbanieae. Full article

The Coelogyne s.l. is one of the emblematic genera of the Asian orchids, with high horticultural and medicinal values. However, the phylogenetic relationships of the genus inferred from previous studies based on a limited number of DNA markers remain ambiguous. In this study, we newly sequenced and assembled the complete plastomes of seven Coelogyne species: C. bulleyia, C. fimbriata, C. flaccida, C. prolifera, C. tricallosa, C. uncata, and an unknown taxa, Coelogyne sp. The plastomes of Coelogyne exhibited a typical quadripartite structure, varying in length between 157,476 bp and 160,096 bp, accompanied by a GC content spanning from 37.3% to 37.5%. A total of 132 genes were annotated for each plastome, including 86 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Among these, 19 genes underwent duplication within the inverted repeat (IR) regions, and 18 genes exhibited the presence of introns. Additionally, we detected 54 to 69 simple sequence repeats (SSRs) and 30 to 49 long repeats. In terms of codon usage frequency, leucine (Leu) emerged with the highest frequency, while cysteine (Cys) exhibited the lowest occurrence. Furthermore, eight hypervariable regions (atpB-rbcL, psbK-psbI, rps8-rpl14, rps16-trnQ^UUG, psaC-ndhE, ndhF-rpl32, psbB-psbT, and ycf1) were identified. Phylogenetic analyses using complete plastomes and protein-coding genes indicated that Coelogyne s.l. was monophyletic. Moreover, the results robustly supported the division of Coelogyne s.l. into five clades. This study provides a comprehensive analysis of the structural variation and phylogenetic analysis of the Coelogyne s.l. based on plastome data. The findings offer significant insights into the plastid genomic characteristics and the phylogenetic relationships of Coelogyne s.l., contributing to a deeper understanding of its evolutionary history. Full article

Brownlowia tersa and Brownlowia argentata are two true mangroves in the genus Brownlowia in Malvaceae, and they are a near-threatened and a data-deficient species, respectively. However, the genomic resources of Brownlowia have not been reported for studying their phylogeny and evolution. Here, we report the chloroplast genomes of B. tersa and B. argentata based on stLFR data that were 159,478 and 159,510 base pairs in length, respectively. Both chloroplast genomes contain 110 unique genes and one infA pseudogene. Sixty-eight RNA-editing sites were detected in 26 genes in B. argentata. A comparative analysis with related species showed similar genome sizes, genome structures, and gene contents as well as high sequence divergence in non-coding regions. Abundant SSRs and dispersed repeats were identified. Five hotspots, psbI-trnS, trnR-atpA, petD-rpoA, rpl16-rps3, and trnN-ndhF, were detected among four species in Brownlowioideae. One hotspot, rps14-psaB, was observed in the two Brownlowia species. Additionally, phylogenetic analysis supported that the Brownlowia species has a close relationship with Pentace triptera. Moreover, rpoC2 was a candidate gene for adaptive evolution in the Brownlowia species compared to P. triptera. Thus, these chloroplast genomes present valuable genomic resources for further evolutionary and phylogenetic studies of mangroves and plant species in Malvaceae. Full article

Danxiaorchis yangii is a fully mycoheterotrophic orchid that lacks both leaves and roots, belonging to the genus Danxiaorchis in the subtribe Calypsoinae. In this study, we assembled and annotated its mitochondrial genome (397,867 bp, GC content: 42.70%), identifying 55 genes, including 37 protein-coding genes (PCGs), 16 tRNAs, and 2 rRNAs, and conducted analyses of relative synonymous codon usage (RSCU), repeat sequences, horizontal gene transfers (HGTs), and gene selective pressure (dN/dS). Additionally, we sequenced and assembled its plastome, which has a reduced size of 110,364 bp (GC content: 36.60%), comprising 48 PCGs, 26 tRNAs, and 4 rRNAs. We identified 64 potential chloroplast DNA fragments transferred to the mitogenome. Phylogenomic analysis focusing on 33 mitogenomes, with Vitis vinifera as the outgroup, indicated that D. yangii is grouped as follows: D. yangii + ((Dendrobium wilsonii + Dendrobium wilsonii henanense) + Phalaenopsis aphrodite). Phylogenetic analysis based on 83 plastid PCGs from these species showed that D. yangii is grouped as follows: (D. yangii + Pha. aphrodite) + (Den. wilsonii + Den. henanense). Gene selective pressure analysis revealed that most mitochondrial and plastid genes in D. yangii are under purifying selection, ensuring functional stability, and certain genes may have undergone positive selection or adaptive evolution, reflecting the species’ adaptation to specific ecological environments. Our study provides valuable data on the plastomes and mitogenomes of D. yangii and lays the groundwork for future research on genetic variation, evolutionary relationships, and the breeding of orchids. Full article

Background: The shift to a parasitic lifestyle in plants often leaves distinct marks on their plastid genomes, given the central role plastids play in photosynthesis. Studying these unique adaptations in parasitic plants is essential for understanding the mechanisms and evolutionary patterns driving plastome reduction in angiosperms. By exploring these changes, we can gain deeper insights into how parasitism reshapes the genomic architecture of plants. Method: This study analyzed and compared the plastomes of 113 parasitic plants from different families. Results: The Orobanchaceae family (hemiparasitic plants) displayed the largest plastome size, while Apodanthaceae exhibited the shortest. Additionally, Orobanchaceae showcased little to no gene loss in their plastomes. However, holoparasitic species typically had reduced plastome sizes. Convolvulaceae exhibited significantly reduced plastome sizes due to high gene loss, and Apodanthaceae retained only a few genes. Gene divergence among different families was also investigated, and rps15, rps18, and rpl33 in Orobanchaceae; accD and ycf1 in Convolvulaceae; atpF and ccsA in Loranthaceae; and rpl32 in Santalaceae showed greater divergence. Additionally, Orobanchaceae had the highest numbers of all repeat types, whereas Loranthaceae and Convolvulaceae exhibited the lowest repeat numbers. Similarly, more simple sequence repeats were reported in Loranthaceae and Santalaceae. Our phylogenetic analysis also uncovered a distinct clade comprising Loranthaceae, with a single Schoepfiaceae species clustering nearby. Contrary to expectations, parasitic and hemiparasitic plants formed mixed groupings instead of segregating into separate clades. Conclusions: These findings offer insights into parasitic plants’ evolutionary relationships, revealing shared and divergent genomic features across diverse lineages. Full article