Search Results (134)

Background: Grewia is a genus of flowering plants belonging to the Malvaceae family. Grewia tembensis is used in traditional medicine for the treatment of several microbial diseases as well as a livestock feed. Methods: In the current study, the complete chloroplast (cp) genome of G. tembensis was constructed using data derived from high-throughput sequencing, followed by comprehensive analyses and comparison with phylogenetically related species. Results: The chloroplast genome of G. tembensis is 158,040 bp long and has the typical quadripartite structure found in angiosperms. The large single-copy (LSC) segment measures 86,956 bp, whereas the small single-copy (SSC) regions encompass 20,142 bp. The two inverted repeat (IRa and IRb) regions have an identical length of 25,471 bp and display a higher degree of conservation relative to the single-copy (SC) regions based on nucleotide diversity analysis. The genome of G. tembensis possesses 130 genes. The simple sequence repeat (SSR) numbers ranged between 202 and 234 repeats in Grewioideae subfamily species under this study. Furthermore, nucleotide diversity analysis demonstrated a marked elevation in polymorphism information (Pi) values across 30 genes in Grewioideae. Conclusions: cpSSRs can be used for the examination of population genetic variability within and between Grewia species, as well as the categorization of populations and their biogeographical distribution. In addition, loci with high Pi values can contribute substantial genetic variability, which is crucial for addressing taxonomic dilemmas in phylogenetic investigations. Full article

Background/Objectives: Fissidens crispulus Brid. is a dioicous moss with conspicuous axillary hyaline nodules and serrulate leaf margins. It features Neoamblyothallia-type peristome teeth and serves as an ecologically significant model for studying adaptation in the hyperdiverse genus Fissidens (>440 species). Methods: In this study, the complete chloroplast genome of F. crispulus was sequenced and de novo assembled, enabling detailed comparative genomic, phylogenetic, and codon usage bias studies. Results: As the third fully sequenced member of Fissidentaceae, this study deciphers its 124,264–124,440 bp quadripartite genome encoding 129 genes (83 CDS, 32 tRNAs, 8 rRNAs). Repeat analysis identified 125–127 SSRs, dominated by mono-/di-nucleotide A/T repeats (>70%), and dispersed repeats predominantly forward (F) and palindromic (P) (>85%), confirming profound AT-biased composition (GC content: 28.7%). We established 7 hypervariable loci (matK, ycf2, etc.) as novel Dicranidae-wide phylogenetic markers. Codon usage exhibited significant A/U-ending preference, with 12 optimal codons (e.g., GCA, UGU, UUU) determined. Maximum likelihood analyses resolved F. crispulus and F. protonematicola as sister groups with high support value (MBP = 100%). Conclusions: This work provides the foundational cpDNA resource for Fissidens, filling a major gap in bryophyte chloroplast genomics and establishing a framework for resolving the genus’s infrageneric conflicts. Furthermore, it offers critical insights into bryophyte plastome evolution and enables future codon-optimized biotechnological applications. Full article

Background: Ash dieback, driven by the invasive fungal pathogen Hymenoscyphus fraxineus, has precipitated severe declines in Fraxinus excelsior L. populations across Europe, threatening genetic diversity and ecosystem stability. Methods: This study investigates the interplay between phenotypic vitality and genetic variation in five Polish ash stands using nuclear simple sequence repeat (nSSR) and chloroplast DNA (cpDNA) markers. Vitality assessments of 186 trees across three reserves (from Białowieża Primeval Forest and Wolica Reserve) were conducted. Results: Vitality assessments revealed a slight predominance of dying individuals (36%, 3rd degree of Roloff classification). Nuclear analyses indicated moderate to high diversity (mean H_E = 0.826), significant inbreeding (F_IS = 0.178, p < 0.001), and low inter-population differentiation (F_ST = 0.044) among all five stands. Chloroplast markers showed elevated differentiation ($\mathsf{\Phi }$_ST = 0.228, p < 0.0001), reflecting phylogeographic structure. Vitality degrees assessed in three chosen populations (Browsk FD, Hajnówka FD, and Chojnów FD) exhibited negligible genetic differentiation (nSSR F_ST = 0.009; cpDNA $\mathsf{\Phi }$_ST = 0.003), suggesting gene flow mitigates pathogen-induced selection. Bayesian clustering (STRUCTURE, K = 3) revealed admixture with distinct genotypes in dying trees, potentially linked to susceptibility. Conclusions: These findings underscore the resilience of ash genetic pools and advocate for selective breeding in nurseries to prevent the spread of dieback, prioritizing resistant genotypes for conservation. Full article

The genus Manglietia Blume is an important group of Magnoliaceae that has high economic and ornamental value. Owing to the small morphological differences among most Manglietia species and the limited sample sizes in previous molecular-level studies, its infrageneric classification remains unclear, and interspecific relationships for some species are still contentious. Clarifying the phylogenetic relationships within the genus Manglietia is crucial for species classification, genetic diversity assessment, and evolutionary developmental studies. This study sequenced, assembled, and annotated the chloroplast (cp) genomes of Manglietia guangnanica, Manglietia hookeri, and Manglietia longirostrata. The results indicated that these cp genomes are canonical quadripartite structures with total lengths of 160,067 bp, 160,067 bp, and 160,076 bp, respectively. All three cp genomes were annotated with 133 genes, comprising 88 protein-coding genes, 37 tRNAs, and 8 rRNAs. A total of 31, 30, and 30 dispersed repeats and 53, 53, and 56 SSRs were detected, respectively. ENC plot, neutrality plot, and PR2 plot analyses indicated that codon usage bias was influenced primarily by natural selection. Nucleotide diversity analysis revealed 8 highly variable regions in the cp genomes, among which petA-psbJ, rpl32-trnL, and ccsA-ndhD are recommended as candidate molecular markers for Manglietia species. Phylogenetic analysis revealed four highly supported clades: Clade I (18 species), Clade II (M. decidua only), Clade III (9 species), and Clade IV (M. caveana only). Among these clades, Clade IV is a newly discovered monotypic clade in this study, which differs from the results of all previous studies. Further investigations of Clades I and III, which include multiple Manglietia species, revealed that the presence or absence of hairs on Twigs, Stipules, and the abaxial surface of the leaf are important morphological characteristics for distinguishing species between these two clades. Furthermore, the results revealed that M. guangnanica and M. calcarea are two distinct species, and the treatment of M. longirostrata as a variety of M. hookeri was not supported by our study. This study enriches the cp genome data of Manglietia, provides new insights into infrageneric classification, and lays a foundation for further phylogenetic and evolutionary studies of Manglietia. Full article

Background: Collabieae is a medium-sized group within the orchid subfamily Epidendroideae that is distributed primarily across tropical Asia. Most Collabieae species are known for their considerable ornamental and medicinal merits. However, habitat destruction and overharvesting have led to severe decline in their wild populations. Chloroplast (cp) genomes are highly valued in evolutionary studies, due to comparative conservation and accumulation of genomic variations. Elucidating the structure of chloroplast genome is instrumental in conserving genetic diversity within the Collabieae. Methods: we explored the chloroplast genome characteristics of Collabieae. We incorporated three newly sequenced genomes from species (Acanthophippium sylhetense, Eriodes barbata, and Spathoglottis plicata), along with seven related species. Results: all analyzed cp genomes displayed a typical quadripartite circular structure. The total lengths ranged from 157,036 bp to 158,321 bp. Each genome contained 136 genes: 88 protein-coding genes, 38 tRNA genes, eight rRNA genes, and two pseudogenes. Across the ten Collabieae species, gene number, order, orientation, GC content, and codon usage bias were highly consistent, indicative of strong sequence conservation. However, notable structural divergence was observed at the plastome junctions, alongside variations in SSR and repetitive element frequencies. Moreover, six hypervariable regions were identified. Noncoding regions exhibited higher variability compared to protein-coding regions. Phylogenetic analysis indicated that E. barbata forms a distinct, small branch sister to the rest of the Collabieae members. Genera Acanthophippium and Spathoglottis were sister to the remaining groups within the tribe. Conclusions: this overall phylogenetic framework aligns well with previous findings. Our study provides valuable cp genomic resources and advances evolutionary research in Collabieae. Full article

Chimonanthus praecox, a traditional ornamental plant in China, is admired for its ability to bloom during the cold winter season and is recognized as an outstanding woody cut flower. MADS-box genes encode transcription factors essential for plant growth and development, with key functions in regulating flowering time and the formation of floral organs. In this study, 74 MADS-box genes (CpMADS1–CpMADS74) were identified and mapped across 11 chromosomes, with chromosome 1 harboring the highest number (13 genes) and chromosome 3 the fewest (3 genes). Physicochemical property analysis revealed that all CpMADS proteins are hydrophilic and predominantly nuclear-localized. Phylogenetic analysis classified these genes into Type I and Type II subfamilies, highlighting a clear divergence in domain structure. Eighty simple sequence repeat (SSR) loci were detected, with dinucleotide repeats being the most abundant, and the majority located in Type II MADS genes. From 23 C. praecox samples, 10 polymorphic SSR markers were successfully developed and PCR-validated, enabling a cluster analysis that grouped these cultivars into three distinct clusters. This study offers significant insights into the regulation of flowering, floral organ development, genetic linkage map construction, and the application of marker-assisted selection in C. praecox. Full article

The Dalbergia genus, a morphologically diverse group within the Fabaceae family, encompasses species of significant value in furniture production and medicinal and aromatic applications. The taxonomy of Dalbergia has relied on morphological traits, chloroplast (cp) DNA fragments, and cp genomic data. However, genomic resources for tropical liana species within this genus remain scarce. In this study, we assembled and analyzed the cp genomes of 3 liana species—Dalbergia peishaensis, D. pinnata, and D. tsoi—and compared them with those of 26 other Dalbergia species to explore their cp genome characteristics and evolutionary patterns. We employed a combination of traditional cp genome analysis and methods adapted from plant whole-genome sequencing. Phylogenetic analysis revealed that D. peishaensis has a close relationship with D. cultrata, forming a recently diverged clade, whereas D. tsoi and D. pinnata are positioned within a basal clade of the Dalbergia genus, suggesting an earlier divergence. The Dalbergia cp genomes exhibit considerable variation in size, with evidence of pseudogenization, gene loss, and duplication observed in the three liana species. Notably, the infA gene, previously reported as absent in the chloroplast genomes of Dalbergia species, was identified in the cp genomes of these three liana Dalbergia species. A total of 4533 simple sequence repeats (SSRs) were identified, providing valuable insights into cp genome evolution and facilitating future population genetics studies, particularly when combined with the high structural variation observed in the genus through whole-genome analysis methods. Additionally, seven highly divergent regions were identified as potential DNA barcode hotspots. This study enhances the genomic characterization of liana Dalbergia species and offers a robust framework for future plant cp genome analyses by integrating methodologies originally developed for whole-genome studies. Full article

Background/Objectives: In South China, Lithocarpus species dominate mixed evergreen broadleaf forests, forming symbiotic relationships with ectomycorrhizal fungi and serving as food resources for diverse fauna, including frugivorous birds and mammals. The limited understanding of chloroplast genomes in this genus restricts our insights into its species diversity. This study investigates the chloroplast genome (cp genome) sequences from seven Lithocarpus species, aims to elucidate their structural variation, evolutionary relationships, and functional gene content to provide effective support for future genetic conservation and breeding efforts. Methods: We isolated total DNA from fresh leaves and sequenced the complete cp genomes of these samples. To develop a genomic resource and clarify the evolutionary relationships within Lithocarpus species, comparative chloroplast genome studies and phylogenetic investigations were performed. Results: All studied species exhibited a conserved quadripartite chloroplast genome structure, with sizes ranging from 161,495 to 163,880 bp. Genome annotation revealed 130 functional genes and a GC content of 36.72–37.76%. Codon usage analysis showed a predominance of leucine-encoding codons. Our analysis identified 322 simple sequence repeats (SSRs), which were predominantly palindromic in structure (82.3%). All eight species exhibited the same 19 SSR categories in similar proportions. Eight highly variable regions (ndhF, ycf1, trnS-trnG-exon1, trnk(exon1)-rps16(exon2), rps16(exon2), rbcL-accD, and ccsA-ndh) have been identified, which could be valuable as molecular markers in future studies on the population genetics and phylogeography of this genus. The phylogeny tree provided critical insights into the evolutionary trajectory of Fagaceae, suggesting that Lithocarpus was strongly supported as monophyletic, while Quercus was inferred to be polyphyletic, showing a significant cytonuclear discrepancy. Conclusions: We characterized and compared the chloroplast genome features across eight Lithocarpus species, followed by comprehensive phylogenetic analyses. These findings provide critical insights for resolving taxonomic uncertainties and advancing systematic research in this genus. Full article

Canna, the sole member of the Cannaceae family, is widely cultivated as an ornamental plant for its decorative flowers and foliage and is also a potential tuber crop due to its high starch content. This study sequenced, assembled, and analyzed the complete chloroplast (cp) genomes of three common Canna species with distinct leaf colors (green, purple, and variegated). The four cp genomes ranged from 164,427 to 164,509 bp in length, had a GC content of 36.23–36.25%, and exhibited identical gene content and codon preferences. Each genome contained 130 genes, including 110 unique genes (78 protein-coding genes, four of unknown function, four rRNAs, and 28 tRNAs), 18 duplicated genes located in the IR regions (six protein-coding genes, two of unknown function, four rRNAs, and eight tRNAs), and two trnM-CAU genes in the LSC region. SSR and long-repeat showed differences in long repeats numbers and distributions among the four cp genomes, highlighting potential molecular markers for Canna species identification and breeding. Comparative analysis showed high conservation across Canna cp genomes. Phylogenetic analysis confirmed a close relationship between Cannaceae and Marantaceae and supported a [Musaeceae (Cannaceae + Marantaceae)] clade as a sister group to Costaceae. The cp genome data generated in this study provide valuable insights for developing molecular markers, resolving taxonomic classifications, and advancing phylogenetic and population genetic studies in Canna species. Full article

Background/Objectives: Illicium verum Hook. f. and Illicium difengpi K. I. B.et K. I. M. are two important medicinal plants which grow in the mountainous areas of Guangxi, China. Their similar morphological characteristics frequently lead to their misidentification. Chloroplast genome (cp)-based barcode technology has been used to effectively identify two closely related species; however, at present, there is no systematic comparative study of the cp genome sequences between I. verum and I. difengpi. Methods: Here, the cp genomes of the two plants were sequenced and analyzed. Results: The cp genome sizes were 142,689 and 142,689 bp for I. verum and I. difengpi, respectively. Each of the cp genomes annotated 122 genes, with 79 protein coding genes, 8 ribosomal RNA genes, and 35 transfer RNA genes. Amino acid frequencies of 1.17–10.19% (I. verum) and 1.18–10.17% (I. difengpi) were found in the coding genes. There were also 104 and 96 SSRs as well as 26 and 25 long repeats identified in I. verum and I. difengpi, respectively, among which the most common were A/T base repeats. Both cp genomes had SSC/IRa junctions located in gene ycf1-trnN. The ycf1 and trnL-trnV-rps7 genes were positioned at the IRb/SSC and LSC/IR boundaries, respectively. A phylogenetic relationship was constructed and the two species were fully nested within the genus Illicium. Conclusions: The comparative cp genomes of I. verum and I. difengpi are presented in this study, and this provides valuable phylogenetic information for subsequent molecular marker development and research of I. verum and I. difengpi. Full article

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. Full article

Chestnut trees are an essential source of both food and timber. However, the severe threats from invasive pests and diseases compromise their existence and productivity. In Europe, chestnut hybridization programs have been initiated to produce resilient rootstocks in response to ink disease. However, the gap in the identification of these hybrid plants is typically based on field observations and morphological features and remains a challenge. Our study presents a marker set for distinguishing between chestnut hybrid CA90 (Castanea sativa × Castanea crenata), a hybrid with demonstrated resistance to Phytophthora cinnamomi, and other varieties using microsatellite (SSR) markers and bioinformatics tools. We used 35 chestnut samples, including three CA90 controls, hybrids sampled within Portugal, with an aim to define the profiles of the chestnut hybrids and varieties in this study based on band patterns and SSR motifs. We selected and modified nine distinct SSR primers with null allelic features from 43 already developed simple sequence repeat (SSR) markers. PCR amplification and agarose gel electrophoresis were used to amplify and visualize the DNA bands. To confirm genetic variations, 27 amplified bands were sequenced by Sanger sequencing. This analysis identified 31 SSRs across 22 SSR-containing sequences, with trinucleotide (67.74%) repeats being the most common, followed by repeats of dinucleotide (22.58%), mononucleotide (6.45%), and hexanucleotide (3.23%). A total of 18 alleles were observed for the nine loci. The alleles ranged from one to three per locus for the 35 samples. The novel locus CP4 could only be found in CA90 hybrids. This tool can aid in identifying and selecting disease-resistant hybrids, thereby contributing to chestnut production and management strategies. Full article

Objectives: This study investigates the cpDNA sequences from six Hevea species, aiming to explore their genomic characteristics, gene content, and genetic relationships. The objectives include understanding the structure of these genomes, identifying potential gene rearrangements, and providing insights into genetic improvement and conservation strategies for the Hevea genus. Methods: cpDNA sequences from six Hevea species were sequenced and analyzed. Genome sizes, GC content, gene encoding potential, and structural integrity were assessed. Simple sequence repeats (SSRs) and codon usage were analyzed, with a focus on optimal codons and their frequency. Phylogenetic analysis was conducted to determine the genetic relationships within the Hevea genus. Results: The cpDNAs from the six species exhibited genome sizes ranging from 161,093 bp to 161,254 bp, with GC content between 35.72% and 35.75%. Each genome contained 91 to 92 protein-coding genes, with the infA gene consistently present. No significant gene rearrangements were detected, and SSR analysis revealed mono-repeats primarily composed of A/T bases. Codon usage analysis indicated that leucine is predominantly encoded by the UUA codon, and 31 optimal codons were identified, mainly ending in A or U. Phylogenetic analysis clarified the genetic relationships among the species. Conclusions: The study provides detailed insights into the cpDNA characteristics of Hevea species, highlighting stable genome structures, conserved genes, and specific patterns of codon usage. These findings are valuable for conservation efforts, genetic improvement strategies, and the sustainable use of Hevea germplasm. Full article

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. Camellia 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 ycf1 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 (rps16, psaJ, rpl33, rps8, and rpl16) and two gene intervals (atpH-atpI and petD-rpoA) 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. Full article

Exploring the gene flow and its causes in complex habitats of forest trees is valuable for understanding species’ adaptive evolution. Pinus yunnanensis var. tenuifolia (PYT) is mainly distributed in the dry–hot valleys along the Nanpan-Hongshui rivers in southwest China, an ecologically fragile area. In this study, we analyzed 1056 seeds from eleven natural populations of PYT across its range using twelve cpSSR markers to explore haplotype polymorphisms and correlations with environmental factors. The results revealed a high genetic diversity (H_E = 0.83), with the private haplotypes significantly exceeding the shared haplotypes. A genealogical structure was observed among the populations, with a moderate differentiation (F_ST = 0.162). The population clustering and haplotype network demonstrated localized areas of pollen exchange, especially in the middle and lower reaches of the river. Redundancy analysis showed that, as the populations were closer to the river, genetic diversity tended to decrease significantly, implying that the pollen dispersal is restricted by the foehn effect in the valley. Variability in genetic differentiation among the offspring populations was primarily influenced by geographic factors, such as mountains and rivers, which, along with local environmental adaptations, shaped the pollen distribution pattern. These findings may facilitate the sustainable management and conservation of PYT and other species under similar habitats. Full article