Unique Rearrangement Research Articles

New branch on the tree of life of Gastrotricha: establishment of a new genus for limno-terrestrial species

Abstract Gastrotricha encompass a diversity of free-living micrometazoans typically associated with aquatic or semi-aquatic environments. The discovery of a gastrotrich species in limno-terrestrial habitats challenges existing taxonomic classifications and expands our understanding of their ecological diversity. This study describes Dendroichthydium ibyrapora gen. et sp. nov., a new gastrotrich from epiphytic mosses found in Atlantic rainforest within Serra do Japi biological reserve, and establishes its taxonomic status through morphological and molecular analyses. Morphological characterization was conducted using light microscopy, scanning electron microscopy, and confocal laser scanning microscopy, revealing that D. ibyrapora exhibits distinctive adaptations suited to limno-terrestrial environments, including unique cuticular adaptations and rearrangement of locomotory cilia. Molecular phylogenetics, using 18S and 28S ribosomal DNA sequences, supports the recognition of Dendroichthydium as a new genus, distinctly separated from known genera within Paucitubulatina. Furthermore, we propose reclassifying Chaetonotus (Chaetonotus) silvaticus to Dendroichthydium silvaticus comb. nov. based on shared morphological traits. The establishment of the genus Dendroichthydium reflects the ongoing need to re-evaluate gastrotrich diversity and taxonomy, highlighting the role of underexplored limno-terrestrial habitats in hosting unique life forms. This study underscores the importance of integrating morphology and genetics to improve our understanding of phylogenetics and the evolutionary dynamics of Gastrotricha.

Selective and Divergent Synthesis of Naphthalene- and Phenanthrene-Fused Azahelicenes by Turning Rearrangement On or Off.

The Scholl reaction has been used to synthesizea variety of polycyclic aromatic hydrocarbons, where 1,2-aryl shifts have sometimes occurred to yield unique rearrangement products. However, such 1,2-aryl shifts are often uncontrollable, and the selective and divergent synthesis with or without rearrangement is desired. Here, we achieved thecontrol of the rearrangementin the Scholl reaction of carbazoles by theN-substituents.The Scholl reaction of3,6-bis{2-(2-naphthyl)phenyl}carbazoles and 3,6-bis{2-(9-phenanthrenyl)phenyl}carbazoleswith anN-benzyl group gave multiple azahelicenes via double rearrangement, while those with anN-benzoyl group gave aza[9]helicene and quadruple [4]helicene in the former and latter cases, respectively. The reaction mechanisms on the divergent reaction pathways were investigated by DFT calculations, which well supported the experimental results.

Immune Repertoires in Various Dermatologic and Autoimmune Diseases.

The immune repertoire (IR) is a term that defines the combined unique genetic rearrangements of antigen receptors expressed by B and T lymphocytes. The IR determines the ability of the immune system to identify and respond to foreign antigens while preserving tolerance to host antigens. When immune tolerance is disrupted, development of autoimmune diseases can occur due to the attack of self-antigens. Recent technical advances in immune profiling allowed identification of common patterns and shared antigen-binding sequences unique to diverse array of diseases. However, there is no current literature to date evaluates IR findings in autoimmune and skin inflammatory conditions. In this review, we provide an overview of the past and current research findings of IR in various autoimmune and dermatologic conditions. Enriching our understanding of IRs in these conditions is critical for understanding the pathophysiology behind autoimmune skin disease onset and progression. Furthermore, understanding B-cell and T-cell IR will help devise therapeutic treatments in the hopes of restoring immune tolerance and preventing disease onset and progression.

Mechanistic Investigation of the Pseudo-Halogen Effect in Enantioselective Aminocatalyzed [6 + 4] and [10 + 6] Cycloadditions: Enabling Unique Favorskii-Like Rearrangements.

A mechanistic investigation into the novel combination of the pseudo-halogen effect with enantioselective aminocatalysis unravels the mechanistic intricacies of [6 + 4] and [10 + 6] higher-order cycloadditions and the succeeding new Favorskii-like rearrangements. By introducing the OTf-group into the tropone framework, it can serve both as an activator for the cycloaddition and as a proficient leaving group within the corresponding cycloadduct, thus enabling unprecedented ring-contracting Favorskii-like rearrangements. Integrating the -OTf group creates an electron-deficient 6π-component leveraging the pseudo-halogen effect by enhancing the polarization and introducing new strategic interaction points. This modification complements electron-rich 4π- and 10π-components from amino-activated 2,4-dienals or indene-carbaldehydes. A comprehensive DFT investigation supported by experimental results demonstrates that the [6 + 4] system proceeds through a rate-limiting stepwise exo-cycloaddition leading to a cycloadduct initially in a boat-conformation, subsequently transitioning to the more stable chair-conformation. The change in conformation ensures an SN1-like expulsion of the -OTf group, generating a stable carbocation bridgehead primed for a novel Favorskii-like seven-to-six ring-contracting rearrangement, resulting in the experimentally observed product. As proof-of-concept for the cycloaddition/Favorskii-like rearrangement, it is demonstrated that this approach can be extended to an unprecedented [10 + 6] cycloaddition. In contrast to the [6 + 4] system, the [10 + 6] system distinguishes itself with a concerted SN1-like/Favorskii-like six-to-five ring-contracting rearrangement, representing the rate-limiting step. This novel concept results in the experimental isolation of structurally complex products in high peri-, diastereo-, and enantioselectivity with moderate yield. These findings demonstrate the pseudo-halogen effect's multifaceted role in promoting and enabling novel reactivity.

Modification of cobalt bis(dicarbollide) ions with nitrile groups on carbon atoms: a unique low-temperature skeletal rearrangement due to the specific electron-donor character of CN substitution.

Herein, we report on the synthesis and stereochemistry of mono- and isomeric dinitrile derivatives of [(1,2-C2B9H11)2-3,3'-Co]- ions. The shape and electronic properties of CN groups can apparently surmount the strain associated with the substitution of two vicinal carbon positions. Owing to electron donation to the cage, this results in a substituent-induced rearrangement of one of the carbon atoms to the upper pentagonal ring. The molecular structure of this isomer was confirmed using sc-XRD and DFT chemical computations.

Black flies (Diptera: Simuliidae) in the Galapagos Islands: Native or adventive?

Invasive species are a threat to ecosystems worldwide, but determining if a species is adventive or native is not always straightforward. The black flies that inhabit the Galapagos Islands, long known as Simulium ochraceum, are blood-feeding pests of humans and livestock. They first came to the attention of residents in 1989, suggesting a recent arrival. Earlier colonization, however, has been suggested, based largely on polymorphic genetic loci. To address questions of origin, provenance, and length of residency, we conducted a macrogenomic analysis of the polytene chromosomes of the S. ochraceum complex from seven sites in the Galapagos Islands and 30 sites in mainland Ecuador, Central America, and the Caribbean. Among 500 analyzed larvae, we discovered 88 chromosomal rearrangements representing 13 cytoforms, at least seven of which are probably full species. All evidence points to a single, cohesive cytoform with full species status in the Galapagos, conspecific with mainland populations, and widely distributed in the Neotropical Region. It has an identical, nearly monomorphic banding sequence with 10 novel fixed inversions and a subtle but unique Y-linked chromosomal rearrangement across all populations sampled in the Galapagos, the mainland, and the Caribbean. We recalled the name Simulium antillarum from synonymy with S. ochraceum and applied it to the Galapagos black flies, and we established that wolcotti is a junior synonym of antillarum. The time(s) and mode(s) of arrival of S. antillarum in the Galapagos remain uncertain, although the wide geographic distribution, including islands in the Caribbean, suggests that the species is an adept colonizer. Regardless of how long it has been in the archipelago, S. antillarum might have assumed a functional role in the streams of San Cristobal, but otherwise has had a detrimental effect on humans and livestock and potentially on the unique birds and mammals of the Galapagos Islands.

Inside-Out Rational Design of Ornithine Cyclodeaminase RlOCD from Rhizobium leguminosarum by a Multiregion Synergy Strategy for Efficient Synthesis of l-Pipecolic Acid.

Lysine cyclodeaminase (LCD)-mediated synthesis of l-pipecolic acid (l-PA) from l-lysine (l-Lys) is a promising approach. However, only one LCD has been reported, and its inadequate activity limits industrial applications. To address this problem, a substrate analogue-guided enzyme mining strategy was employed. A novel ornithine cyclodeaminase (OCD) from Rhizobium leguminosarum (RlOCD) was identified in combination with directed macrogenomic approaches. RlOCD displayed a conversion rate of 28% at a substrate loading as high as 1000 mM. A multiregion synergy strategy consisting of pocket reshaping, dynamical cross-correlation matrix-guided coevolutionary design, and surface modification was used to design RlOCD from the inside-out. A quadruple mutant (V93C/L119C/I170T/R90L) designated Mu4 with significantly increased activity was obtained, which showed a 28.46-fold increase in the catalytic efficiency. The conversion of Mu4 was 91% within 10 h at 1000 mM (146.19 g L-1) loading. The space-time yield of 282.1 g L-1 d-1 is the highest level ever reported. Molecular dynamics simulations and interaction analyses revealed that efficient pocket expansion and unique conformational rearrangements increased the affinity for the substrate, resulting in a more catalytically active conformation. This study expands the toolbox for the production of l-PA and demonstrates the effectiveness and potential of Mu4 for its production.

Complete mitogenome and intra-family comparative mitogenomics showed distinct position of Pama Croaker Otolithoides pama

The Pama Croaker, Otolithoides pama, is an economically important fish species in Bangladesh. Intra-family similarities in morphology and typical barcode sequences of cox1 create ambiguities in its identification. Therefore, morphology and the complete mitochondrial genome of O. pama, and comparative mitogenomics within the family Sciaenidae have been studied. Extracted genomic DNA was subjected to Illumina-based short read sequencing for De-Novo mitogenome assembly. The complete mitogenome of O. pama (Accession: OQ784575.1) was 16,513 bp, with strong AC biasness and strand asymmetry. Relative synonymous codon usage (RSCU) among 13 protein-coding genes (PCGs) of O. pama was also analyzed. The studied mitogenomes including O. pama exhibited consistent sizes and gene orders, except for the genus Johnius which possessed notably longer mitogenomes with unique gene rearrangements. Different genetic distance metrics across 30 species of Sciaenidae family demonstrated 12S rRNA and the control region (CR) as the most conserved and variable regions, respectively, while most of the PCGs undergone a purifying selection. Different phylogenetic trees were congruent with one another, where O. pama was distinctly placed. This study would contribute to distinguishing closely related fish species of Sciaenidae family and can be instrumental in conserving the genetic diversity of O. pama.

Flash vacuum pyrolysis of steroid propargyl ethers

Owing to its unique rearrangement and cyclization processes via flash vacuum pyrolysis (FVP), the acetylenic moiety has attracted considerable attention by organic chemists as a key building block in the construction of innovative organic architects. Herein, a series of seven steroid propargyl ether precursors have been successfully synthesized and pyrolyzed. Analysis and characterization of the FVP products revealed that the propargyl ethers of phenolic steroids undergo Claisen-rearrangement to give 2-indanone and benzo cyclobutene derivatives, while propargyl ethers of non-aromatic steroids resulted in the corresponding α, β-unsaturated ketones.

Cofactor-independent C-C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis.

Biosynthesis of atypical angucyclines involves unique oxidative B-ring cleavage and rearrangement reactions, which are catalyzed by AlpJ-family oxygenases, including AlpJ, JadG, and GilOII. Prior investigations established the essential requirement for FADH2/FMNH2 as cofactors when utilizing the quinone intermediate dehydrorabelomycin as a substrate. In this study, we unveil a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor-dependent reactions of AlpJ-family oxygenases. Furthermore, the AlpJ- and JadG-catalyzed reactions of CR1 could be quenched by superoxide dismutase, supporting a catalytic mechanism wherein the substrate CR1 reductively activates molecular oxygen, generating a substrate radical and the superoxide anion O2 •-. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or cofactor-independent manner.

Individualized Cell-Free DNA Monitoring With Chromosomal Junctions for Mesothelioma

IntroductionThe spatially complex nature of mesothelioma and interventions like pleurodesis, surgery, and radiation often complicate imaging-based assessment. Further, cell-free DNA (cfDNA) based monitoring strategies are inadequate for mesothelioma, given the presence of a few recurring nonsynonymous somatic variants. However, patient-specific chromosomal rearrangements are commonly found in mesothelioma. Our study objective was to develop an individualized cfDNA assay to enable blood-based monitoring using circulating tumor DNA (ctDNA) in mesothelioma. We hypothesized that the unique chromosomal rearrangement junctions found in mesothelioma could be employed for individualized ctDNA detection and disease monitoring. MethodsDNA was extracted from tumor specimens for whole genome sequencing. Chromosomal junctions, prioritized by highest allele frequency and low homology to the rest of the genome, were selected for detection. Primers and Taqman probes were designed to span the junctions, forming personalized junction panels. Patient plasma obtained before therapy and at response assessment was tested for the presence of personalized junctions via quantitative polymerase chain reaction. ResultsOur study included nine patients, four with peritoneal and five with pleural mesothelioma. 763 chromosomal junctions were identified in the tumors of all cases. We selected three to five junctions per sample for quantitative polymerase chain reaction. We detected 25/30 (83%) of selected junctions in the plasma of seven out of nine patients (78%). Cell-free junction detection at follow-up was concordant with disease status: cfDNA junctions were detected in three patients with persistent disease, and not detected in a patient with no evidence of disease after surgery. ConclusionsWith further validation, individualized ctDNA junction assays could supplement imaging for disease monitoring in mesothelioma.

Defect Induced Structural Transition and Lipase Immobilization in Mesoporous Aluminum Metal-Organic Frameworks.

The transition from disorder to order and structural transformation are distinctive metal-organic framework (MOF) features. How to adapt or control both behaviors in MOF has rarely been studied. In this case, we demonstrate that our successful synthesis of [Al(OH)(PDA)]n (AlPDA-53-DEF, AlPDA-53-H, and AlPDA-68) with H2PDA=4,4'-[1,4-phenylenebis(ethyne-2,1-diyl)]-di benzoic acid has shown the intricate world of Aluminum Metal-Organic Frameworks (Al-MOFs). It offers profound insights into defect structures to order and transformations. AlPDA-53-DEF, in particular, revealed a fascinating interplay of various pore sizes within both micro and mesoporous regions, unveiling a unique lattice rearrangement phenomenon upon solvent desorption. Defects and disorders emerged as crucial impacts of transforming AlPDA-53-DEF, with its initially imperfect crystallinity, into the highly crystalline, hierarchically porous AlPDA-53-H.

Characteristics and Comparative Analysis of the Complete Plastomes of Apostasia fujianica and Neuwiedia malipoensis (Apostasioideae)

Apostasioideae, the early divergent subfamily of Orchidaceae, comprises Apostasia and Neuwiedia genera with approximately 20 species. Despite extensive research on Apostasioideae, previous studies have struggled to resolve taxonomic issues, particularly concerning the position of species within this subfamily. Here, we sequenced and annotated plastomes of Apostasia fujianica and Neuwiedia malipoensis, unveiling their phylogenetic relationships and shared plastome features with the other five published plastomes. We identified and analyzed the length, GC content, repeat sequences, and RSCU values of the chloroplast genomes. It is noteworthy that the chloroplast genome of N. malipoensis stands out as the largest among all known chloroplast genomes within the Apostasioideae subfamily, primarily due to contributions from both the LSC and SSC regions. Furthermore, our analysis revealed three unique structural rearrangements located approximately 10k–47k bp (ycf3–trnS-GCU) and 58k–59k bp(accD) in the LSC region and 118k–119k (ndhI) bp in the SSC region of the chloroplast genomes across all five species within the Apostasia genus, which presents a potential avenue for identifying distinctive chloroplast genetic markers, setting them apart from other orchid plants. And a total of four mutational hotspots (rpoC2, atpH, rps4, ndhK, and clpP) were identified. Moreover, our study suggested that Apostasia and Neuwiedia formed a monophyletic group, with Apostasia being sister to Neuwiedia. Within the Apostasia genus, five species were classified into two major clades, represented as follows: (A. odorata (A. shenzhenica and A. fujianica) (A. ramifera and A. wallichii)). These findings hold significance in developing DNA barcoding of Apostasioideae and contribute to the further phylogenetic understanding of Apostasioideae species.

Revelations from Comparative Mitochondrial Genome Analysis in Four Orders of Class Insecta

The largest and most diverse group of organisms in the animal kingdom are insects. Molecular markers are powerful tools that can tackle a wide range of insect ecological research issues. These provide a more effective way to study the massive unexplored genetic diversity and gene pool of insects. Recent trends of use of DNA marker techniques in varied domains of insect ecological studies demonstrate that mitochondrial DNA has made a significant contribution towards advancing our knowledge of genetic basis of insect diversity. To shed light on various aspects such as genome organization, base composition, gene rearrangements, and other features, we integrated 165 mitochondrial genomes (mitogenomes) consisting of 37 genes and a noncoding control region, from four major insect orders (Diptera, Lepidoptera, Orthoptera and Hemiptera) for comparative genomic analysis. The same 37 genes were found in the majority of mitochondrial genomes, however the order of genes was found disturbed in a few mitochondrial genomes. The nucleotide composition was found strongly biased towards AT content. Usually, protein-coding genes prefer ATA, ATT and ATG as a canonical start codon. However, inconsistency was observed for few PCGs particularly for COI. The loss of DHU arm was found specific to trnS1 gene. In Zeugodacus tau (Pumpkin fruit fly), trnF gene lacked the TΨC arm. Majority of the mismatches (G-U (most common), U-U, U-C, A-A, A-C, A-G and T-T) were found within the acceptor arm, DHU arm and anticodon stem of tRNA genes but few in TΨC stem. Interestingly, a unique gene rearrangement from trnW (W codes for Tryptophan) to trnU (U codes for Selenocysteine) in the mitochondrial genome of Boettcherisca peregrine (Flesh fly) was observed. AT-rich control region remains highly variable among most of the insects. The review is aimed to draw conclusions for better interpretations of mitochondrial DNA evolution.

Uncovering rearrangements in the Tibetan antelope via population-derived genome refinement and comparative analysis with homologous species.

Introduction: The Tibetan antelope (Pantholops hodgsonii) is a remarkable mammal thriving in the extreme Qinghai-Tibet Plateau conditions. Despite the availability of its genome sequence, limitations in the scaffold-level assembly have hindered a comprehensive understanding of its genomics. Moreover, comparative analyses with other Bovidae species are lacking, along with insights into genome rearrangements in the Tibetan antelope. Methods: Addressing these gaps, we present a multifaceted approach by refining the Tibetan Antelope genome through linkage disequilibrium analysis with data from 15 newly sequenced samples. Results: The scaffold N50 of the refined reference is 3.2Mbp, surpassing the previous version by 1.15-fold. Our annotation analysis resulted in 50,750 genes, encompassing 29,324 novel genes not previously study. Comparative analyses reveal 182 unique rearrangements within the scaffolds, contributing to our understanding of evolutionary dynamics and species-specific adaptations. Furthermore, by conducting detailed genomic comparisons and reconstructing rearrangements, we have successfully pioneered the reconstruction of the X-chromosome in the Tibetan antelope. Discussion: This effort enhances our comprehension of the genomic landscape of this species.

On-Surface Synthesis of Anthracene-Fused Zigzag Graphene Nanoribbons from 2,7-Dibromo-9,9'-bianthryl Reveals Unexpected Ring Rearrangements.

On-surface synthesis has emerged as a powerful strategy to fabricate unprecedented forms of atomically precise graphene nanoribbons (GNRs). However, the on-surface synthesis of zigzag GNRs (ZGNR) has met with only limited success. Herein, we report the synthesis and on-surface reactions of 2,7-dibromo-9,9'-bianthryl as the precursor toward π-extended ZGNRs. Characterization by scanning tunneling microscopy and high-resolution noncontact atomic force microscopy clearly demonstrated the formation of anthracene-fused ZGNRs. Unique skeletal rearrangements were also observed, which could be explained by intramolecular Diels-Alder cycloaddition. Theoretical calculations of the electronic properties of the anthracene-fused ZGNRs revealed spin-polarized edge-states and a narrow bandgap of 0.20 eV.

Approach to Acute Myeloid Leukemia with Increased Eosinophils and Basophils

There is remarkable morphologic and genetic heterogeneity in acute myeloid leukemia (AML). In a small percentage of cases of AML, increased eosinophils and/or basophils are present in the bone marrow and sometimes in the peripheral blood. This is often a puzzling diagnostic situation but also an important finding that requires special investigation. Unique chromosomal rearrangements have been correlated with an increased number of eosinophils and basophils in AML. The identification of the underlying genetic lesion that promotes eosinophilia and basophilia can dramatically change both the prognosis and the treatment of the patient. Thus, clinicians must be vigilant in searching for the cause of eosinophilia and basophilia in patients with AML, since the different causes may lead to different treatments and survival outcomes. In this article, we examine the significance of increased eosinophils and/or basophils in the context of AML, provide guidance that simplifies the differential diagnosis, and give prognostic and therapeutic information about specific subtypes of AML associated with eosinophilia and/or basophilia. Evidence supporting personalized (molecularly targeted) therapy for these patients is also presented.

Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing–Based Clonality Testing in B-Cell and Plasma Cell Neoplasms

Next generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, we describe our approach and clinical experience with an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R=0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within our laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R=0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.

Daphnia sp. (Branchiopoda: Cladocera) Mitochondrial Genome Gene Rearrangement and Phylogenetic Position Within Branchiopoda.

In high-altitude (4500 m) freshwater lakes, Daphnia is the apex species and the dominant zooplankton. It frequently dwells in the same lake as the Gammarid. Branchiopoda, a class of Arthropoda, Crustacea, is a relatively primitive group in the subphylum Crustacea, which originated in the Cambrian period of the Paleozoic. The complete mitogenome sequence of Daphnia sp. (Branchiopoda: Cladocera) was sequenced and annotated in this study and deposited in GenBank. The sequence structure of this species was studied by comparing the original sequences with BLAST. In addition, we have also researched the mechanisms of their mitochondrial gene rearrangement by establishing a model. We have used the Bayesian inference [BI] and maximum likelihood [ML] methods to proceed with phylogenetic analysis inference, which generates identical phylogenetic topology that reveals the phylogenetic state of Daphnia. The complete mitogenome of Daphnia sp. shows that it was 15,254 bp in length and included two control regions (CRs) and 37 genes (13 protein-coding genes, 22 tRNAs and two ribosomal RNAs [16S and 12S]). In addition to tRNA-Ser (GCT), other tRNAs have a typical cloverleaf secondary structure. Meanwhile, the mitogenome of Daphnia sp. was clearly rearranged when compared to the mitogenome of typical Daphnia. In a word, we report a newly sequenced mitogenome of Daphnia sp. with a unique rearrangement phenomenon. These results will be helpful for further phylogenetic research and provide a foundation for future studies on the characteristics of the mitochondrial gene arrangement process in Daphnia.

Mitochondrial phylogenomics of bumblebees, Bombus (Hymenoptera: Apidae): a tale of structural variation, shifts in selection constraints, and tree discordance

Abstract The mitochondrial DNA (mtDNA) of bumblebees (Bombus) has been widely used for phylogenetic studies, but its evolution is still underexplored. Here we report a comprehensive analysis of 60 bumblebee mitogenomes, including 40 newly assembled ones, to investigate bumblebee mtDNA structure, composition, and informativeness under a phylogenetic framework. Our mtDNA dataset supports the monophyly of Bombus and its subgenera, although we found a high degree of tree discordance in deeper nodes when using different inference methods or matrix composition. Concerning mitogenome structure, our results show that tRNA genes were often rearranged, with unique rearrangements indicating shared ancestry across bumblebee subgenera, illustrating their potential for subgeneric classification. Our results also challenge the notion that faster evolving mtDNA exhibits higher gene rearrangement rates. Finally, we explicitly assessed shifts in selection constraints of mtDNA genes in obligate social parasites of subgenus Psithyrus and found that their mtDNA evolved under relaxed selective constraints. Our findings show the utility of mtDNA in providing insights into bumblebee phylogenetics, evolution, and genome trait diversification. We also highlight the potential for comparative mitogenomics to uncover previously unknown aspects of bumblebee evolution, offering exciting opportunities for future research in this field.