CPGAVAS2, an integrated plastome sequence annotator and analyzer

Phylogenomics provides new insight into the phylogeny and diversification of Asian Lappula (Boraginaceae)

The application of omics data serves as a powerful tool for investigating the roles of incomplete lineage sorting (ILS) and hybridization in shaping genomic diversity, offering deeper insights into complex evolutionary processes. In this study, we utilized deep genome sequencing data from 76 individuals of Lappula and its closely allied genera, collected from China and Central Asia. By employing the HybPiper and Easy353 pipelines, we recovered 262-279 single-copy nuclear genes (SCNs) and 352-353 Angiosperms353 genes, respectively. We analyzed multiple datasets, including complete chloroplast genomes and a filtered set of 475 SCNs, to conduct phylogenetic analyses using both concatenated and coalescent-based methods. Furthermore, we employed Quartet Sampling (QS), coalescent simulations, MSCquartets, HyDe, and reticulate network analyses to investigate the sources of phylogenetic discordance. Our results confirm that Lappula is polyphyletic, with L. mogoltavica clustering with Pseudolappula sinaica and forming a sister relationship with other taxa included in this study. Additionally, three Lepechiniella taxa nested within distinct clades of Lappula. Significant gene tree discordance was observed at several nodes within Lappula. Coalescent simulations and hybrid detection analyses suggest that both ILS and hybridization contribute to these discrepancies. Flow cytometry (FCM) analyses confirmed the presence of both diploid and tetraploid taxa within Lappula. Phylogenetic network analyses further revealed that Clades IV and VII likely originated through hybridization, with the tetraploids in Clade IV arising from two independent hybridization events. Additionally, the "ghost lineage" identified as sister to Lappula redowskii serves as one of the donors in allopolyploidization. In conclusion, our study provides new insights into the deep phylogenetic relationships of Asian Lappula and its closely allied genera, contributing to a more comprehensive understanding of the evolution and diversification of Lappula.

A new synonym for Viburnum erosum (Viburnaceae) in East China, based on morphological and molecular evidence

The critical observations of living plants in the field, along with the examination of type specimens and protologues, led us to conclude that the key characteristics, including the length of the petiole, stipules and peduncles, as well as the shape of leaves of Viburnum fengyangshanense, all fall within the variation range of V. erosum. Additionally, molecular analysis of nuclear ribosomal internal transcribed spacer (nrITS) and three plastid DNA markers (rbcL, matK and ndhF) indicates that V. fengyangshanense and V. erosum are deeply nested within a clade. Therefore, based on morphological and molecular evidence, it is demonstrated that V. fengyangshanense should be regarded as a new synonym of V. erosum.

Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Hippophae salicifolia

This study reports the first complete mitochondrial genome assembly of Hippophae salicifolia, an ecologically and economically important plant endemic to the Himalayas. The 475,105 bp genome has a 44.80% GC content and an overall AT bias, comprising 74 genes (37 protein-coding, 31 tRNA, three rRNA, and three pseudogenes). We identified extensive repetitive elements, including 188 SSRs, 20 tandem repeats, and 455 dispersed repeats, and explored their potential roles in genome evolution. Codon usage analysis showed a bias for codons ending in A or U, while RNA editing analysis revealed 415 sites that mostly convert hydrophilic to hydrophobic amino acids. Phylogenetic and collinearity analyses clarified evolutionary relationships within Hippophae and uncovered genome rearrangements. In addition, extensive gene transfer was detected between the mitochondrial and chloroplast genomes. Ka/Ks and nucleotide diversity analyses indicate that most genes are under purifying selection, with some possibly undergoing positive selection. Overall, these findings enhance our understanding of the structural and evolutionary features of the H. salicifolia mitochondrial genome and provide valuable insights for the genetic improvement and conservation of Hippophae species.

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

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

Comparative chloroplast genomics provides insights into the phylogenetic relationships and evolutionary history for Actinidia species

Actinidia species are fruit trees with various functions, such as providing edible fruit, serving as ornamental plants, and having medicinal benefits. However, the taxonomy of Actinidia species is controversial due to widespread hybridization, the history of divergence and polyploid speciation among Actinidia species also remains unclear. In this study, we conducted comparative analyses of the chloroplast genomes and ploidy among multiple Actinidia species. The genes clpP, infA, ndhD, ndhK, and rpl20 were absent from these chloroplast genomes. The ycf2 and rpl20 genes in the Actinidia species were under positive selection. Several regions (rps16-trnQ-UUG, trnS-GCU-trnR-UCU, ndhC-trnV-UAC, rbcL-accD, rps12-psbB, trnN-GUU-ndhF, ycf1-trnN-GUU, and trnH-GUG-psbA) and genes (ycf1, ycf2, accD, rpl20) exhibited high variability, which could potentially serve as molecular markers in species delineation and other phylogenetic studies. Through divergence time estimation, the Actinidia genus originated 23 million years ago (Ma), and experienced a tetraploidization event in ~ 20 Ma. Subsequently, Actinidia has undergone extensive diploidization. Our findings will provide valuable information in species identification, breeding programs, and conservation efforts for Actinidia species.

Decoding the mitogenome of rosemary (Salvia rosmarinus): insights into genome evolution, structural dynamics and prospects for mitochondrial engineering

BACKGROUND

Rosemary (Salvia rosmarinus), an aromatic evergreen shrub of the Salvia (Lamiaceae), is native to the Mediterranean region, thriving in rocky or arid soils. Widely used in food, pharmaceuticals, and cosmetics, its clonal reproduction poses significant challenges for breeding and germplasm innovation. While mitogenome engineering holds promise for introducing heritable mutations, incomplete mitogenome information for rosemary has hindered such efforts. This study addresses this gap by assembling and analyzing the complete mitogenome of S. rosmarinus, focusing on its structure, repetitive sequences, RNA editing events, intracellular gene transfer (IGT), and phylogenetic relationships.

RESULTS

The S. rosmarinus mitogenome spans 384,113 bp with a GC content of 44.8%, containing 34 unique protein-coding genes and 114 simple sequence repeats. Comparative analysis revealed 28 homologous segments shared between the mitogenome and plastome, totaling 18,675 bp in length. Furthermore, homologous fragments between nuclear and organellar genomes were identified, including 1,069,255 bp of organelle-derived sequences in the nuclear genome, with 194,689 bp from nuclear plastid DNA transfers (NUPTs) and 15,192 bp from nuclear mitochondrial DNA transfers (NUMTs). NUPTs were more abundant and contributed more significantly to the total length. Synteny analysis of eight Lamiales species revealed extensive mitogenomic recombination and structural rearrangements. These findings highlight the dynamic nature of mitogenomes, offering insights into genome evolution and supporting future breeding programs to enhance the genetic diversity and adaptability of S. rosmarinus.

CONCLUSIONS

This study provides the first complete mitogenome of S. rosmarinus, revealing dispersed repeats, RNA editing, and horizontal gene transfer between the nuclear and organelle genomes. The mitogenome exhibits a typical circular structure with evidence of frequent recombination, providing valuable insights into Salvia mitochondrial genetics, genome evolution, and molecular biology.

Assembly and Comparative Analysis of the Complete Mitochondrial Genomes of Smilax glabra and Smilax zeylanica

BACKGROUND

Smilax glabra (S. glabra) and Smilax zeylanica (S. zeylanica), two medicinally important species within the genus Smilax, have been widely used in Traditional Chinese Medicine (TCM) for the treatment of rheumatism, traumatic injuries, and related ailments. Despite their medicinal significance, research on the mitochondrial DNA (mtDNA) of Smilax species remains limited.

METHODS

We utilized NovaSeq 6000 and PromethION sequencing platforms to assemble the complete mitochondrial genomes of Smilax glabra and Smilax zeylanica, and conducted in-depth comparative genomic and evolutionary analyses.

RESULTS

The complete mitochondrial genomes of S. glabra and S. zeylanica were assembled and annotated, with total lengths of 535,215 bp and 471,049 bp, respectively. Both genomes encode 40 unique protein-coding genes (PCGs), composed of 24 core and 16 non-core genes, alongside multiple tRNA and rRNA genes. Repetitive element analysis identified 158 and 403 dispersed repeats in S. glabra and S. zeylanica, respectively, as well as 123 and 139 simple sequence repeats (SSRs). RNA editing site predictions revealed C-to-U conversions in both species. Additionally, chloroplast-to-mitochondrial DNA migration analysis detected 34 homologous fragments in S. glabra and 28 homologous fragments in S. zeylanica. Phylogenetically, S. glabra and S. zeylanica cluster within the Liliales order and Smilacaceae family, closely related to Lilium species. Collinearity analysis indicated numerous syntenic blocks between Smilax and three other Liliopsida species, though gene order was not conserved.

CONCLUSIONS

This study presents high-quality mitochondrial genome assemblies for S. glabra and S. zeylanica, providing valuable insights into molecular identification and conservation efforts of these traditional medicinal plants.

Complete chloroplast genomes of five Aegilops aucheri Boiss. accessions having different geographical origins

The subject of this study is Aegilops aucheri Boiss. 1844: a member of the section Sitopsis, subsection Truncata. This species is infrequently included in phylogenetic studies and is commonly regarded as a heterotypic synonym of Aegilops speltoides Tausch. The aim of this study was to detect genetic differences between Ae. aucheri and Ae. speltoides using the phylogenetic signal retrieved from chloroplast genomes. Plastomes of five Ae. aucheri accessions from different geographical locations were sequenced, annotated, and subjected to a phylogenetic analysis. Plastome sizes were found to range between 135,666 and 135,668 bp in Ae. aucheri. Comparative analysis of the chloroplast genome sequences from five Ae. aucheri accessions revealed single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) relative to the Ae. speltoides plastome. To gain a more comprehensive understanding of the genetic divergence within the Truncata subsection, sequencing the nuclear genome of Ae. aucheri and comparing it to that of Ae. speltoides is essential.

Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group

Melanoseris, a diverse genus in the Lactucinae subtribe, has 21 species in China, with 13 being endemic. The high diversity of this genus presents taxonomic challenges, particularly in the M. cyanea group, where overlapping distributions and transitional morphological traits complicate classification. This study aims to analyze the chloroplast genomes of Melanoseris, with a focus on the M. cyanea group, to explore structural differences and phylogenetic relationships among these closely related species. We analyzed the chloroplast genomes of 16 Melanoseris samples, including 12 new genomes from the M. cyanea group. The genome sizes ranged from 152,255 to 152,558 bp and exhibited a typical quadripartite structure, with an average GC content of 37.7%. Each genome encodes 132 genes, including 87 protein-coding genes, 37 tRNAs, and 8 rRNAs. Repeat analysis identified 89 to 105 dispersed repeats, 24 to 28 tandem repeats, and 35 to 39 SSRs, with mononucleotide A/T repeats being the most common. Sequence alignment revealed that variable regions were mainly concentrated in the single-copy regions. Nucleotide diversity ranged from 0 to 0.00485, highlighting 10 mutation hotspot regions. Phylogenetic analysis showed a limited differentiation among species within the M. cyanea group. This research enhances our understanding of the genetic diversity of Melanoseris, laying the foundation for future taxonomic and phylogenetic studies.

The complete chloroplast genomes of Petrocodon mirus and Petrocodon hancei (Gesneriaceae)

The genus Petrocodon is uniquely distributed in karst areas and exhibits high floral morphological diversity. We assembled and characterized the complete chloroplast genomes of Petrocodon mirus X.Z.Shi, J.X.Fu & L.H.Yang 2024 and Petrocodon hancei (Hemsl. 1890) A.Weber & Mich.Möller 2011. The genome sizes are 153,547 bp and 153,294 bp, respectively. Phylogenetic analysis revealed that P. hancei is closely related to P. multiflorus, while the position of P. mirus remains unclear. These findings provide genomic resources for studying genetic diversity in Petrocodon and Gesneriaceae.

Assembly and comparative analysis of the complete mitochondrial of Spodiopogon sagittifolius, an endemic and protective species from Yunnan, China

BACKGROUND

Spodiopogon sagittifolius, a C4 plant closely related to cultivated crops, is an edible resource and a Class II nationally protected species in China. Endemic to Yunnan, its populations are declining due to habitat destruction, highlighting its resource and conservation importance. Despite its significance, the molecular phylogenetic relationships and genetic mechanisms of adaptive evolution in the genus Spodiopogon remain poorly understood.

RESULTS

We successfully assembled and annotated the first mitochondrial genome of S. sagittifolius using HiFi sequencing and the PMAT tool. The genome is 500,699 bp in length with a GC content of 43.15%. Synteny and dN/dS analyses revealed structural and functional conservation of mitochondrial genomes in closely related species, with most protein-coding genes under purifying selection (dN/dS < 1). Notably, nad2 exhibited signs of positive selection (dN/dS = 1.49), indicating potential adaptive evolution. Extensive RNA editing events were detected across 27 protein-coding genes, predominantly involving C-to-U conversions, with synonymous mutations accounting for 49.65% of the edits. Strong codon usage bias favoring A/U-ending codons and the identification of repeat sequences suggest enhanced mitochondrial efficiency and stress adaptation. Phylogenetic analyses confirmed the taxonomic placement of S. sagittifolius within the Andropogoneae tribe.

CONCLUSIONS

This study provides the first insights into the mitochondrial genome evolution of S. sagittifolius, highlighting key features linked to stress tolerance and adaptive evolution. These findings establish a foundation for its conservation and potential domestication, with implications for crop improvement and ecological resilience.

Genomic variation and evolutionary patterns in organelle genomes between annual and perennial Glycine species

BACKGROUND

The complexity of structural variations and long stretches of repetitive DNA make the analysis of plant mitochondrial genomes (mitogenomes) exceptionally challenging. A thorough investigation of plant mitogenomes is essential for uncovering the evolutionary processes of plant organelles and optimizing traits related to plant cellular metabolism. The genus Glycine includes groups with both perennial and annual life strategies, making it an ideal subject for studying the complexity and variations of plant mitogenomes during evolution across different life strategies.

RESULTS

Here, we assembled 20 complete mitochondrial and plastid genomes of Glycine accessions, including both annual and perennial species using the latest organelle genome assembly tool. Significant structural variations and differences in tRNA content were observed in the mitogenomes between the two life-history strategy subgenera, while protein-coding genes and rRNAs content were highly conserved. Distinct patterns of nuclear plastid DNAs and nuclear mitochondrial DNAs (NUPTs/NUMTs) were uncovered among annual and perennial species. Genes residing in NUMTs (NUMGs) showed a substantial presence in Glycine accessions, with annual soybeans exhibiting a higher proportion of protein-coding genes fully integrated into the nuclear genome. Phylogenetic analysis indicated a closely related evolutionary trajectory between mitochondrial and nuclear genomes in Glycine, providing supplementary evidence relevant to the evolutionary history of Glycine.

CONCLUSIONS

This study showed the structural variations and evolutionary patterns of mitochondrial genomes between annual and perennial Glycine species. These findings contribute to our understanding of plant organelle complexity, variation and history of intracellular genomic integration.

Nine complete chloroplast genomes of the Camellia genus provide insights into evolutionary relationships and species differentiation

The genus Camellia, known for species such as Camellia japonica, is of significant agricultural and ecological importance. However, the genetic diversity and evolutionary relationships among Camellia species remain insufficiently explored. In this study, we successfully sequenced and assembled the complete chloroplast (cp) genomes of nine Camellia accessions, including the species Camellia petelotii, and eight varieties of C. Japonica (C. Japonica 'Massee Lane', C. Japonica 'L.T.Dees', C. Japonica 'Songzi', C. Japonica 'Kagirohi', C. Japonica 'Sanyuecha', C. Japonica 'Xiameng Hualin', C. Japonica 'Xiameng Wenqing', and C. Japonica 'Xiameng Xiaoxuan'). These genomes exhibited conserved lengths (~ 156,580-157,002 bp), indicating minimal variation in genome size. They consistently predicted 87 protein-coding genes, although variations were observed in the rRNA and tRNA genes. Structural and evolutionary analyses revealed the highly conserved nature of these cp genomes, with no significant inversions or gene rearrangements detected. Consistent codon usage patterns were observed across these accessions. Five hypervariable regions (rpsbK, psbM, ndhJ, ndhF, and ndhD) were identified as potential molecular markers for species differentiation. Phylogenetic analysis of 82 accessions from the Camellia genus, along with outgroup accessions revealed close genetic relationships among certain C. japonica varieties, including Songzi, Sanyuecha, L.T.Dees, and Kagirohi, which formed sister groups. Massee Lane was located within Sect. Camellia. Moreover, Xiameng Hualin, Xiameng Wenqing, Xiameng Xiaoxuan, and C. petelotii demonstrated a strong genetic affinity. These findings provide valuable insights into the structural and evolutionary dynamics of Camellia cp genomes, contributing to species identification and conservation.

Comparative analysis of chloroplast genomes on Meliaceae species: insights into the evolution and species identification

Introduction

Meliaceae, a significant group in Sapindales, possesses material and medicinal value due to its applications in timber and bioactive compounds. However, the high morphological diversity of the Meliaceae species and the lack of comparative studies of chloroplast (cp) genomes have led to great challenges in the classification and identification of Meliaceae species.

Methods

In this study, we sequenced the complete cp genomes of three Toona species (Toona fargesii, Toona ciliata, and Toona sinensis), and conducted comparative analyses of these cp genomes along with 29 previously published cp genomes of Meliaceae. Additionally, we performed the phylogenetic analyses and estimated the divergence times of Meliaceae.

Results

The cp genomes of 32 Meliaceae species ranged from 158,558 bp to 160,978 bp in length. Specifically, the cp genomes of Toona varied from 159,242 bp to 159,617 bp in length. These cp genomes contained a total of 135 unique genes, comprising 90 protein-coding, 8 rRNA, and 37 tRNA genes. Divergence time estimation revealed that the Meliaceae family diverged into two subfamilies (Cedreloideae and Melioideae) approximately 72.92 Ma (95% HPD: 60.62-87.01 Ma) in the Late Cretaceous. The diversification of Cedreloideae (47.86 Ma, 95% HPD: 47.42-48.22 Ma) occurred later than that of Melioideae (66.60 Ma, 95% HPD: 55.41-79.73 Ma). Furthermore, comparative genomic analysis identified 52 to 116 simple sequence repeats (SSRs) and twelve highly variable regions (HVRs) found among the cp genomes of Meliaceae.

Discussion

Divergence time estimation indicates that most Meliaceae species have a relatively recent origin, with rapid divergence occurring during the Late Oligocene or Early Miocene epochs. Comparative analysis of cp genomes revealed that Meliaceae exhibits relative conservation in terms of cp genome size, inverted-repeat (IR) boundary, genome structure, HVRs and codon patterns. Although differences exist between the Cedreloideae and Melioideae subfamilies, the overall similarity remains notably high. Furthermore, the ycf1, trnK-rps16, and ndhF-rpl32 regions exhibited the highest nucleotide polymorphism within Meliaceae, while the rpl22 gene displayed significant genetic diversity within both subfamilies. As candidate molecular markers, these regions may effectively distinguish among species. These findings not only provide insights into the evolution and species identification but also establish a scientific foundation for future systematics within Meliaceae.

Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment

Iodes seguinii is a woody vine known for its potential therapeutic applications in treating rheumatoid arthritis (RA) due to its rich bioactive components. Here, we achieved the first chromosome-level assembly of the nuclear genome of I. seguinii using PacBio HiFi and chromatin conformation capture (Hi-C) sequencing data. The initial assembly with PacBio data produced contigs with an N50 length of 9.71 Mb, and Hi-C data anchored these contigs into 13 chromosomes, achieving a total length of 273.58 Mb, closely matching the estimated genome size. Quality assessments, including BUSCO, long terminal repeat assembly index, transcriptome mapping rates, and sequencing coverage, confirmed the high quality, completeness, and continuity of the assembly, identifying 115.28 Mb of repetitive sequences, 1062 RNA genes, and 25,270 protein-coding genes. Additionally, we assembled and annotated the 150,599 bp chloroplast genome using Illumina sequencing data, containing 121 genes including key DNA barcodes, with maturase K (matK) proving effective for species identification. Phylogenetic analysis positioned I. seguinii at the base of the Lamiales clade, identifying significant gene family expansions and contractions, particularly related to secondary metabolite synthesis and DNA damage repair. Metabolite analysis identified 84 active components in I. seguinii, including the discovery of luteolin, with 119 targets predicted for RA treatment, including core targets like AKT1, toll-like receptor 4 (TLR4), epidermal growth factor receptor (EGFR), tumor necrosis factor (TNF), TP53, NFKB1, janus kinase 2 (JAK2), BCL2, mitogen-activated protein kinase 1 (MAPK1), and spleen-associated tyrosine kinase (SYK). Key active components such as flavonoids and polyphenols with anti-inflammatory activities were highlighted. The discovery of luteolin, in particular, underscores its potential therapeutic role. These findings provide a valuable genomic resource and a scientific basis for the development and application of I. seguinii, addressing the genomic gap in the genus Iodes and the order Icacinales and underscoring the need for further research in genomics, transcriptomics, and metabolomics to fully explore its potential.

Phylogenomic analyses re-evaluate the backbone of Corylus and unravel extensive signals of reticulate evolution

Phylogenomic analyses have shown that reticulate evolution greatly affects the accuracy of phylogenetic inferences, and thus may challenge the authority of bifurcating phylogenetic trees. In this study, we re-evaluated the phylogenetic backbone of the genus Corylus based on complete taxon sampling and genomic data. We assembled 581 single-copy nuclear genes and whole plastomes from 64 genome resequencing datasets to elucidate the reticulate relationships within Corylus. Nuclear coalescent and concatenation phylogenies revealed identical and fully supported backbone, clarifying the sisterhood between sect. Acanthochlamys and sect. Siphonochlamys as well as the phylogenetic position of C. fargesii and C. wangii, which have yet been addressed in previous phylogenetic studies. However, the monophyly of C. jacquemontii and C. kwechowensis and the distinction between C. ferox and C. ferox var. thibetica were not supported. Gene trees-species tree conflicts and cytonuclear discordance were identified, with multiple evidences supporting that hybridization/introgression, coupled with incomplete lineage sorting, have led to substantial phylogenetic incongruence in Corylus. Moreover, typical geographical clustering rather than strict monophyletic pattern in plastome phylogeny implies chloroplast capture within Corylus and offers evidence of cytoplasmic introgression. Overall, this study provides a robust phylogenomic backbone for Corylus and unravels that reticulate evolution can greatly shape taxonomic revision.

Comprehensive analysis of the mitochondrial genome of Iris domestica emphasizing multichromosomal organization and repeat-mediated homologous recombination

Background

Iris domestica is a perennial herb valued for both its ornamental and medicinal properties. Despite its significance, no comprehensive analysis of its mitochondrial genome has been previously reported. Plant mitochondrial genomes are known for their large size, structural complexity, and frequent recombination events. This study aims to provide the first complete assembly and characterization of the mitochondrial genome of I. domestica, with a focus on its structure, gene content, repeat elements, and RNA editing sites.

Results

We used GetOrganelle and Unicycler software to hybrid assemble Nanopore and Illumina data to obtain the mitochondrial genome of I. domestica. The mitochondrial genome of I. domestica consists of four contigs: contig1 (222,498 bp), contig2 (90,780 bp), contig3 (42,563 bp), and contig4 (39,247 bp). Two repeat sequences, R1 (7,784 bp) and R2 (3,519 bp), facilitate the conformation of three circular chromosomes, suggesting a complex multi-chromosomal structure. A total of 34 protein-coding genes, including 24 core genes and 10 non-core genes were identified. Analysis of tandem repeat elements revealed significant variability, with Chromosome 1 showing the highest diversity of SSRs and scattered repeats. Additionally, 20 homologous fragments were identified between the mitochondrial and chloroplast genomes, accounting for 1.10% of the mitochondrial genome. Phylogenetic analysis based on 24 conserved mitochondrial genes placed I. domestica in close relation to Iris domestica and Crocus sativus. Furthermore, 545 RNA editing sites were identified, with notable variations across genes, suggesting that RNA editing plays a significant role in regulating mitochondrial gene expression.

Conclusion

The complete assembly of the I. domestica mitochondrial genome reveals a complex multichromosomal structure characterized by recombination events. The high number of RNA editing sites and the presence of transferred plastid DNA highlight the dynamic nature of the genome, contributing to its adaptability and evolution. These findings provide a genetic foundation into the plant's medicinal properties, adaptive mechanisms, and potential for environmental resilience.

The Complete Mitochondrial Genome of Thymus mongolicus and Its Phylogenetic Relationship with Lamiaceae Species

Thymus mongolicus (Lamiaceae) is a plant commonly found throughout China, in which it is widely used in chemical products for daily use, traditional medicinal preparations, ecological management, and cooking. In this study, we have assembled and annotated for the first time the entire mitochondrial genome (mitogenome) of T. mongolicus. The mitochondrial genome of T. mongolicus is composed in a monocyclic structure, with an overall size of 450,543 base pairs (bp) and a GC composition of 45.63%. It contains 32 unique protein-encoding genes. The repetitive sequences of the T. mongolicus mitogenome include 165 forward repetitive sequences and 200 palindromic repetitive sequences, in addition to 88 simple sequence repeats, of which tetramers accounted for the highest proportion (40.91%). An analysis of the mitogenome codons revealed that synonymous codons generally end with A/U. With the exception of nad4L, which uses ACG/ATG as an initiation codon, all other genes begin with the ATG start codon. Codon analysis of the mitogenome also showed that leucine (909) are the most abundant amino acid, while tryptophan (134) are the least prevalent. In total, 374 RNA editing sites were detected. Moreover, 180 homologous segments totaling 105,901 bp were found when the mitochondrial and chloroplast genomes of T. mongolicus were compared. Phylogenetic analysis further indicated that T. mongolicus is most closely related to Prunella vulgaris in the Lamiaceae family. Our findings offer important genetic insights for further research on this Lamiaceae species. To the best of our knowledge, this study is the first description of the entire mitogenome of T. mongolicus.

Mitogenome of Uncaria rhynchophylla: genome structure, characterization, and phylogenetic relationships

BACKGROUND

Uncaria rhynchophylla is listed in the Chinese pharmacopoeia as one of the five botanical sources of the traditional medicine Gou-Teng, which has been utilized for the treatment of mental and cardiovascular disorders. This particular species is well-known in China for its hook-like structures originating from the leaf axils. Despite available reports on its chloroplast genome, there persists a notable lack of understanding concerning the structural variations and evolution of its mitochondrial genome. This knowledge gap hinders our ability to fully comprehend its genetic attributes.

RESULTS

We successfully assembled the mitochondrial genome of U. rhynchophylla by seamlessly integrating Illumina short reads with Nanopore long reads, resulting in a non-circular genome comprising 1 circular contig and 2 linear contigs. The total length of this genome is 421,660 bp, encompassing 36 PCGs. The identification of 4 distinct pairs of repeats has unveiled their pivotal role in repeat-mediated recombination. Of the 28 homologous fragments derived from chloroplasts, the majority were observed to have been transferred from the inverted repeat (IR) regions of the chloroplast genome to the mitochondrial genome. The mitochondrial DNA provides a distinctive resolution for the positioning of several species within the Gentianales phylogenetic framework, which remains unresolved by chloroplast DNA.

CONCLUSION

By utilizing a newly assembled, high-quality mitochondrial genome of U. rhynchophylla, we have elucidated its intricate genomic structure, distinctive sequence characteristics, and potential for phylogenetic analysis. These findings mark significant strides in advancing our comprehension of the genetics of Uncaria.

The complete chloroplast genome of Malva cathayensis M.G.Gilbert, Y.Tang & Dorr 2007 and its phylogenetic analysis

Malva cathayensis, a wild medicinal and edible Malvaceae species, lacked genomic data until now. In this study, we presented its first complete chloroplast genome (158,793 bp), featuring a quadripartite structure: 87,215 bp LSC, 20,766 bp SSC, and two 25,406 bp IRs. The genome contains 129 genes (85 protein-coding, 36 tRNA, 8 rRNA) with 37.1% GC content. Phylogenetic analysis revealed two Malva clades, with M. cathayensis grouping alongside M. crispa, M. verticillata, and M. parviflora. This study provides essential molecular data for Malva's evolutionary relationships and diversification, enabling future comparative genomic research in this genus.

Characterization of the complete chloroplast genome of Garcinia xanthochymus Hook. f. ex T. Anderson 1874 (Clusiaceae) and its phylogenetic implications

Garcinia xanthochymus is renowned for sweet, water-rich pulp fruits. Despite some phytochemical analyses highlighting its economic and medicinal value, research on its phylogeny is scarce. To fill this void, we sequenced the first chloroplast genome of G. xanthochymus. The genome was 157,688 bp long with a typical quadripartite structure, consisting of two IR (27,017 bp each), a LSC (85,998 bp), and a SSC (17,656 bp). It contained 125 unique genes, including 80 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Forming a distinct branch, G. pedunculata, G. subelliptica and G. mangostana showed the closest phylogenetic relationships.

Evidence for evolution of a new sex chromosome within the haploid-dominant Marchantiales plant lineage

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Dicranum motuoense (Bryophyta): A New Taxon from China, with Special References to Its Complete Organelle Genomes

Dicranum is one of the most diverse and widespread genera within the family Dicranaceae, encompassing ca. 110 accepted species worldwide. However, the taxonomy of this genus remains notoriously complex, with the circumscription of several species still unresolved, thereby limiting our understanding of the Dicranum's diversity. During a recent survey of Dicranum in China, we found an intriguing species characterized by a unique combination of morphological traits including stiff and fragile leaves, sharply denticulate leaf apices, elongated, rectangular and porose laminal cells throughout, bistratose or partially bistratose laminal cells in the distal part, 1-2 stratose alar cells, and a transverse section of the costa in the lower portion of leaf with two stereid bands and undifferentiated epidermal layers. Morphological and molecular phylogenetic analyses, based on five chloroplast markers and one nuclear marker, support the recognition of this moss as a new species, which we described here as Dicranum motuoense sp. nov. Furthermore, we present the complete organellar genomes of this newly identified species. The chloroplast genome of D. motuoense is 123.94 kb in length, while the mitochondrial genome is 105.77 kb in length. A total of 127 genes and 66 genes were identified in the chloroplast and mitochondrial genomes, respectively. This study not only advances our understanding of species diversity with Dicranum but also contributes to the broader knowledge of its evolution. Additionally, a key for the identification of Dicranum species with fragile leaves is included.

Whole plastome sequence of Hibiscus moscheutos L. 1753 (Malvaceae) and its phylogenetic analysis

Hibiscus moscheutos, a perennial herb in the Malvaceae family, has medicinal properties but lacks molecular data. This study sequenced and analyzed its first complete plastome using next-generation sequencing. The 160,208 bp circular plastome has a typical quadripartite structure with 130 genes and 36.93% GC content. Phylogenetic analysis showed that H. mutabilis is sister to H. taiwanensis. This study provides essential molecular data for future research on Hibiscus phylogeny, taxonomy, and evolution.

The population chloroplast genomes of Populus reveal the phylogenetic relationship between three new taxa of sect. Leucoides and their parents

BACKGROUND

Poplars are important woody plants, which are widely distributed in the forests from the subtropics to the north of the Northern Hemisphere. Poplars have high ecological and economic value. However, there are frequent interspecific and intraspecific hybrids in Populus, resulting in a large number of intermediate taxa, which makes the morphological identification of Populus very challenging. Plastid genome is an important tool to study the evolutionary relationship of plants. Therefore, comparison and phylogenetic analysis were carried out based on the population chloroplast genomes of 34 individuals from 7 taxa.

RESULTS

In this study, seven newly assembled and annotated chloroplast genomes of Populus were reported. They all had typical quadripartite structures with the same GC content (37.6%), but there were differences within the population, and the genome size ranged from 155,736 bp to 156,812 bp. In all Populus species, 134 genes were identified, including 88 protein coding genes (PCGs), 37 tRNA and 8 rRNA genes. The gene sequences alignment of different taxa showed that the gene sequences and content were relatively conservative, there was no gene rearrangement, and only 3 highly variable regions (psbZ-trnG, ndhC-trnV and trnN-trnR) were identified, which can be used as molecular markers. Most PCGs had high codon usage bias and 3 positive selection genes (rps7, rps12 and rpl16) have been identified. The analysis of population genetic structure and phylogeny showed that the chloroplast genomes supported that Populus was a monophyletic taxon, which could be divided into four sections (Abaso, Turanga, Populus and ATL (Aigeiros, Tacamahaca and Leucoides)). Among them, P. dafengensis, P. butuoensis and P. szechuanica had the closest genetic relationship, P. gonggaensis and P. cathayana had the closest genetic relationship, it was speculated that the taxa of Sect. Tacamahaca may be the main female parent of the three new taxa from Sect. Leucoides.

CONCLUSION

In general, this study provides valuable insights for new species identification, phylogenetic relationships, breeding and resource development, and genetic diversity of Populus.

The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar "Yuexiangzao"

Camellia sinensis var. sinensis cultivar "Yuexiangzao" (YXZ) was a new tea cultivar in China. In this study, we reported a complete chloroplast (CP) genome based on the DNGSEQ sequencing technology. The CP genome sequence of YXZ was 157,041 bp in length and contained a large single copy (LSC, 86,594 bp), a small single copy (SSC, 18,291 bp), and two inverted repeats (IRs, 26,078 bp). The GC contents of LSC, SSC, and two IRs were 35.31%, 30.53%, and 42.94%, respectively. The phylogenetic analysis showed that YXZ was closely related to C. sinensis cv. "Tieluohan" and C. sinensis cv. "Xinyang 10."

Complete chloroplast genome of the marine eelgrass Zostera pacifica (Zosteraceae, Plantae) from Monterey, California

We present the complete chloroplast genome of the eelgrass Zostera pacifica from Monterey, California. The genome is circular and 144,675  bp in length. It consists of 82 protein-coding, 31 transfer RNA, and 8 ribosomal RNA genes and is 99.44%-99.42% similar in nucleotide pairwise identity to the closely related species Zostera marina.

Comparative and phylogenetic analysis of Potentilla and Dasiphora (Rosaceae) based on plastid genome

BACKGROUND

Potentilla L. and Dasiphora L. are predominantly perennial herbs, occasionally manifesting as annuals or shrubs, primarily found in the northern temperate zone. However, taxonomic classification within this group remains contentious, particularly regarding genus boundaries and species delineation. Therefore, this study sequenced and analyzed the complete plastid genomes of 19 species from Potentilla and Dasiphora, comparing them with five previously published plastid sequences. Our objectives included reconstructing phylogenetic relationships within Potentilla and Dasiphora and investigating cytonuclear discordance among them.

RESULTS

These plastid genomes were highly conserved in structure, GC content, and overall genome composition, comprising 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Notably, all Dasiphora plastid genomes lacked the unique intron for rpl2. Comparative genomic analyses revealed that variations in plastid genome size were due to differences in the lengths of the LSC, SSC, and IR regions. The IR region was predominantly conserved, while non-coding regions exhibited higher variability than coding regions. We screened SSR and identified seven highly variable loci that serve as potential molecular markers, offering valuable insights into the intergeneric relationships between Potentilla and Dasiphora. Phylogenetic analyses based on nuclear (ITS, ETS) and cytoplasmic (plastid, mitochondrial) genes confirmed the monophyly of Potentilla and Dasiphora, with results largely consistent with previous studies and supported by robust reliability metrics. We identified cytonuclear conflicts within Potentilla, which frequently disrupt its monophyly. We hypothesize that these conflicts may result from interspecific hybridization or incomplete lineage sorting events during the evolutionary history of the genus.

CONCLUSIONS

This study offers a theoretical foundation for advancing molecular identification and phylogenetic research on Potentilla and Dasiphora species. However, future work could benefit from greater detail on the criteria for selecting mitochondrial gene sequences and nrDNA datasets.

Gastrochilusobovatifolius (Orchidaceae, Aeridinae), a new species from the Daba Mountains of Chongqing, China

Gastrochilusobovatifolius, a new species discovered in the Dabashan of northeast Chongqing (China), is described and illustrated. The novelty morphologically resembles G.affinis, G.balangshanensis and G.heminii in having a glabrous and smooth epichile. but can be distinguished by the unique obovate shape of the leaves, smaller epichile, and flower color. The results of molecular phylogenetic analysis, based on nuclear ribosome internal transcribed spacer (nrITS) and four chloroplast DNA fragments (matK, psbA-trnH, psbM-trnD, and trnL-F) of 55 Gastrochilus species, support the inclusion of G.obovatifolius in G.sect.Microphylli, being most closely related to G.balangshanensis from Sichuan. The new species is a trunk epiphyte in evergreen broad-leaved forest.

Complete mitogenome characteristics and phylogenetic analysis of traditional Chinese medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family

BACKGROUND

Tinospora sagittata, a member belongs to the genus Tinospora of Menispermaceae family. Its tuberous roots have been used as traditional Chinese medicine (TCM) for pharmacological properties and are commonly known name as "Jin Guo Lan". Although its plastome and nuclear genome had been sequenced, its mitochondrial genome has not been explored, which significantly hampers conservation efforts and further research for this species. In addition, previous efforts based on multiple molecular markers providing profound insights into an intergeneric phylogenetic framework for Burasaieae and sampled species of T. sagittata are placed in a superclades, species delimitation of T. sagittata still need to be comprehensively evaluated.

RESULTS

Flow cytometry revealed that Tinospora sagittata has two cytotypes and a wide range in genome sizes. We further sequenced and assembled the organelle genomes of T. sagittata, including the mitogenome (513,210-513,215 bp) and plastome (163,621-164,006 bp). The plastomes were highly similar in gene content and exhibited a typical quadripartite structure, but a translocation as well as two inversions were detected in mitogenomes. The repeats patterns in both organelles are generally similar, but significant difference in the codon bias of the genes of Tinospora organelle genomes. Interesting, both organelle genomes had shown that inter-gene spacer regions could be used as effective molecular markers for further phylogenetic analyses and species identification. Comprehensive analysis of protein coding genes of organelle genomes showed that significant difference in Ka, Ks, and Ka/Ks values among the organelle genomes. Phylogenetic analysis identified a tree that was basically consistent with the phylogeny of Ranunculales described in the APG IV system.

CONCLUSIONS

We provided a high-quality and well-annotated organelle genome for Tinospora sagittata. The study present here advances our understanding of the intricate interplay between plastome and mitogenome. Moreover, our results also laid the foundation for further studying the course, tempo and mode of organelle genome evolution of Menispermaceae.

Phylogenetic Inferences and Historical Biogeography of Onocleaceae

The family Onocleaceae represents a small family of terrestrial ferns, with four genera and around five species. It has a circumboreal to north temperate distribution, and exhibits a disjunct distribution between Eurasia and North America, including Mexico. Historically, the taxonomy and classification of this family has been subject to debate and contention among scholars, leading to contradictory classifications and disagreements on the number of genera and species within the family. Furthermore, due to this disjunct intercontinental distribution and the lack of detailed study across its wide range, this family merits further study to clarify its distributional pattern. Maximum likelihood and Bayesian phylogenetic reconstructions were based on a concatenated sequence dataset for 17 plastid loci and one nuclear locus, which were generated from 106 ingroup and six outgroup taxa from three families. Phylogenetic analyses support that Onocleaceae is composed of four main clades, and Pentarhizidium was recovered as the first branching lineages in Onocleaceae. Molecular dating and ancestral area reconstruction analyses suggest that the stem group of Onocleaceae originated in Late Cretaceous, with subsequent diversification and establishment of the genera Matteuccia, Onoclea, Onocleopsis, and Pentarhizidium during the Paleogene and Neogene. The ancestors of Matteuccia, Onoclea, and Onocleopsis could have migrated to North America via the Beringian land bridge or North Atlantic land bridge which suggests that the diversification of Matteuccia + Onoclea + Onocleopsis closely aligns with the Paleocene-Eocene Thermal Maximum (PETM). In addition, these results suggest that Onocleaceae species diversity peaks during the late Neogene to Quaternary. Studies such as this enhance our understanding of the mechanisms and climatic conditions shaping disjunct distribution in ferns and lycophytes of eastern Asia, North America, and Mexico and contribute to a growing body of evidence from other taxa, to advance our understanding of the origins and migration of plants across continents.

Comparative analysis of chloroplast genomes reveals molecular evolution and phylogenetic relationships within the Papilionoideae of Fabaceae

BACKGROUND

The structure of chloroplast genomes (cpDNAs) in Fabaceae (Fab.) has undergone significant evolutionary modifications. Within the Papilionoideae (Pap.), the emergence of the Inverted Repeat-Lacking Clade (IRLC) represents a major genomic alteration. However, the molecular evolution and phylogenetic relationships within Pap. remain poorly resolved due to limited molecular data and incomplete research, highlighting the need for systematic investigation.

PURPOSE

This study presents an in-depth analysis of the cpDNAs within the Pap., with the aim of unraveling the molecular evolution and phylogenetic interconnections among its species.

METHODS

Complete cpDNAs of 18 Pap. species were sequenced using the Illumina Novaseq 6000 platform, followed by assembly and annotation. Comparative genomic analyses were conducted to elucidate structural variations and phylogenetic relationships.

RESULTS

The research has uncovered significant differences in the structure and characteristics of the cpDNAs within the Pap.. The lengths of the cpDNAs of 18 species range from 121,190 bp to 158,539 bp, and they contain between 107 and 112 unique genes. Five species, namely Desmodium elegans and Indigofera bracteata, exhibit a typical quadripartite structure, while thirteen species from genera such as Astragalus (Ast.), Hedysarum (Hed.), and Caragana (Car.) are grouped within the Inverted Repeat-Lacking Clade (IRLC). Genetic characteristic analysis revealed a plentiful presence of SSR loci, with single-nucleotide repeats and dinucleotide (A/T) repeats being the most predominant. Notably, the cpDNAs of five species including D. elegans have experienced significant rearrangements. For example, an inversion of approximately 23 kilobase (kb) pairs was observed in Pueraria peduncularis and Sophora moorcroftiana. These species exhibit pronounced differences in their non-coding regions. Comparative genomic variations at cpDNA sites were identified. Moreover, by using D. elegans as a reference, six genes (ycf4, clpP, ycf1, trnI-GAU, accD, rpl32) displayed high nucleotide polymorphism (Pi > 0.1), and the Ka/Ks ratio for all protein-coding genes was determined to be less than 1. The topological structure of the constructed phylogenetic tree of 85 species was basically consistent with that of Pap.. Seven main clades were formed and relatively high bootstrap values were exhibited, further clarifying the evolutionary relationships among them.

CONCLUSION

This study provides novel insights into the molecular evolution and phylogeny of Pap., offering a foundational resource for future taxonomic and evolutionary research.

The complete chloroplast genome of Barringtonia asiatica (L.) Kurz (Lecythidaceae)

Genomic resources for Barringtonia asiatica (L.) Kurz, a pantropical beach forest species native to the Philippines, have not been published to date, despite its medicinal importance and potential for biomedical applications. In this study, we assembled and characterized the first complete chloroplast genome of B. asiatica using Illumina paired-end sequencing technology. It displayed a typical quadripartite structure with a sequence length of 158,794 bp, comprised of a large single copy of 88,196 bp, small single-copy of 18,448 bp, and a pair of inverted repeat regions of 26,075 bp each. The cp genome contained 35 tRNA genes, eight rRNA genes, and 86 protein-coding genes with an overall GC content of 36.8%. Phylogenetic analysis revealed a close evolutionary relationship between B. racemosa and B. fusicarpa, forming a monophyletic group with B. asiatica with high bootstrap support, thereby enhancing our understanding of the phylogeny, systematics, and genetics of Asian Lecythidaceae species.

The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera

BACKGROUND

Pseudogalium is a new monotypic genus with two subspecies in China and one in Japan, which holds a distinctive phylogenetic position and ecological significance within the tribe Rubieae. Chloroplast genomes contain abundant information for resolving phylogenetic relationships. To investigate the phylogenetics of P. paradoxum and its related genera, we first sequenced, assembled, and annotated the chloroplast genome of two subspecies of P. paradoxum in China and reconstructed the phylogenetic trees. Due to the lack of samples of P. paradoxum subsp. franchetianum from Japan, this study only analyzed and discussed P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei.

RESULTS

This study had shown that the complete chloroplast genomes of Pseudogalium ranged from 153,093 bp to 153,333 bp in length with 130 genes in total, all of which had typical circular structures consisting of a large single-copy region, a small single-copy region and a pair of inverted repeat regions. The comparative analysis showed that the chloroplast genome of P. paradoxum was conserved in the inverted repeat regions. Additionally, we identified 60 dispersed repeat sequences, 61-63 simple sequence repeats, and 30 codons within the 82 protein-coding genes that exhibited RSCU values greater than one. Furthermore, we detected highly divergent regions that hold potential as new DNA barcodes for species identification. Compared with Pseudogalium, the gene number, gene length, and GC content in the chloroplast genomes of Galium and Rubia exhibited differential characteristics, and the dispersed repeat sequences and SSRs in Galium and Rubia were significantly different. Phylogenetic analysis based on the whole chloroplast genomes showed that Pseudogalium can be treated as a new genus, with P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei considered as two distinct subspecies of P. paradoxum.

CONCLUSIONS

The complete chloroplast genomes of P. paradoxum were first reported in this study, which provided a new insight into phylogeny and taxonomy of this genus. Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.

De novo assembly and characterization of the complete mitochondrial genome of Phellodendron amurense reveals three repeat-mediated recombination

Phellodendron amurense Rupr., a rare herb renowned for its medicinal and ecological significance, has remained genetically unexplored at the mitochondrial level until now. This study presents the first-ever systematic assembly and annotation of the complete mitochondrial genome of P. amurense, achieved through a hybrid strategy combining Illumina and Nanopore sequencing data. The mitochondrial genome spans 566,285 bp with a GC content of 45.51 %, structured into two circular molecules. Our comprehensive analysis identified 32 protein-coding genes (PCGs), 33 tRNA genes, and 3 rRNA genes, alongside 181 simple sequence repeats, 19 tandem repeats, and 310 dispersed repeats. Notably, multiple genome conformations were predicted due to repeat-mediated homologous recombination. Additionally, we assembled the chloroplast genome, identifying 21 mitochondrial plastid sequences that provide insights into organelle genome interactions. A total of 380 RNA-editing sites within the mitochondrial PCGs were predicted, enhancing our understanding of gene regulation and function. Phylogenetic analysis using mitochondrial PCGs from 30 species revealed evolutionary relationships, confirming the homology between P. amurense and Citrus species. This foundational study offers a valuable genetic resource for the Rutaceae family, facilitating further research into genetic evolution and molecular diversity in plant mitochondrial genomes.

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus

Background

Asparagus L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved.

Methods

To identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among Asparagus species, we employed a plastid genome (plastome) dataset consisting of 25 Asparagus species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses.

Results

All Asparagus plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among Asparagus plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. Although the phylogenetic relationships of most Asparagus species aligned with previous study findings, the phylogenetic positions of A. munitus, A. subscandens, A. gobicus, and A. dauricus were newly determined.

Conclusions

The plastomes of Asparagus are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within Asparagus. In addition, special SSR motifs and divergent hotspot regions identified from Asparagus plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within Asparagus. Overall, this study offers a wealth of informative genetic resources pertinent to Asparagus, thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

Genome skimming provides evidence to accept two new genera (Apiaceae) separated from the Peucedanum s.l

Background

The Peucedanum s.l. genus, the backbone member of subfamily Apioideae, includes many medically and economically important plants. Although previous studies have proved that the genus was not a natural taxonomic unit and taxonomists also conducted several taxonomic revisions for taxa of this genus, classifications of numerous taxa of the genus still have not been satisfactorily resolved, especially for those endemic to China. Therefore, we conducted a comprehensive taxonomic revision of taxa within the polyphyletic Peucedanum s.l. genus in this study.

Methods

We used two molecular datasets (103 plastomes and 43 nrDNA sequences) generated by genome skimming to reconstructed a reliable phylogenetic framework with high support and resolution. In addition, we also investigated the divergence time of core clade of endemic taxa.

Results and Discussion

Both analyses failed to recover Peucedanum s.l. as a monophyletic group and robustly supported that P. morisonii, the representative of Peucedanum s.s., was distantly related to other Peucedanum s.l. members, which implied that these Peucedanum s.l. taxa were not "truly Peucedanum plants". Among these Peucedanum s.l. members, plastid-based phylogenies recognized two monophyletic clades, clade A (four species) and clade B (10 taxa). Meanwhile, obvious recognized features for morphology, plastome, and chromosome number for each clade were detected: dorsally compressed and glabrous mericarps with filiform dorsal ribs, winged lateral ribs, numerous vittae in commissure and each furrow, IRa/LSC border falling into rpl23 gene, an overall plastome size of 152,288-154,686 bp, and chromosome numbers of 2n=20 were found in clade A; whereas dorsally compressed and pubescent mericarps with filiform dorsal ribs, winged lateral ribs, numerous vittae in commissure and each furrow, IRa/LSC border falling into the ycf2 gene, an overall plastome size of 146,718-147,592 bp, and chromosome numbers of 2n=22 were discovered in clade B. Therefore, we established two new genera (Shanopeucedanum gen. nov. and Sinopeucedanum gen. nov.) to respectively accommodate the taxa of clades A and B. Furthermore, molecular dating analysis showed that the diversification of clades A and B occurred in the early Pleistocene and late Pliocene, respectively, which may have been driven by the complex geological and climate shifts of these periods. In summary, our study impelled a revision of Peucedanum s.l. members and improved the taxonomic system of the Apiaceae family.

Molecular phylogeny and comparative chloroplast genome analysis of the type species Crucigenia quadrata

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.

The complete chloroplast genome of Heracleum hemsleyanum Diels (Apioideae), a traditional medicinal herb in China

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.

Unveiling the conserved nature of Heliconia chloroplast genomes: insights from the assembly and analysis of four complete chloroplast genomes

Introduction

Heliconia, 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.

Methods

In 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.

Results

The 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.

Discussion

This 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.

Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae.

Complete Chloroplast Genomes of 9 Impatiens Species: Genome Structure, Comparative Analysis, and Phylogenetic Relationships

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.

Mitochondrial genome structural variants and candidate cytoplasmic male sterility-related gene in sugarcane

BACKGROUND

Sugarcane is a crucial crop for both sugar and bioethanol production. The nobilization breeding and utilization of wild germplasm have significantly enhanced its productivity. However, the pollen sterility in Saccharum officinarum restricts its role to being a female parent in crosses with Saccharum spontaneum during nobilization breeding, resulting in a narrow genetic basis for modern sugarcane cultivars. Mitochondria, often referred to as the intracellular "energy factories", provide energy for plant life activities, and are also implicated in cytoplasmic male sterility (CMS).

RESULTS

We performed mitochondrial genome assembly and structural analysis of two Saccharum founding species. We discovered that the proportions of repeat sequences are the primary factor contributing to the variations in mitochondrial genome structure and size between the two Saccharum species. Heterologous expression of the mitochondrial chimeric gene ORF113, which is highly expressed in male-sterile S. officinarum flowers, significantly inhibits growth and ATP synthesis in yeast cells, making it a key candidate CMS-related gene in sugarcane. Furthermore, we developed two co-dominant simple sequence repeat (SSR) markers based on the mitochondrial genome, which can effectively distinguish the cytoplasmic types of the two Saccharum species.

CONCLUSION

In this study, we identified structural variants and developed SSR molecular markers in the mitochondrial genomes of both S. officinarum and S. spontaneum. We also identified a novel mitochondrial chimeric ORF as a key candidate CMS-related gene. These findings offer valuable insights into variety identification, genetic resource development, and cross-breeding strategies in sugarcane.

Complete chloroplast genome of eight Phaius (Orchidaceae) species from China: comparative analysis and phylogenetic relationship

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.

Comparative analysis of mitochondrial genomes of Stemona tuberosa lour. reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

BACKGROUND

Stemona tuberosa, a vital species in traditional Chinese medicine, has been extensively cultivated and utilized within its natural distribution over the past decades. While the chloroplast genome of S. tuberosa has been characterized, its mitochondrial genome (mitogenome) remains unexplored.

RESULTS

This paper details the assembly of the complete S. tuberosa mitogenome, achieved through the integration of Illumina and Nanopore sequencing technologies. The assembled mitogenome is 605,873 bp in size with a GC content of 45.63%. It comprises 66 genes, including 38 protein-coding genes, 25 tRNA genes, and 3 rRNA genes. Our analysis delved into codon usage, sequence repeats, and RNA editing within the mitogenome. Additionally, we conducted a phylogenetic analysis involving S. tuberosa and 17 other taxa to clarify its evolutionary and taxonomic status. This study provides a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

CONCLUSION

Our study provides the inaugural comprehensive analysis of the mitochondrial genome of S. tuberosa, revealing its unique multi-branched structure. Through our investigation of codon usage, sequence repeats, and RNA editing within the mitogenome, coupled with a phylogenetic analysis involving S. tuberosa and 17 other taxa, we have elucidated its evolutionary and taxonomic status. These investigations provide a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

A complete chloroplast genome of Sedum lushanense S. S. Lai 2004 (Crassulaceae: Crassuloideae)

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.

The haplotype-resolved T2T genome for Bauhinia × blakeana sheds light on the genetic basis of flower heterosis

BACKGROUND

The Hong Kong orchid tree Bauhinia × blakeana Dunn has long been proposed to be a sterile interspecific hybrid exhibiting flower heterosis when compared to its likely parental species, Bauhinia purpurea L. and Bauhinia variegata L. Here, we report comparative genomic and transcriptomic analyses of the 3 Bauhinia species.

FINDINGS

We generated chromosome-level assemblies for the parental species and applied a trio-binning approach to construct a haplotype-resolved telomere-to-telomere (T2T) genome for B. blakeana. Comparative chloroplast genome analysis confirmed B. purpurea as the maternal parent. Transcriptome profiling of flower tissues highlighted a closer resemblance of B. blakeana to its maternal parent. Differential gene expression analyses revealed distinct expression patterns among the 3 species, particularly in biosynthetic and metabolic processes. To investigate the genetic basis of flower heterosis observed in B. blakeana, we focused on gene expression patterns within pigment biosynthesis-related pathways. High-parent dominance and overdominance expression patterns were observed, particularly in genes associated with carotenoid biosynthesis. Additionally, allele-specific expression analysis revealed a balanced contribution of maternal and paternal alleles in shaping the gene expression patterns in B. blakeana.

CONCLUSIONS

Our study offers valuable insights into the genome architecture of hybrid B. blakeana, establishing a comprehensive genomic and transcriptomic resource for future functional genetics research within the Bauhinia genus. It also serves as a model for exploring the characteristics of hybrid species using T2T haplotype-resolved genomes, providing a novel approach to understanding genetic interactions and evolutionary mechanisms in complex genomes with high heterozygosity.

Assembly and analysis of the first complete mitochondrial genome sequencing of main Tea-oil Camellia cultivars Camellia drupifera (Theaceae): revealed a multi-branch mitochondrial conformation for Camellia

BACKGROUND

Tea-oil Camellia within the genus Camellia is renowned for its premium Camellia oil, often described as "Oriental olive oil". So far, only one partial mitochondrial genomes of Tea-oil Camellia have been published (no main Tea-oil Camellia cultivars), and comparative mitochondrial genomic studies of Camellia remain limited.

RESULTS

In this study, we first reconstructed the entire mitochondrial genome of C. drupifera to gain insights into its genetic structure and evolutionary history. Through our analysis, we observed a characteristic multi-branched configuration in the mitochondrial genomes of C. drupifera. A thorough examination of the protein-coding regions (PCGs) across Camellia species identified gene losses that occurred during their evolution. Notably, repeat sequences showed a weak correlation between the abundance of simple sequence repeats (SSRs) and genome size of Camellia. Additionally, despite of the considerable variations in the sizes of Camellia mitochondrial genomes, there was little diversity in GC content and gene composition. The phylogenetic tree derived from mitochondrial data was inconsistent with that generated from chloroplast data.

CONCLUSIONS

In conclusion, our study provides valuable insights into the molecular characteristics and evolutionary mechanisms of multi-branch mitochondrial structures in Camellia. The high-resolution mitogenome of C. drupifera enhances our understanding of multi-branch mitogenomes and lays a solid groundwork for future advancements in genomic improvement and germplasm innovation within Tea-oil Camellia.

Unveiling the intricate structural variability induced by repeat-mediated recombination in the complete mitochondrial genome of Cuscuta gronovii Willd

Cuscuta gronovii Willd., a member of the Convolvulaceae family, is noted for its potential medicinal and nutritional benefits. In this study, we utilized a combination of Illumina and Oxford Nanopore sequencing technologies to successfully assemble the complete circular mitochondrial genome (mitogenome) of C. gronovii. The mitogenome, spanning 304,467 base pairs, includes 54 genes: 33 protein-coding genes, three ribosomal RNA (rRNA) genes, and 18 transfer RNA (tRNA) genes. Beyond its primary circular structure, we discovered and validated several alternative genomic conformations, driven by five specific repeat sequences. Three inverted repeats were found to initiate rearrangements, resulting in the creation of seven distinct chromosomal structures, while two direct repeats split a larger molecule into two subgenomic entities. We also mapped 421 RNA editing sites across the protein-coding sequences, influencing 33 protein-coding genes with varying distribution, particularly noting high frequencies in the nad4 and ccmB genes. Sixteen of these RNA editing sites were experimentally validated through PCR amplification and Sanger sequencing, confirming their presence with 100 % accuracy. This research not only introduces the first mitochondrial genome of C. gronovii but also highlights its complex conformational variability induced by repeat-mediated recombination, providing a valuable genomic resource for further molecular breeding efforts and phylogenetic evolution within the genus Cuscuta.

Chloroplast Genome Sequencing and Comparative Analysis of Six Medicinal Plants of Polygonatum

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.