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At least 19 recordsLinked to original sources
PubMed2026

First complete mitochondrial genome of Uzelothrips scabrosus (Thysanoptera: Uzelothripidae) provides insights into gene rearrangements and phylogenetic position within Terebrantia.

The family Uzelothripidae is represented by a single genus Uzelothrips and can be distinguished from others by the presence of whip-like antennae, a circular ventral sensorium on antennal segment III, a well-developed tentorium, and a membranous ovipositor. Here, we generated the first complete mitochondrial genome of Uzelothrips scabrosus (15,674 bp) using next-generation sequencing to explore the gene rearrangements and phylogenetic relationships. It consists of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two putative control regions. The genome exhibits strong AT bias (71.35%) with negative AT and GC skew. Codon usage analyses indicate a strong bias towards A/U-ending codons and influenced by both natural selection and mutation pressure. All PCGs were under purifying selection, with cox1 being the most conserved and nad4L the most variable. The gene order of the family Uzelothripidae is highly rearranged compared to the ancestral insect gene order. Comparative analysis revealed that gene block B was the most widely conserved, whereas the remaining gene blocks exhibited family or lineage-specific conservation patterns, reflecting extensive mitochondrial gene rearrangements during the evolution of the Thysanoptera. Moreover, 228 synapomorphic and 68 autapomorphic gene boundaries were identified across thysanopteran mitogenomes. Phylogenies indicated that the family Uzelothripidae is in a sister relationship with Stenurothripidae, and the Uzelothripidae + Stenurothripidae clade is sister to Thripidae. This study provides the first mitogenomic insights into Uzelothripidae and highlights the need for broader taxon sampling and nuclear genomic data to resolve deep evolutionary relationships within Thysanoptera.

Comparative analysis↗
PubMed2026

Comparative mitogenomics of Ocnus glacialis reveals lineage-specific evolutionary rates and complex gene rearrangements in Dendrochirotida.

The order Dendrochirotida (Class Holothuroidea) is a species-rich echinoderm group, yet its internal evolutionary history remains poorly resolved due to limited mitogenomic resources. In this study, we characterized the first complete mitochondrial genome of Ocnus glacialis and conducted comparative analyses to elucidate its phylogenetic position and molecular evolutionary patterns. The circular mitogenome of O. glacialis is 16,776 bp in length, containing the canonical set of 37 genes. Among the analyzed dendrochirotids, O. glacialis exhibited the highest A + T content (70.88%) and a near-zero AT-skew, a compositional profile often linked to lineage-specific evolution in specialized environments. Selection pressure analyses, including branch-model tests, revealed that these compositional features are associated with relaxed purifying selection and an accelerated rate of sequence evolution. Branch-site analyses further identified specific codon sites in cytb, nad2, nad4l, nad5, and nad6 under positive or relaxed constraints. Structurally, O. glacialis displayed the most complex gene rearrangement pattern among the studied species, characterized by multiple tandem duplication-random loss (TDRL) events and extensive intergenic sequences. Furthermore, divergence time estimation suggests that these structural and compositional shifts occurred in tandem with the lineage's diversification. We propose that these mitogenomic signatures reflect a synergistic outcome of habitat transition toward Arctic cold-water and deep-sea environments, coupled with demographic factors such as reduced effective population sizes inherent to its benthic life history. By resolving taxonomic uncertainties, this study provides a robust temporal and molecular framework for understanding the evolutionary history and ecological diversification of the Ocnus lineage.

Animals↗
PubMed2026

NOTCH3 Internal Tandem Duplication Defines a Novel Oncogenic Activation Mechanism of NOTCH Signaling.

NOTCH signaling is activated in tumors through multiple mechanisms, including mutations, gene rearrangements, and gene amplification. We report a novel activation mechanism, an internal tandem duplication (ITD) near the NOTCH3 negative regulatory region (NRR), found in a myogenic mesenchymal neoplasm. This 17-amino acid residue duplication disrupts the tightly autoinhibited structure surrounding the S2 cleavage site, resulting in ligand-independent S2 cleavage and constitutive pathway activation, as demonstrated by increased expression of the NOTCH3 target gene HES1. Cells expressing NOTCH3-ITD showed increased nuclear localization of the receptor and exhibited malignant phenotypes, including enhanced proliferation and migration. Together, these findings support the oncogenic role of NOTCH3-ITD.

Receptor, Notch3↗
PubMed2026

One-time duplication and ongoing loss of mitochondrial tRNA genes in Cryptocercus cockroaches.

Mitochondrial genome is a popular marker in phylogenetics and species diversity estimations. Mitogenome is relatively compact and conserved, while gene rearrangements were found in some species across various organisms. Models to explain the origin and evolution of gene rearrangement have been proposed but seldom demonstrated; empirical evidence from closely related species is particularly scarce. Here, through an intensive case study of the cockroach genus Cryptocercus Scudder, 1862, we elucidate the evolution of mitochondrial gene order. This study utilized 51 new samples and re-assembled raw reads of 26 published samples. A diversity of rearrangement patterns is recovered, especially in the tRNA gene cluster between ND3 and ND5, which is effectively explained by the duplication - random loss model. Specifically, the entire tRNA gene cluster was duplicated; this duplication is potentially facilitated by chance binding between the 3' end of ND5 gene and the ND3-trnA region during DNA replication. Furthermore, we reveal that one of the gene copies degenerated stochastically across lineages, directly contributing to the observed diversity in gene arrangement. Gene rearrangement patterns are apomorphies for certain clades, providing additional evidence for the inferred phylogeny and serving as potential indicators of species. This study underscores the importance of intensive sampling and rigorous data curation for deciphering the evolutionary mechanisms.

Duplication–random loss model↗
PubMed1976

Genetic relatedness in the family Enterobacteriaceae.

Five criteria of genetic relatedness are considered. The first, transfer of plasmids between groups, is frequently not a good criterion, because transfer is possible between all genera of the Enterobacteriaceae and also to genera in other families. Though transfer to closely related groups is most frequent, host restriction and the properties of the plasmid may influence the transfer frequency as much as the relatedness of the donor and recipient. The second criterion is interspecies recombination (integration) of chromosomal genes transferred by Hfr strains. Crosses between closely related genera (E. coli and Shigella) gave high frequency of stable hybrids, but crosses between less related genera (E. coli and Salmonella) result in lower recombination, with the donor genes frequently integrated in nonallelic positions on the chromosome, or remaining as autonomous CCC-DNA. In crosses between distantly related genera such as E. coli and Proteus, all the donor DNA remained as CCC, with no detectable integration into the chromosome. Third, the linkage maps of different strains of a species such as E. coli or of closely related species are very similar. The linkage maps of E. coli and S. typhimurium are also similar, with one gene rearrangement, an inversion, distinguishing them. There are some indications of differences in gene order between E. coli and Yersinia and between E. coli and S. marcescens and considerable evidence for rearrangements in gene order between E. coli and P. mirabilis. No similarity between the linkage maps of E. coli and of nonenteric bacteria such as Pseudomonas was observed. Thus within the enteric bacteria there is striking similarity in order of genes between closely related genera, but major changes when less related genera, such as E. coli and P. mirabilis, are observed. are observed...

Bacterial Proteins↗
PubMed2026

A new species of Gryllotalpa (Orthoptera, Gryllotalpidae) from northwestern China, with notes on its mitochondrial genome.

A new species of mole cricket, Gryllotalpa xinjiangica Gu & Miao, sp. nov., is described from Xinjiang, northwestern China, based on morphological characters and molecular data. The new species belongs to the G. gryllotalpa species complex and represents the second confirmed species of this complex known from East Asia. It can be distinguished from related species by the absence of inner subapical spurs on the hind tibiae, tegminal venation, and the structure of the male phallic complex. The complete mitochondrial genome of G. xinjiangica Gu & Miao, sp. nov. was sequenced, revealing a novel tRNA gene rearrangement (trnE-trnN-trnS1). Phylogenetic analyses based on the mitochondrial cox1 gene support the distinctiveness of the new species and recover it as sister to the G. gryllotalpa + G. vineae clade. An identification key to the known Chinese species of Gryllotalpidae is provided.

Gene rearrangement↗
PubMed2026

The first two complete mitochondrial genomes for the genus Neotrichoporoides (Hymenoptera, Eulophidae) and their phylogenetic analysis.

Neotrichoporoides belongs to the family Eulophidae (Hymenoptera: Chalcidoidea). As a group of parasitic wasps, it plays an indispensable role in the biological control of agricultural and forest pests and in maintaining ecosystem balance. To date, only nine complete mitochondrial genomes of Eulophidae have been sequenced worldwide, including the two newly sequenced species in this study. To enrich our understanding of the mitochondrial genomic diversity of Eulophidae and to provide preliminary insights into its phylogenetic relationships, we sequenced and comparatively analyzed the mitochondrial genomes of two Neotrichoporoides species. The mitogenomes of N. nyemitawus (GenBank: PZ188956; 15,164 bp) and N. viridimaculatus (GenBank: PX794932; 15,297 bp) contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR), and exhibit a strong AT bias, with AT contents of 85.5% and 85.0%, respectively. We further analyzed mitochondrial gene rearrangements across 17 species from Encyrtidae, Eulophidae and Pteromalidae and summarized family-specific rearrangement characteristics. tRNA rearrangements were detected in all three families. Eulophidae harbors conserved PCGs, while the inverse transposition of trnA and transposition of trnV are likely reported for the first time within this family. The two Neotrichoporoides species differ only in the arrangement of several tRNAs. Comparative analysis of PCGs revealed differences in molecular evolutionary rates among genes, with ATP8, ND2 and ND4 evolving faster than the others. Phylogenetic analysis based on mitochondrial genome sequences showed that species from two subfamilies formed a monophyletic group, and congeneric species clustered into a single clade. This study contributes to resolving phylogenetic relationships within Eulophidae and further deepens our understanding of this family.

Eulophidae↗
PubMed2026

Nucleotide Combination Proportions Across Algae, Monocotyledons and Dicotyledons: Insights into Plant Genome Evolution.

Plant evolution started with unicellular algae, gradually evolving multicellularity and terrestrial colonization. These evolutionary events were accompanied by the interplay of chromosome polyploidization, rearrangement, gene loss, and point mutation. We counted the proportion of nucleotide combinations in the genome sequences of 64 sequenced plants, and analyzed the significant difference in these nucleotide combination proportions among algae, monocotyledons and dicotyledons. The correlation of highly significant different and no significant different nucleotide combinations was analyzed respectively. Nucleotide combinations and their reverse complementary sequence proportions were analyzed in different functional regions of the genome. These results reveal that some nucleotide combinations are subject to strict selection, and these combinations have a higher proportion in the CDS regions and lower proportion in the intergenic regions. Meanwhile, there are some nucleotide combinations that are under less selective pressure, and these combinations have a higher proportion in the intergenic regions and lower proportion in the CDS regions. Cluster analysis based on trinucleotide to octanucleotide combination proportions reveals that plant genome evolution is accompanied by clade-wide differentiation of genome-wide nucleotide composition patterns, in addition to well-documented chromosomal polyploidization, structural rearrangement and gene loss events. We analyzed the changes in the proportion of nucleotide combinations at the genome level in 64 sequenced plants, providing a new idea for studying genome evolution in the plant kingdom.

comparative genomics↗
PubMed1978

Sequences of mouse immunoglobulin light chain genes before and after somatic changes.

We have determined the nucleotide sequences of the germ line gene as well as a corresponding somatically mutated and rearranged gene coding for a mouse immunoglobulin lambdaI type light chain. These sequencing studies were carried out on three Eco RI-DNA fragments which had been cloned from BALB/c mouse embryos or a lambdaI chainsecreting myeloma, H2020. The embryonic DNA clone Ig 99lambda contains two protein-encoding segments, one for the majority of the hydrophobic leader (L) and the other for the rest of the leader and the variable (V) region of the lambda0 chain (Cohn et al., 1974); these segments are separated by a 93 base pair (bp) intervening sequence (I-small). The coding of the V region ends with His at residue 97. The second embryonic DNA clone Ig 25lambda includes a 39 bp DNA segment (J) coding for the rest of the conventionally defined V region (that is, up to residue 110), and also contains the sequence coding for the constant (C) region approximately 1250 untranslated bp (I-large) away from the J sequence. The J sequence is directly linked with the V-coding sequence in the myeloma DNA clone, Ig 303lambda, which has the various DNA segments arranged in the following order: 5' untranslated region, L, l-small, V linked with J, l-large, C, 3' untranslated sequence. The lg 303lambda V DNA sequence codes for the V region synthesized by the H2020 myeloma and is different from the lg 99lambda V DNA sequence by only two bases. No silent base change was observed between the two DNA clones for the entire sequence spanning the 5' untranslated regions and the V-coding segments. These results confirm the previously drawn conclusion that an active complete lambdaI gene arises by somatic recombination that takes place at the ends of the V-coding DNA segment and the J sequence. No sequence homology was observed at or near the sites of the recombination.

Animals↗
PubMed2025

Exploring the Genetic Landscape of Primary Marginal Zone Lymphoma of the Urinary Bladder.

Extranodal marginal zone B-cell lymphoma (MZL) of mucosa-associated lymphoid tissue is the most frequent primary lymphoma of the urinary bladder. Although MZLs from various anatomical sites are often associated with autoimmune disorders, infections, and site-characteristic genetic alterations, the molecular foundations and potential infectious triggers of urinary bladder MZL remain poorly understood. To elucidate the disease etiology and correlation with MZLs arising in other locations, we examined a cohort of 17 cases (11 women and 6 men) diagnosed with primary bladder MZL between 2005 and 2025. Immunohistochemical analysis confirmed the literature, with all samples testing positive for the pan B-cell markers CD20 and CD79a and negative for CD5 (except 1), cyclin D1, and SOX11. Thirteen samples exhibited secretory differentiation and displayed immunoglobulin light chain restriction (9 κ and 4 λ). No gene rearrangements in BCL2, BCL6, BCL10, IRF4, MALT1, and MYC were detected. High-throughput sequencing identified 31 pathogenic/likely pathogenic somatic mutations across 18 genes, with TBL1XR1 (n = 8), MAP2K1 (n = 4), and TNFAIP3 (n = 2) being the most frequently mutated ones. Additionally, all cases included variants of unknown significance. The sample of 1 patient tested positive for Chlamydia trachomatis, human betaherpesvirus 6B, and Epstein-Barr virus. Escherichia coli was detected in 5 samples. We provide compelling evidence that urinary bladder MZL is a point mutation-driven disease rather than gene fusion-driven disease and that E coli is present in approximately one-third of tumor biopsies. These tumors frequently harbor pathogenic mutations in genes encoding components regulating plasma cell differentiation and the pleiotropic MAPK/ERK signaling pathway. TBL1XR1, which was unexpectedly frequently mutated, is generally linked to more aggressive variants of MZL and diffuse large B-cell lymphoma; however, its prognostic significance in urinary bladder MZL remains to be determined. Comparative analysis highlighted partial overlap of urinary bladder MZL mutational profiles with those found in salivary gland MZL.

Humans↗
PubMedDate not supplied

The arrangement and rearrangement of antibody genes.

Cloned segments of mouse chromosomal DNA provide direct evidence for the somatic rearrangement of kappa variable and constant region genes in antibody producing cells. This rearrangement apparently affects only one member of an allelic pair of light chain genes.

Animals↗
PubMed2026

Detection of a Rare Intra-ALK Inversion and ALK Rearrangement in a Lung Adenocarcinoma Patient by FoundationOne Liquid CDx and Successful Treatment with Alectinib: Case Report.

A 50-year-old woman with stage IVB lung adenocarcinoma tested negative for driver mutations using the Oncomine Dx Target Test Multi-CDx system (Thermo Fisher Scientific, Waltham, MA). After undergoing chemotherapy and immunotherapy, FoundationOne Liquid CDx (Foundation Medicine, Inc., Cambridge, MA) identified a rare EML4-ALK gene rearrangement. Treatment with alectinib led to rapid clinical improvement and sustained disease control for more than 7 months. This case highlights the value of next-generation sequencing-based profiling in detecting rare actionable alterations missed by standard tests. We also include a discussion on why the EML4-AKL fusion was not detected in the usual test.

ALK-EML4 rearrangement↗
PubMed2026

Myoepithelioma-like tumor of the vulvar region shows a quiet genome and heterogeneous detectable mechanisms of SMARCB1 inactivation: Integrated analysis of two cases and review of the literature.

Myoepithelioma-like tumor of the vulvar region (MELTVR) is a rare SMARCB1-deficient mesenchymal neoplasm of adult women that can mimic malignant vulvar sarcomas, particularly epithelioid sarcoma. Although loss of SMARCB1/INI1 expression is a defining feature, the comprehensive genomic landscape of MELTVR remains poorly characterized. We report two cases of MELTVR and performed integrated histopathologic, immunophenotypic, and molecular analyses, including whole-exome sequencing (WES) with copy number assessment and targeted RNA-based fusion testing using the Archer FusionPlex Sarcoma panel. Histologically, both tumors consisted of relatively uniform epithelioid to short spindle cells in solid nests and cords within focal myxoid stroma, with complete loss of INI1 and positivity for smooth muscle markers and focal ER/EMA expression. Genomic profiling demonstrated a quiet molecular background in both cases, with low tumor mutation burden (0.45 and 1.03 mut/Mb) and no pathogenic SNVs/indels in major cancer-associated genes. One case showed a focal homozygous deletion of the SMARCB1 locus at 22q11.2, whereas the other case exhibited INI1 loss without detectable SMARCB1 mutation or copy number loss, suggesting heterogeneous mechanisms of inactivation. CDKN2A copy number remained neutral in both tumors. No canonical sarcoma-associated gene rearrangements, including EWSR1, FUS, PLAG1, or NR4A3, were identified. Together with a review of previously reported cases, these findings support MELTVR as an SMARCB1-inactivated neoplasm with low genomic complexity and highlight the diagnostic value of NGS-based profiling in excluding malignant mimics and preventing overtreatment.

Humans↗
PubMed2026

Mitogenomic phylogeny of the aquatic subterranean Bathynellacea (Crustacea, Malacostraca) and implications for the monophyly of Syncarida.

The crustacean order Bathynellacea is a specialized monophyletic lineage restricted to aquatic subterranean environments and comprises approximately 340 extant species from three families. Despite advances in sequencing technologies that have significantly increased the number of sequenced crustacean mitogenomes, no bathynellacean mitogenomes have been reported to date. In this study, we report the first complete mitogenomes for Bathynellacea-Allobathynella sp., Arisubathynella cheongmiensis, Hangangbathynella mihoensis (Parabathynellidae), and Bathynella cf. rufa (Bathynellidae)-from two families. These mitogenomes, ranging from 14,422 to 16,645 bp in length, are characterized by extensive gene rearrangements, pronounced compositional biases, and accelerated evolutionary rates. Phylogenetic analyses based on malacostracan mitogenomic data strongly support the monophyly of Bathynellacea. However, the exceptionally long branches separating bathynellacean taxa suggest that extensive morphological simplification, driven by parallel adaptations to subterranean environments, may mask the ancestral diagnostic signals required to resolve their deep-level relationships. Most notably, our results indicate that the two extant orders within the superorder Syncarida-Bathynellacea and Anaspidacea-are phylogenetically distant, supporting the polyphyly of Syncarida. This suggests that their shared morphological features (e.g., the absence of a carapace and the loss of the mandibular lacinia mobilis) are likely products of convergent evolution rather than common ancestry. Our study provides mitogenomic resources for Bathynellacea and underscores the necessity of mitogenomic evidence in reassessing the taxonomic status of subterranean crustacean lineages.

Animals↗
PubMed1978

Change in quantity and size distribution of small circular DNAs during development of chicken bursa.

Small circular DNAs ranging in contour length from 0.06 to 3.5 micrometers have been isolated from bursas of 19-day chicken embryos and 4- to 5-week-old chickens. Small circular DNA is present in bursas of 19-day embryos at approximately 0.2 molecules per cell and is very heterogeneous, lacking distinct size classes; most molecules have contour lengths of less than 0.04 micrometers. In contrast, small circular DNA is present in bursas of 4- to 5-week old chickens at about 4 molecules per cell, and although this DNA is still heterogeneous, it contains a major distinct class of molecules 0.8 micrometers in size. These small circular DNAs may be products of developmental gene rearrangements occurring in the chromosomal DNA of lymphocytes in the bursa.

Animals↗
PubMed1978

Incomplete dosage compensation in an evolving Drosophila sex chromosome.

Cellular autoradiography was used to measure relative rates of chromosomal RNA synthesis and to examine the regulatory phenomenon of X-linked dosage compensation in Drosophila miranda, a species containing two distinct, nonhomologous X chromosomes (X1 and X2). The X1 chromosome was found to be dosage-compensated, since the rate of RNA synthesis along the single X1 chromosome in males equaled that of both X1 chromosomes in females. Unlike other sex chromosomes that have been studied, the more recently evolved X2 heterochromosome exhibited regional differences in transcriptional activity when males and females were compared. The distal 10% of the X2 was not dosage-compensated, whereas the majority of an interior segment, representing 30% of the X2 chromosome's length, was found to be dosage-compensated. Our data are consistent with the idea that the evolution of X2 dosage compensation has paralleled the differentiation of the X2 sex chromosome. In addition, gene rearrangement seems to have accompanied the acquisition of a dosage-compensory mechanism in the X2.

Animals↗