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PubMed1975

Acetylcholine receptors at neuromuscular synapses: phylogenetic differences detected by snake alpha-neurotoxins.

Phylogenetic differences in acetylcholine receptors from skeletal neuromuscular synapses of various species of snakes and lizards have been investigated, using the snake venom alpha-neurotoxins alpha-atratoxin (cobrotoxin) and alpha-bungarotoxin. The acetylcholine receptors of the phylogenetically primitive lizards, like those from all other vertebrates previously tested, are blocked by these alpha-neurotoxins. In contrast, receptors from snakes and advanced lizards are insensitive to one or both of the toxins. It is suggested that toxin-resistant acetylcholine receptors appeared early in the evolution of Squamata and preceded the appearance of alpha-neurotoxins.

Animals↗

PubMed1975

A phylogenetic perspective for social behavior in primates.

Three selected groups of studies of primate social behavior and development are discussed. In the first group of studies the social development of rhesus monkeys reared in different environments is considered. Rhesus show remarkable similarity in behavior in diverse environments, demonstrating a phylogenetic set to develop species-typical behavioral repertoires. The second set of studies reports on three species (Macaca mulatta, Macaca fasicularis, and Erythrocebus patas) reared in similar settings. Species differences observed in these settings were a result of phylogenetic set. Finally, mother-infant seperation studies conducted with several monkey species are reviewed. The results of these studies were interpreted to be the product of each species, the specific setting or apparatus used, and the independent variable manipulation employed. Caution is recommended in cross-species generalization within primates.

Aggression↗

PubMed2026

SNaQ.jl: Improved scalability for level-1 phylogenetic network inference.

MOTIVATION: Phylogenetic networks represent complex biological scenarios that are overlooked in trees, such as hybridization and horizontal gene transfer. Although numerous methods have been developed for phylogenetic network inference, their scalability is severely limited by the computational demands of likelihood optimization and the vastness of network space. Composite (or pseudo-) likelihood approaches like SNaQ have improved computational tractability for network inference, but they remain inadequate for datasets of sizes routinely handled by tree inference methods. RESULTS: Here, we introduce SNaQ.jl, a new standalone Julia package with the composite likelihood inference originally implemented within PhyloNetworks.jl as well as new scalability features that enhance computational efficiency through (i) parallelization of quartet likelihood calculations during composite likelihood computation, (ii) weighted random selection of quartets, and (iii) probabilistic decision-making during network search. Through a simulation study and empirical data analysis, we show that this new version of SNaQ.jl (version 1.1) improves average runtimes by up to 499% on average with no change in function parameters or method accuracy. AVAILABILITY AND IMPLEMENTATION: SNaQ.jl is a new open source Julia package available at https://github.com/JuliaPhylo/SNaQ.jl.

Phylogeny↗

PubMed2025

MyESL: A Software for Evolutionary Sparse Learning in Molecular Phylogenetics and Genomics.

Evolutionary sparse learning uses supervised machine learning to build evolutionary models where genomic sites loci are parameters. It uses the Least Absolute Shrinkage and Selection Operator with bi-level sparsity to connect a specific phylogenetic hypothesis with sequence variation across genomic loci. The MyESL software addresses the need for open-source tools to perform evolutionary sparse learning analyses, offering features to preprocess input phylogenomic alignments, post-process output models to generate molecular evolutionary metrics, and make Least Absolute Shrinkage and Selection Operator regression adaptable and efficient for phylogenetic trees and alignments. The core of MyESL, which constructs models with logistic regressions using bi-level sparsity, is written in C++. Its input data preprocessing and result post-processing tools are developed in Python. Compared to other tools, MyESL is more computationally efficient and provides evolution-friendly inputs and outputs. These features have already enabled the use of MyESL in two phylogenomic applications, one to identify outlier sequences and fragile clades in inferred phylogenies and another to build genetic models of convergent traits. In addition to the use in a Python environment, MyESL is available as a standalone executable compatible across multiple platforms, which can be directly integrated into scripts and third-party software. The source code, executable, and documentation for MyESL are openly accessible at https://github.com/kumarlabgit/MyESL.

Phylogeny↗

PubMed2025

The distribution of fitness effects varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients () of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of DFE variation have not been systematically investigated across species with divergent phylogenetic histories and ecological functions. Here, we inferred the DFE in natural populations of eleven animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We find that the DFE co-varies with phylogeny, where the expected mutation effects are more similar in closely related species (). Additionally, mammals have a higher proportion of strongly deleterious mutations (22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Population size is significantly negatively correlated with the expected impact of new deleterious mutations (), and the proportion of new beneficial mutations (). These findings align with Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. Consistent with the FGM's predictions, we observe that mutations are more deleterious in complex organisms, while beneficial mutations occur more frequently in smaller populations to compensate for the drift load. Our study demonstrates strong phylogenetic constraints in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of global epistasis, long-term population size and organismal complexity drive variation in the DFE across animals.

Fisher’s geometric model↗

PubMed2025

Comparison of phylogenetic metrics of transmission in symptomatic and asymptomatic tuberculosis.

BACKGROUND: Understanding drivers of Mycobacterium tuberculosis (Mtb) transmission remains a critical challenge in high-burden settings. Tuberculosis control efforts traditionally target symptomatic individuals, yet the role of asymptomatic cases in sustaining transmission is increasing recognized. METHODS: We conducted a genomic and epidemiological analysis of Mtb isolates collected in Mato Grosso do Sul, Brazil, between 2008 and 2024. From 2017 to 2022, active case finding was performed in three of the state's largest prisons, whereby sputum was collected from individuals irrespective of symptoms and tested by GeneXpert and culture. We evaluated several metrics of recent transmission from symptomatic and asymptomatic individuals, including phylogenetic clustering, Time-scaled Haplotype Density (THD), Local Branching Index (LBI), and transmission probabilities inferred using the Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH). FINDINGS: We sequenced 2,362 Mtb strains, of which 3.5% (115/2,362) were resistant to at least one drug, and 0.6% (16/2,362) were multi-drug resistant. Most strains were lineage 4, and 78.2% of all isolates were part of a genomic cluster. Among 2,362 individuals with tuberculosis, 1,137 were incarcerated at the time of diagnosis. Among these, 505 were identified through active case finding: 277 had symptomatic disease and 228 had asymptomatic tuberculosis. There was no significant difference in phylogenetic clustering proportion (77% vs. 85%; p= 0.816), THD (median 0.50 vs. 0.39; p = 0.120), or LBI (median 0.00863 vs. 0.00871; p = 0.086) between symptomatic and asymptomatic individuals. Bayesian transmission trees revealed no significant difference in the number of secondary infections inferred from symptomatic compared with asymptomatic individuals (p = 0.56). These findings were consistent across genomic clusters and robust to model assumptions. INTERPRETATION: We identified no differences in transmission from symptomatic compared with asymptomatic individuals, using several genomic measures of transmission, underscoring the substantial contribution that asymptomatic tuberculosis makes to transmission at the population level.

Asymptomatic↗

PubMed2026

Target Capture of Ancient Shell DNA Enables Phylogenetic Reconstruction of Deep-Sea Molluscs.

Target capture is widely used to enrich endogenous DNA from calcium phosphate skeletal material in vertebrates, but its performance on calcium carbonate hard parts widely produced by invertebrates remains poorly understood. Here, we compared DNA recovery from four fresh and 12 ancient (eight radiocarbon-dated to 1671-1135 years old before present) deep-sea vesicomyid clam shells, including species Archivesica marissinica, A. nanshaensis and A. okutanii, using whole-genome sequencing (WGS) or target capture of ultraconserved elements (UCEs). WGS achieved 16.65% on-target read recovery of UCEs from fresh soft tissue, but < 1% from shell specimens. By contrast, UCE capture in the same specimen increased on-target reads by up to 155-fold, reaching 29.84% in fresh shells and up to 72-fold, reaching 19.89% in ancient shells. Target capture of UCEs recovered 142-1001 loci per sample compared to 0-230 with WGS alone. Ancient shells of A. marissinica and A. okutanii, based on reads mapped with bwa-mem2 and bbmap, exhibited characteristic post-mortem DNA damage signals, with average 5'-end C-to-T misincorporation rates of 3.46% and 15.97%, respectively, exceeding the levels observed in fresh A. marissinica shells (maximum 1.24%). UCE-based phylogenetic reconstructions incorporating shell ancient DNA recovered two major clades within Pliocardiinae, consistent with published phylogenomic trees. Together, these findings demonstrate that target-capture enrichment enables effective recovery of highly degraded DNA from ancient mollusc shells and supports robust phylogenetic inference at the intrageneric scale, expanding the utility of shells-one of the most abundant invertebrate remains-for evolutionary, biogeographic and conservation studies.

Animals↗

PubMed2025

Whole genome sequencing and phylogenetic classification accelerate the implementation of respiratory syncytial virus genomic surveillance in Canada: a pilot study.

UNLABELLED: Whole genome sequencing (WGS) has emerged as a powerful tool to facilitate the study of existing and emerging infectious diseases. WGS-based genomic surveillance provides information on the genetic diversity and tracks the evolution of important viral pathogens, including respiratory syncytial virus (RSV). Multiplex tiling polymerase chain reaction (PCR) assays have been used to facilitate sequencing of a variety of pathogens in support of genomics-based surveillance initiatives. We developed, optimized, and implemented multiplex tiling PCR assays for RSVA and RSVB capable of generating near-complete genomes in the majority of contemporaneous specimens tested. A pilot data set comprising 52 RSVA and 37 RSVB genomes derived from Canadian clinical specimens during the 2022-2023 respiratory virus season was used to perform phylogenetic analyses using both near-complete genome and glycoprotein (G) sequences. Overall, the RSV phylogenetic tree built with whole genomes showed identical lineage clusters as compared to the G gene but was more discriminatory. Moreover, the availability of complete genomes enables the identification of a broader range of mutations. For instance, mutations identified in the fusion protein among Canadian isolates tested here, including S377N, K272M, S276N, S211N, S206I, and S209Q, could affect the efficacy of current vaccines or antiviral-based therapeutics. In conclusion, our work reinforces other recent studies demonstrating the utility of multiplex tiling PCR assays to facilitate high-throughput WGS of RSV, which is capable of supporting enhanced genomic surveillance initiatives, as well as the more comprehensive genomic analyses required to inform public health strategies for the development and usage of vaccines and antiviral drugs. IMPORTANCE: We present assays to efficiently sequence genomes of RSVA and RSVB. This enables researchers and public health agencies to acquire high-quality genomic data using rapid and cost-effective approaches. Genomic data-based comparative analysis can be used to conduct surveillance and monitor circulating isolates for efficacy of vaccines and antiviral therapeutics.

Humans↗

PubMed2026

Detection and phylogenetic characterization of Jingmen tick virus in Amblyomma mixtum ticks from Costa Rica.

UNLABELLED: Jingmenviruses are a group of segmented flaviviruses detected in arthropods and vertebrates that have attracted growing public health interest due to the recognition of some members as emerging human arboviral pathogens. As part of a study aimed at deciphering the virome of ticks of medical and veterinary importance in Costa Rica, we detected Jingmen tick virus (JMTV) in host-feeding Amblyomma mixtum ticks collected from horses. We assembled three complete genome segments and one partial segment from tick pools. Phylogenetic analyses revealed that JMTV from Costa Rica (JMTV Costa Rica) shares a common viral ancestor with JMTV viruses identified in ticks from the Caribbean and Latin America. Two distinct clades of Jingmenviruses were identified in the American continent, suggesting two distinct introductions: one from Europe/Asia and the other from Africa/Asia. Of note, JMTV Costa Rica falls in the same clade as viruses from Europe and Western Asia, including sequences found in humans. Our study constitutes the first detection of JMTV in Amblyomma mixtum. This tick species feeds on a wide range of hosts, including wildlife, domestic animals, and frequently parasitizes humans in Central America. Further research involving the detection of active and past infections by JMTV in humans and horses after tick bites is needed to evaluate the risk of spillover in Central America, including Costa Rica. IMPORTANCE: Jingmenviruses are flaviviruses detected in arthropods and vertebrates, reported in several countries worldwide. Some members cause disease and infections in humans; therefore, they are considered emergent human arboviruses. In Costa Rica and Central America, there is no information on tick-associated viruses or the role of ticks as putative vectors of viruses. Here, we report the first regional detection of Jingmen tick virus (JMTV) in Amblyomma mixtum ticks collected from horses. We assembled three complete and one partial viral segment from tick pools. Phylogenetic analysis revealed that the JMTV detected in Costa Rica is closely related to other detections from Latin America and the Caribbean and is located in the same clade as viruses reported in humans. Additionally, we detected two separate introductions of JMTV to Latin America. To determine whether this JMTV is an emergent arbovirus locally, research on past or active infections in humans is required.

Animals↗

PubMed2026

Molecular epidemiology and phylogenetic analysis of Anaplasma ovis and Anaplasma marginale in Ixodidae infesting livestock in northwestern Iran.

BACKGROUND: Anaplasma marginale and Anaplasma ovis are tick-borne obligate intracellular bacteria causing anaplasmosis in cattle and small ruminants, respectively, with considerable economic losses worldwide. Given the favorable ecological conditions for tick survival and the limitation of data on Anaplasma spp. in local tick populations in northwestern Iran, this study aimed to molecular and phylogenetic analysis of A. ovis and A. marginale in Ixodidae infesting livestock in northwestern Iran. METHODS: In this cross-sectional study, a total of 780 ixodid ticks were collected from livestock across 198 herds in 11 counties of Ardabil Province during 2025. Ticks were morphologically identified and grouped into pools based on species and host type. Genomic DNA was extracted using a commercial kit and molecular detection of A. ovis and A. marginale was performed using PCR assays targeting the 16 S rRNA and groEL genes. Positive samples were submitted for Sanger sequencing to confirm the identity of Anaplasma spp., phylogenetic analysis was conducted using reference sequences from GenBank (NCBI) using MEGA software (version 12). Statistical analyses were conducted using SPSS (version 25), and associations between categorical variables were assessed using Fisher's exact test (p < 0.05). RESULTS: Eight tick species belonging to three genera were identified. Among the hosts, sheep exhibited the highest infestation rate (49.3%). Hyalomma anatolicum anatolicum was the most prevalent species (25.3%) and was present in all sampled counties. Tick distribution varied significantly among host species (p = 0.003) and geographic locations (p = 0.002). PCR analysis detected A. ovis DNA in 16.6% (4/24) and A. marginale DNA in 8.3% (2/24) of tick pools. Positive pools were primarily associated with Rhipicephalus spp. and Dermacentor marginatus. According to the results of the statistical analysis a significant association was found between tick species and host type (χ² = 13.87, p = 0.0031), with Hyalomma anatolicum anatolicum more prevalent in sheep (p = 0.001). Tick abundance varied across counties (χ² = 16.42, p = 0.002), with highest densities in Nir, Khalkhal, and Kowsar (χ² = 14.21, p = 0.0028). No significant association was observed between Anaplasma positivity and tick species (p = 0.21) or host type (p = 0.09). CONCLUSIONS: The detection of A. ovis and A. marginale DNA in ixodid tick pools indicates their circulation in Ardabil Province. However, due to pooled sampling and the limited number of positive samples, the infection rate at the individual tick level could not be determined. These findings also highlight the importance of a One Health approach, considering the interconnected roles of animal health, tick vectors, and the environment in the transmission and control of tick-borne diseases.

Animals↗

PubMed2026

The distribution of fitness effects of nonsynonymous mutations varies phylogenetically across animals.

The distribution of fitness effects (DFE) describes the selection coefficients of newly arising mutations and fundamentally influences population genetic processes. However, the extent and mechanisms of differences in the DFE for non-synonymous mutations have not been systematically investigated across species with divergent phylogenetic histories and ecologies. Here, we inferred the DFE in natural populations of 11 animal (sub)species, including humans, mice, fin whales, vaquitas, wolves, collared flycatchers, pied flycatchers, halictid bees, Drosophila, and mosquitoes. We found that mammals have a higher proportion of strongly deleterious mutations (defined as s≤-0.01; 22% to 47% in mammals; 0.0% to 5.4% in insects and birds) and a lower proportion of weakly deleterious mutations than insects and birds. Further, the DFE co-varies with phylogeny, such that the mean mutation effects are more similar in closely related species (Pagel's λ = 0.84, P = 0.01). Next, we investigated whether various summary statistics of the DFE were related to variation in life-history traits across these organisms. We found some support for genome size, body mass, and long-term effective population size being correlated with the DFE. Overall, our findings are consistent with predictions derived independently from the Fisher's Geometric Model (FGM), which defines organismal complexity as the number of phenotypes under selection. FGM predicts that mutations are more deleterious in complex organisms, while strongly deleterious mutations occur more frequently in smaller populations. Our study demonstrates strong phylogenetic signal in the evolution of a fundamental population genetics parameter, and proposes that, through mechanisms of epistasis, long-term population size and organismal complexity could be underlying variation in the DFE across animals.

Journal Article↗

PubMed2022

Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa.

Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019-2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20-49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a "Samoan S. Typhi framework" that supports current and future typhoid surveillance and control efforts in Samoa.

Humans↗

PubMed2025

The Complete Chloroplast Genome and the Phylogenetic Analysis of Panicum bisulcatum (Thumb.) (Poaceae).

The chloroplast (cp) genome of Panicum bisulcatum (Thumb.), a significant agricultural weed, was sequenced and characterized to elucidate its genomic architecture, evolutionary dynamics, and phylogenetic relationships. The complete cp genome was assembled as a circular DNA molecule of 138,489 bp, exhibiting a typical quadripartite structure comprising a large single-copy (LSC, 82,260 bp), a small single-copy (SSC, 12,569 bp), and a pair of inverted repeats (IR, 21,830 bp each) regions. It encodes 135 genes, including 89 protein-coding genes, 49 tRNAs, and 8 rRNAs. Functional annotation revealed that most genes are involved in photosynthesis and genetic system. A total of 51 simple sequence repeats (SSRs) and 62 long repeats (LRs) were identified, providing potential molecular markers. Comparative analysis of IR boundaries highlighted both conserved features and species-specific expansion/contraction events among Panicum species. Phylogenomic analysis robustly placed P. bisulcatum within the genus Panicum, showing a closest relationship with P. incomtum and confirming the monophyly of the genus. Furthermore, single nucleotide polymorphism (SNP) analysis with its closest relative, P. incomtum, revealed 4659 SNPs, with a dominance of synonymous substitutions, indicating the action of purifying selection. This study provides the first comprehensive cp genomic resource for P. bisulcatum, which will facilitate future studies in species identification, phylogenetic reconstruction, population genetics, and the development of sustainable management strategies for this weed.

Phylogeny↗

PubMed1975

The primary structure of a rat kappa Bence Jones protein: phylogenetic relationships of V- and C-region genes.

The complete amino acid sequence of a LOU rat k Bence Jones protein, S211, is presented. The availability of such a sequence makes it possible to re-evaluate the phylogenetic relationships of V- and C-region genes. The data suggest that V- and C-genes, and also V-genes between themselves have evolved at different rates. The Vk1-gene seems to have been preserved during evolution and its products could be identified in three other species. The differences between these Vk1 representative sequence are similar and fall inside the range of inter-subgroup differences. On the other hand, the comparison of Ck-regions from four different species agrees with their recognized phylogenetic relationships. Evidence is presented which suggests that two substitutions within the C-region of the S211 k-chain are unrelated to allotypes and presumably represent somatic events or are evidence for multiple isotypes of rat Ck-region.

Amino Acid Sequence↗

PubMed1978

[Aspects related to the antigenic structure and serological specificity of brucellae phylogenetically related to S- and R-forms and dissociated into R-variants].

The antigenic structures and serological properties of Brucellae S- and R-forms, phylogenetically differentiated, and dissociated R-variants are studied by means of gel-precipitation, immunoelectrophoresis and fixation of the complement. The Brucella suis 1330S, Brucella suis 1330R, Brucella ovis 02 and Brucella abortus 99 are involved in the experiments. Both specific and general antigenic structures are established in all strains studied, but only homologous antibodies from the antigen-antibody complex in the complement-fixation test, induced by the phylogenetically differentiated S- and R-forms (Brucella ovis) or brucellae, diverged into R-variants. Cross complement-fixation tests between the antisera, prepared against S-forms and antigens from natural R-forms (Brucella ovis) or dissociative R-forms (R-variants) have not been observed. Also cross reactions between antisera, induced by R-forms (natural R-forms--Brucella ovis, or dissociative R-variants) and antigens, obtained from S-forms of brucellae are found.

Antigen-Antibody Complex↗

PubMed2026

Complete genome characterization, phylogenetic analysis, and capsid P2 variation of a goose astrovirus genotype 2 isolate from Guizhou, China.

Goose astrovirus genotype 2 (GAstV-2) is associated with gout and renal disease in goslings, but its occurrence in Guizhou Province remains poorly documented. We isolated a GAstV-2 strain, designated GZJP2024, from goslings with visceral gout on a farm in Jinping County, Guizhou Province, China. PCR detected GAstV-2 but not goose parvovirus, goose reovirus, Tembusu virus, fowl adenovirus, or goose astrovirus genotype 1. Serial passage in goose embryos produced mortality and hemorrhagic lesions during the third passage. Whole-genome sequencing yielded a 7,251-nt genome containing three overlapping open reading frames (ORF1a, ORF1b, and ORF2). Sequence identity and phylogenetic analyses assigned GZJP2024 to the GAstV-2 lineage. ORF1b was the most conserved coding region, whereas ORF2 was more variable. Comparison with consensus sequences from representative GAstV-2 strains identified five amino acid substitutions in ORF1a and ten in ORF2. Four ORF2 substitutions (E456D, L540Q, S608T, and A614T) occurred in the capsid P2 domain and overlapped or neighbored predicted B-cell epitope-rich regions. Template-based mapping placed E456D, S608T, and A614T on exposed regions of a spike-like capsid structure. These findings document a GAstV-2 isolate from a gout-affected goose farm in Guizhou and provide sequence data for future regional surveillance.

Capsid P2↗

PubMed2026

The large mitochondrial genome of Syndiclis anlungensis (Lauraceae): Genome structure, comparative analysis, and phylogenetic relationships among Syndiclis species.

The complete mitochondrial genome (mitogenome) of Syndiclis anlungensis, a critically endangered tropical tree, was determined in this study. The mitogenome spans 2,368,454 bp across four contigs and harbors 41 protein-coding genes, 22 tRNA genes, and three rRNA genes. Potential mutation regions, including 1317 repeat sequences and 698 simple sequence repeats (SSRs), were accurately located in the S. anlungensis mitogenome. Sixty-five transferred fragments of the repeats were found between its mitochondrial and chloroplast genomes. When compared to three other Laurales mitogenomes, extensive gene order shuffling is evident, leaving only five conserved gene clusters intact. Codon usage analysis reveals a pronounced A/T bias in both mitochondrial and chloroplast genes, and three mitochondrial genes (atp9, rps19, and sdh3) stand out for their high divergence across eleven Syndiclis taxa. Selection analyses indicate strong purifying pressure on rpl2, rpl16, and sdh3 (Ka/Ks < 1), with no positive selection detected. Using 41 mitochondrial protein-coding gene sequences from sixteen and three individuals of Syndiclis and Beilschmiedia species, respectively, our phylogenetic tree recovers Syndiclis as monophyletic, with two well-supported clades: one includes S. anlungensis, S. chinensis, S. lotungensis, S. marlipoensis, and a putative new Syndiclis species from Yunnan; the other contains S. furfuracea, S. hongkongensis, S. kwangsiensis, and three putative new Syndiclis species from Guangdong and Vietnam.

Genome, Mitochondrial↗

PubMed2026

Mitochondrial genomic characteristics and phylogenetic analysis of Cunninghamella elegans (Mucorales: Cunninghamellaceae).

Cunninghamella, a filamentous fungal genus with important biomedical and biochemical value, lacks any fully annotated mitochondrial genome to date. Herein, we presented the first complete mitogenome of Cunninghamella elegans, a circular 41,552 bp molecule (GC 27.86%) encoding 14 conserved protein-coding genes, 2 rRNA genes, 24 tRNA genes, and 6 non-conserved ORFs. Structural comparison with related species (Absidia glauca and Gongronella sp. w5) revealed dynamic evolution in intron and repeat elements. Phylogenetics places C. elegans within Cunninghamellaceae, with Gongronella as its closest relative. This reference mitogenome will underpin future evolutionary and taxonomic investigations of this industrially and medically significant lineage.

Cunninghamella elegans↗