Initial Assembly Research Articles

Near-complete telomere-to-telomere de novo genome assembly in Egyptian clover (Trifolium alexandrinum).

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to Semi-arid conditions that was domesticated in ancient Egypt since 6,000 years BC and introduced and well adapted to numerous countries including India, Pakistan, Turkey, and Mediterranean region. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for two Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly-fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging two contigs. The total length of the resultant chromosome-level assemblies was 547.7Mb for Helaly and 536.3Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed genomic regions highly differentiated between two cultivars and increased genetic uniformity within each cultivar. Gene ontologies associated with metabolic and biosynthetic processes and developmental processes were enriched in these genomic regions, indicating that these genes may determine the unique characteristics of each cultivar. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.

Comparative Genomic Analysis of an Apiotrichum cacaoliposimilis Strain Isolated from a Patient with Urinary Tract Infection.

Opportunistic infections caused by fungi, particularly those occurring in immunocompromised patients, are considered challenging worldwide. Therefore, a comprehensive understanding of pathogenic fungi is necessary. The present study reports the isolation of a strain of Apiotrichum cacaoliposimilis, which is difficult to detect using conventional clinical assays, from the sterile urine samples of a patient with a urinary tract infection. Sanger sequencing of the internal transcribed spacer regions confirmed the genus of the microbe, while whole-genome sequencing yielded the initial genome assembly of A. cacaoliposimilis. A total of 7,161 predicted proteincoding genes were mapped using multiple databases, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, non-redundant protein database, Pathogen-Host Interactions Database, and Comprehensive Antibiotic Resistance Database. The phenotypic data, biochemical reactions, and antimicrobial susceptibility analyses were conducted to reveal the metabolic properties, virulence, and drug resistance profile of the isolated A. cacaoliposimilis. The rank-sum test revealed the differences in the intergeneric distribution of the highly virulent genes UgeB and Pem2. In addition, other genes exhibited significant overlap in terms of virulence factors with the clinical isolate Apiotrichum mycotoxinivorans GMU1709. Fortunately, similar to most fungi belonging to the Apiotrichum genus, the isolate investigated in the present study was also sensitive to the drug voriconazole (MIC = 0.06 μg/ml). In summary, the phylogenetic placement, potential pathogenic genes, drug sensitivity patterns, and morphological characteristics of the isolated A. cacaoliposimilis were determined precisely in the present study.

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 150,599bp 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.

Evaluation of Augmented Reality instructions based on initial and dynamic assembly tolerance allocation schemes in precise manual assembly

Augmented Reality (AR) assembly instructions can be used to guide precise manual assembly, providing detailed real-time information to assist in executing operations. Most AR instructions for precise manual assembly are based on initial assembly tolerance allocation schemes (ATASs), which provide a precision constrained zone and require assembly according to the initial zone. Dynamic ATASs can adjust the subsequent tolerances according to the completed assembly errors, thereby reducing the assembly difficulty. However, ATASs do not affect the AR cues for assembly guidance, and their effects on the usability of AR instructions are subtle and unclear. This study focuses on evaluating the effects of initial and dynamic ATASs on the usability of AR instructions. An AR instruction based on an initial ATAS and an AR instruction based on a dynamic ATAS were developed for a precise manual assembly task. A user study was conducted with 16 participants to compare the two AR instructions. The results showed significant differences in assembly speed, assembly quality, perceived ease-of-use, and perceived workload. We found that the AR instruction based on the dynamic ATAS can expedite assembly with better perceived ease-of-use and lower perceived workload, but may reduce assembly quality. Based on the results, several recommendations were provided to help researchers and developers design better AR instructions for precise manual assembly.

STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair.

Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and transcription factor IIH (TFIIH) around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. Here, we identify STK19 as a TCR factor facilitating this transition. Loss of STK19 does not impact initial TCR complex assembly or RNAPII ubiquitylation but delays lesion-stalled RNAPII clearance, thereby interfering with the downstream repair reaction. Cryoelectron microscopy (cryo-EM) and mutational analysis reveal that STK19 associates with the TCR complex, positioning itself between RNAPII, UVSSA, and CSA. The structural insights and molecular modeling suggest that STK19 positions the ATPase subunits of TFIIH onto DNA in front of RNAPII. Together, these findings provide new insights into the factors and mechanisms required for TCR.

Theoretical model construction and static performance analysis of multi-leaf journal foil bearings

Abstract Multi-leaf journal foil bearing (MLJFB) structures are complex, making performance prediction challenging, and the accurate prediction of gas film thickness and pressure distributions is crucial. In this study, COMSOL finite-element software was used to establish an initial foil assembly and structural deformation simulation model for an MLJFB with bump foils. Using MATLAB, a compressible gas lubrication model was established and solved using the finite volume method (FVM). Real-time data transfer between COMSOL and MATLAB enabled a fully coupled fluid-structure interaction simulation. This model meticulously accounts for the pre-tension force in the multi-leaf bearing assembly, contact friction between adjacent foils, and the interaction between the top foil and gas film pressure. The effects of journal movement distance, direction, and top foil overlapping ratio on the bearing capacity as well as the effects of different external load directions on the journal equilibrium position were analyzed based on this model. The results indicate that increasing the top foil overlapping ratio enhances the bearing capacity of the MLJFB. Furthermore, compared to the direction of the top foil overlap position, external loads applied in the direction of the top foil midpoint are more beneficial for bearing operational stability.

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.

The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, "telomere-to-telomere" genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT "Duplex" sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used "Pore-C" chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the UL reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and provides a multirun single-instrument solution for the reconstruction of complete genomes.

Impact of timing on the invasion of synthetic bacterial communities.

Microbial communities regularly experience ecological invasions that can lead to changes in composition and function. Factors thought to impact susceptibility to invasions, such as diversity and resource use, vary over the course of community assembly. We used synthetic bacterial communities to evaluate the success and impact of invasions occurring at different times during the community assembly process. Fifteen distinct communities were subjected to each of three bacterial invaders at the initial assembly of the community ("initial invasion"), 24hours into community assembly ("early invasion"), when the community was still undergoing transient dynamics, and 7days into community assembly ("late invasion"), once the community had settled into its final composition. Communities were passaged daily and characterized through sequencing after reaching a stable composition. Invasions often failed to persist over time, particularly in higher richness communities. However, invasions had their largest effect on composition when they occurred before a community had settled into a stable composition. We found instances where an invader was ultimately excluded yet had profound and long-lasting effects on invaded communities. Invasion outcome was positively associated with lower community richness and resource use efficiency by the community, which varied throughout assembly. Our results demonstrate that microbial communities experiencing transient community dynamics are more affected by, and in some instances prone to, invasion, a finding relevant to efforts to modify the composition of microbial communities.

Reinforcement learning for fuselage shape control during aircraft assembly

Critical safety requirements necessitate ultra-high precision quality control during the assembly of large aerospace components to reduce the mismatch between parts to be joined. Traditional methods use heuristic shape adjustment or surrogate model-based control. These methods are limited by reliance on accurate model learning and inadequate robustness to varying initial assembly conditions. To address these limitations, this article proposes a model-free reinforcement learning approach for adaptive fuselage shape control during aircraft assembly. The trained reinforcement learning agent directly adjusts the aircraft components in response to their part variations and enables an autonomous system (like AlphaGo) to learn the optimal shape control policy. Specifically, the reinforcement learning environment is built on the finite element simulator. A reward function is developed to capture the optimization objective and introduces a scheme to enforce the original constraints. The proximal policy optimization algorithm is modified to speed up the learning progress and achieve better final performance. In the case study, the root-mean-square gap between components is reduced by 98.4% on average compared with their initial shape mismatch. Our proposed method outperforms the benchmark methods with smaller final shape errors, smaller maximum forces, and lower variations across different test samples.

Computational design of bifaceted protein nanomaterials with tailorable properties.

Recent advances in computational methods have led to considerable progress in the design of self-assembling protein nanoparticles. However, nearly all nanoparticles designed to date exhibit strict point group symmetry, with each subunit occupying an identical, symmetrically related environment. This property limits the structural diversity that can be achieved and precludes anisotropic functionalization. Here, we describe a general computational strategy for designing multi-component bifaceted protein nanomaterials with two distinctly addressable sides. The method centers on docking pseudosymmetric heterooligomeric building blocks in architectures with dihedral symmetry and designing an asymmetric protein-protein interface between them. We used this approach to obtain an initial 30-subunit assembly with pseudo-D5 symmetry, and then generated an additional 15 variants in which we controllably altered the size and morphology of the bifaceted nanoparticles by designing de novo extensions to one of the subunits. Functionalization of the two distinct faces of the nanoparticles with de novo protein minibinders enabled specific colocalization of two populations of polystyrene microparticles coated with target protein receptors. The ability to accurately design anisotropic protein nanomaterials with precisely tunable structures and functions will be broadly useful in applications that require colocalizing two or more distinct target moieties.

An Integrated Module Performs Selective 'Online' Epoxidation in the Biosynthesis of the Antibiotic Mupirocin.

The delineation of the complex biosynthesis of the potent antibiotic mupirocin, which consists of a mixture of pseudomonic acids (PAs) isolated from Pseudomonas fluorescens NCIMB 10586, presents significant challenges, and the timing and mechanisms of several key transformations remain elusive. Particularly intriguing are the steps that process the linear backbone from the initial polyketide assembly phase to generate the first cyclic intermediate PA-B. These include epoxidation as well as incorporation of the tetrahydropyran (THP) ring and fatty acid side chain required for biological activity. Herein, we show that the mini-module MmpE performs a rare online (ACP-substrate) epoxidation and is integrated ('in-cis') into the polyketide synthase via a docking domain. A linear polyketide fragment with six asymmetric centres was synthesised using a convergent approach and used to demonstrate substrate flux via an atypical KS0 and a previously unannotated ACP (MmpE_ACP). MmpE_ACP-bound synthetic substrates were critical in demonstrating successful epoxidation in vitro by the purified MmpE oxidoreductase domain. Alongside feeding studies, these results confirm the timing as well as chain length dependence of this selective epoxidation. These mechanistic studies pinpoint the location and nature of the polyketide substrate prior to the key formation of the THP ring and esterification that generate PA-B.

Structural profiles of the full phagocyte NADPH oxidase unveiled by combining computational biology and experimental knowledge

The phagocyte NADPH oxidase (NOX2) is an enzyme, crucial for innate immune defense, producing reactive oxygen species necessary for pathogen destruction. Its activation requires the assembly of soluble proteins (p47phox, p40phox, p67phox, and Rac) with the membrane-bound flavocytochrome b558 (cytb558). We combined circular-dichroism analyses, with decades of experimental data, to filter structural models of the NADPH oxidase complex generated by the artificial intelligence program AlphaFold2 (AF2). The predicted patterns tend to closely resemble the active states of the proteins, as shown by the compact structure of the cytb558, whose dehydrogenase domain is stabilized closer to the membrane. The modeling of the interaction of p47phox with cytb558, which is the initial assembly and activation steps of the NADPH oxidase, enables us to describe how the C-terminus of p47phox interacts with the cytb558. Combining the AF2 cytb558 -p47phox model and its classical molecular dynamics simulations, we highlighted new hydrophobic lipid insertions of p47phox, particularly at residues Trp80-Phe81 of its PX domain. The AF2 models also revealed the implications of intrinsically disordered regions, such as the fragment between the PX domain and the SH3 regions of p47phox, in ensuring distant protein-protein and membrane-protein interactions. Finally, the AF2 prediction of the cytb558-Trimera model highlighted the importance of leaving Rac1 as a separate protein to reach an active state of the NADPH oxidase complex. Altogether, our step-by-step approach provides a structural model of the active complex showing how disordered regions and specific lipid and protein interactions can enable and stabilize the multi-subunit assembly.

Progressive bearing failure analysis and strength prediction method for the initial assembly and tensile process of composite bolted joints

Composite bolted joints have extensive application in aerospace and marine equipment. Failure analysis and strength prediction are crucial steps in the design of composite bolted joints. This study proposes a method that can accurately analyze the progressive bearing failure and static strength of composite bolted joints under different initial assembly parameters. This method first obtains an accurate initial assembly state based on the high-fidelity finite element model with detailed thread structure. Then it uses this as an input to analyze the progressive bearing failure process and the bearing strength value. Using the above method, the formation and evolution mechanism of the tightening yielding phenomenon during the assembly process are analyzed. And the influence of the two key assembly parameters, washer type and initial bolt tension, on the bearing strength of composite bolted joints is analyzed. The experimental results verify the effectiveness and accuracy of the simulation methods and results.

Dissecting the role of SMN multimerization in its dissociation from the Cajal body using harmine as a tool compound.

Survival motor neuron protein (SMN), which is linked to spinal muscular atrophy, is a key component of the Gemin complex, which is essential for the assembly of small nuclear RNA-protein complexes (snRNPs). After initial snRNP assembly in the cytoplasm, both snRNPs and SMN migrate to the nucleus and associate with Cajal bodies, where final snRNP maturation occurs. It is assumed that SMN must be free from the Cajal bodies for continuous snRNP biogenesis. Previous observation of the SMN granules docked in the Cajal bodies suggests the existence of a separation mechanism. However, the precise processes that regulate the spatial separation of SMN complexes from Cajal bodies remain unclear. Here, we have employed a super-resolution microscope alongside the β-carboline alkaloid harmine, which disrupts the Cajal body in a reversible manner. Upon removal of harmine, SMN and Coilin first appear as small interconnected condensates. The SMN condensates mature into spheroidal structures encircled by Coilin, eventually segregating into distinct condensates. Expression of a multimerization-deficient SMN mutant leads to enlarged, atypical Cajal bodies in which SMN is unable to segregate into separate condensates. These findings underscore the importance of multimerization in facilitating the segregation of SMN from Coilin within Cajal bodies.

Morphology evolution of supramolecular aggregates from C3-symmetric peptide amphiphiles

During the aging of supramolecular systems, new stable materials with different morphologies, molecular packing, and hierarchical organization may form from the initial assembly. Understanding the mechanisms and pathways accompanying age-related changes may allow for the controlled synthesis of multiple materials from a single molecule in a nature-inspired manner. Herein, we demonstrate the multi-stage evolution of a single solution of C3-symmetric peptide amphiphile containing diphenylalanine fragment and benzyl-1,3,5-tricarboxamide core. Transmission electron microscopy reveals the rapid formation of 20–40 nm wide nanoribbons in an aqueous solution within 60 s after preparation. The lateral edges of nanoribbons contain solvent-exposed aromatic residues that tend to merge via an unconventional edge-to-edge zipping mechanism, leading to the nanoribbon’s growth in width. After reaching a critical width and flexibility, “sticky edges” on the same nanoribbon may merge via a self-zipping mechanism, forming rigid nanotubes. Eventually, mechanical perturbations cause buckling and fracture of nanotubes into shorter nanotubes via flexural or tensile failure. This work reports new evolution pathways in soft 2D assemblies and introduces solution ageing as a promising method to control morphology of peptide amphiphiles.

STK19 facilitates the clearance of lesion-stalled RNAPII during transcription-coupled DNA repair.

Transcription-coupled DNA repair (TCR) removes bulky DNA lesions impeding RNA polymerase II (RNAPII) transcription. Recent studies have outlined the stepwise assembly of TCR factors CSB, CSA, UVSSA, and TFIIH around lesion-stalled RNAPII. However, the mechanism and factors required for the transition to downstream repair steps, including RNAPII removal to provide repair proteins access to the DNA lesion, remain unclear. Here, we identify STK19 as a new TCR factor facilitating this transition. Loss of STK19 does not impact initial TCR complex assembly or RNAPII ubiquitylation but delays lesion-stalled RNAPII clearance, thereby interfering with the downstream repair reaction. Cryo-EM and mutational analysis reveal that STK19 associates with the TCR complex, positioning itself between RNAPII, UVSSA, and CSA. The structural insights and molecular modeling suggest that STK19 positions the ATPase subunits of TFIIH onto DNA in front of RNAPII. Together, these findings provide new insights into the factors and mechanisms required for TCR.

A chromosome-level reference genome assembly and a full-length transcriptome assembly of the giant freshwater prawn (Macrobrachium rosenbergii).

The giant freshwater prawn (Macrobrachium rosenbergii) is a key species in the aquaculture industry in several Asian, African, and South American countries. Despite a considerable growth in its production worldwide, the genetic complexities of M. rosenbergii various morphotypes pose challenges in cultivation. This study reports the first chromosome-scale reference genome and a high-quality full-length transcriptome assembly for M. rosenbergii. We employed the PacBio High Fidelity (HiFi) sequencing to obtain an initial draft assembly and further scaffolded it with the chromatin contact mapping (Hi-C) technique to achieve a final assembly of 3.73-Gb with an N50 scaffold length of 33.6 Mb. Repetitive elements constituted nearly 60% of the genome assembly, with simple sequence repeats and retrotransposons being the most abundant. The availability of both the chromosome-scale assembly and the full-length transcriptome assembly enabled us to thoroughly probe alternative splicing events in M. rosenbergii. Among the 2,041 events investigated, exon skipping represented the most prevalent class, followed by intron retention. Interestingly, specific isoforms were observed across multiple tissues. Additionally, within a single tissue type, transcripts could undergo alternative splicing, yielding multiple isoforms. We believe that the availability of a chromosome-level reference genome for M. rosenbergii, along with its full-length transcriptome, will be instrumental in advancing our understanding of the giant freshwater prawn biology and enhancing its molecular breeding programs, paving the way for the development of M. rosenbergii with valuable traits in commercial aquaculture.

Initiation of hnRNPA1 Low-Complexity Domain Condensation Monitored by Dynamic Light Scattering.

Biomolecular condensates (BMCs) exhibit physiological and pathological relevance in biological systems. Both liquid and solid condensates play significant roles in the spatiotemporal regulation and organization of macromolecules and their biological activities. Some pathological solid condensates, such as Lewy Bodies and other fibrillar aggregates, have been hypothesized to originate from liquid condensates. With the prevalence of BMCs having functional and dysfunctional roles, it is imperative to understand the mechanism of biomolecular condensate formation and initiation. Using the low-complexity domain (LCD) of heterogenous ribonuclear protein A1 (hnRNPA1) as our model, we monitored initial assembly events using dynamic light scattering (DLS) while modulating pH and salt conditions to perturb macromolecule and condensate properties. We observed the formation of nanometer-sized BMCs (nano-condensates) distinct from protein monomers and micron-sized condensates. We also observed that conditions that solubilize micron-sized protein condensates do not solubilize nano-condensates, indicating that the balance of forces that stabilize nano-condensates and micron-sized condensates are distinct. These findings provide insight into the forces that drive protein phase separation and potential nucleation structures of macromolecular condensation.

Fast and Accurate EEG/MEG BEM-Based Forward Problem Solution for High-Resolution Head Models.

A BEM (boundary element method) based approach is developed to accurately solve an EEG/MEG forward problem for a modern high-resolution head model in approximately 60 seconds using a common workstation. The method utilizes a charge-based BEM with fast multipole acceleration (BEM-FMM) and a "smart" mesh pre-refinement (called b-refinement) close to the singular source(s). No costly matrix-filling or direct solution steps typical for the standard BEM are required; the method generates on-skin voltages as well as MEG magnetic fields for high-resolution head models in approximately 60 seconds after initial model assembly. The method is verified both theoretically and experimentally.

Assembly and comparative analysis of the initial complete mitochondrial genome of Primulina hunanensis (Gesneriaceae): a cave-dwelling endangered plant

BackgroundPrimulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.ResultsIn this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.ConclusionsThis study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.