Search Results (165)

In the traditional classification system of the Lauraceae family based on morphology and anatomy, the phylogenetic position of the genus Sassafras has long been controversial. Chloroplast (cp) evolution of Sassafras has not yet been illuminated. In this study, we first sequenced and assembled the complete cp genomes of Sassafras, and conducted the comparative cp genomics, phylogenomics, and divergence time estimation of this ecological and economic important genus. The whole length of cp genomes of the 10 Sassafras ranged from 151,970 bp to 154,011 bp with typical quadripartite structure, conserved gene arrangements and contents. Variations in length of cp were observed in the inverted repeat regions (IRs) and a relatively high usage frequency of codons ending with T/A was detected. Four hypervariable intergenic regions (ccsA-ndhD, trnH-psbA, rps15-ycf1, and petA-psbJ) and 672 cp microsatellites were identified for Sassafras. Phylogenetic analysis based on 106 cp genomes from 30 genera within the Lauraceae family demonstrated that Sassafras constituted a monophyletic clade and grouped a sister branch with the Cinnamomum sect. Camphora within the tribe Cinnamomeae. Divergence time between S. albidum and its East Asian siblings was estimated at the Middle Miocene (16.98 Mya), S. tzumu diverged from S. randaiense at the Pleistocene epoch (3.63 Mya). Combined with fossil evidence, our results further revealed the crucial role of the Bering Land Bridge and glacial refugia in the speciation and differentiation of Sassafras. Overall, our study clarified the evolution pattern of Sassafras cp genomes and elucidated the phylogenetic position and divergence time framework of Sassafras. Full article

Caenogastropoda is a highly speciose and ecologically diverse subclass of Gastropoda but its higher order classification remains unclear, especially within its largest constituent group, Hypsogastropoda. Two nominal taxa encompassing most of the great diversity of Hypsogastropoda are in current widespread use: one is Latrogastropoda, which has been repeatedly redefined resulting in changes to the second, Littorinimorpha, which is generally not supposed to be monophyletic. We examined the utility of these divisions by assembling single-gene data sets of nuclear 28S ribosomal RNA (28S rRNA) and mitochondrial 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit I from many genera. Capuloidea was consistently found with strong support within Latrogastropoda, so this taxon is redefined here to include that superfamily. The analyses also suggested the redefinition of some superfamilies within Littorinimorpha, particularly for the clade comprising Truncatelloidea, Vanikoroidea and Rissooidea, and the Littorinoidea. Littorinimorpha was monophyletic (albeit lacking strong support) in the combined analysis of 28S rRNA and 16S rRNA and was resolved as the sister group of Latrogastropoda which was also monophyletic, with bootstrap support of 66%. Littorinimorpha was not monophyletic in other analyses. In these, the sister group of Latrogastropoda comprised clades of multiple littorinimorph superfamilies but these relationships were also not strongly supported. Full article

China’s southwestern karst landscapes support remarkable cavefish diversity, especially within Sinocyclocheilus, the world’s largest cavefish genus. Using integrative taxonomic methods, we describe Sinocyclocheilus wanlanensis sp. nov., found in a subterranean river in Guizhou Province. This species lacks horn-like cranial structures; its eyes are either reduced to a dark spot or absent. It possesses a pronounced nuchal hump and a forward-protruding, duckbill-shaped head. Morphometric analysis of 28 individuals from six species shows clear separation from related taxa. Nano-CT imaging reveals distinct vertebral and cranial features. Phylogenetic analyses of mitochondrial cytb and ND4 genes place S. wanlanensis within S. angularis group as sister to S. bicornutus, with p-distances of 1.7% (cytb) and 0.7% (ND4), consistent with sister-species patterns within the genus. Sinocyclocheilus wanlanensis is differentiated from S. bicornutus by its eyeless or degenerate-eye condition and lack of bifurcated horns. It differs from S. zhenfengensis, its morphologically closest species, in having degenerate or absent eyes, shorter maxillary barbels, and pelvic fins that reach the anus. The combination of morphological and molecular evidence supports its recognition as a distinct species. Accurate documentation of such endemic and narrowly distributed taxa is important for conservation and for understanding speciation in cave habitats. Full article

Diptera comprises more than 154,000 described species, representing approximately 10–12% of insects. Members have successfully colonized all continents and a wide range of habitats. However, higher-level phylogenetic relationships within Diptera have remained ambiguous. Mitochondrial genomes (mitogenomes) have been used as valuable molecular markers for resolving phylogenetic issues. To explore the effect of such markers in solving the higher-level phylogenetic relationship of Diptera, we sequenced and annotated the mitogenomes of 25 species, combined with 180 mitogenomes from 33 superfamilies of dipteran insects to conduct a phylogenetic analysis based on the PCGsrRNA and PCGs12rRNA datasets using IQ-TREE under the partition model. The phylogenetic analysis failed to recover the monophyly of the two suborders Nematocera and Brachycera. Two of six infraorders within the Nematocera—Tipulomorpha and Ptychopteromorpha—were monophyletic. The ancestral Deuterophlebiidae were a strongly supported sister group of all remaining Diptera, but Anisopodidae, as the closest relative of Brachycera, received only weak support. Three of four infraorders within Branchycera—Tabanomorpha, Xylophagomorpha, and Stratiomyomorpha—were, respectively, supported as a monophyletic clade, except Muscomorpha due to the strong long-branch attraction between Cecidomyiidae and Nycteribiidae. The inferred infraordinal relationships followed the topology Tabanomorpha + (Xylophagomorpha + (Stratiomyomorpha + Muscomorpha)). However, the proposed topology lacks strong statistical support, suggesting alternative relationships remain plausible. Based on mitogenome data alone, we infer that Diptera originated earlier than the Late Triassic at 223.43 Mya (95% highest posterior density [HPD] 166.60–272.02 Mya) and the earliest brachyeran Diptera originated in the mid-Jurassic (171.61 Mya). Full article

Background and Clinical Significance: Inherited thrombocytopenia (IT) is a heterogeneous group of disorders caused by mutations in over 45 genes. Among these, ANKRD26-related thrombocytopenia (ANKRD26-RT) accounts for a notable subset and is associated with variable bleeding tendencies and an increased risk of myeloid malignancies. However, the extent of this oncogenic risk appears to vary between specific gene variants. Understanding the genotype–phenotype relationship is essential for patient counseling and management. This report presents a multigenerational family carrying the rare c.−118C > G variant in the 5′ untranslated region of ANKRD26, contributing to the discussion on variant-specific cancer predisposition. Case Presentation: Two sisters aged 57 and 60 presented with lifelong bleeding diathesis and moderate thrombocytopenia. Their symptoms included easy bruising, menorrhagia, and excessive postoperative bleeding. Genetic testing confirmed heterozygosity for the ANKRD26 c.−118C > G variant. Bone marrow analysis revealed abnormal megakaryopoiesis without evidence of dysplasia or somatic mutations. One sister underwent major surgery without complications when managed with prophylactic hemostatic therapy. Their family history included multiple female relatives with similar symptoms, although formal testing was limited. Notably, none of the affected individuals developed hematologic malignancy, and only one developed esophageal cancer, with no current evidence linking this variant to solid tumors. Conclusions: This case underscores the importance of distinguishing between ANKRD26 variants when assessing malignancy risk. While ANKRD26-RT is associated with myeloid neoplasms, the c.−118C > G variant may confer a lower oncogenic potential. Variant-specific risk stratification and genetic counseling are crucial for optimizing surveillance and avoiding unnecessary interventions in low-risk individuals. Full article

This study investigates the taxonomic status, phylogenetic relationships, and genetic diversity of Japanese chestnut (Castanea crenata Siebold & Zucc.) in Liaodong, China, and across East Asia. Additionally, it evaluates core germplasm resources through cluster and population structure analyses using simple sequence repeat (SSR) marker data from 13 Castanea henryi, 18 Castanea seguinii, and 27 Castanea mollissima, and 142 Japanese chestnut resources. The results show that the East Asian Castanea genus forms a monophyletic group with distinct interspecific boundaries. Japanese chestnut and two varieties/lines of C. seguinii (187 and 170) form a sister clade, indicating a close phylogenetic relationship. All Japanese chestnut resources are divided into two branches, with considerable admixture. The genetic diversity analysis revealed that the 142 Japanese chestnut varieties/lines collectively possessed 141 allelic loci, with genetic distances (GDs) ranging from 0.429 to 0.880 with an average of 0.740. Based on unique characteristics, seven resources with distinctive features were selected as mandatory. A total of 41 core germplasm resources were finally determined using the simulated annealing method. The comparative analysis revealed that, aside from a notable difference in polymorphic information loci, the core germplasm and original germplasm showed no significant differences in other genetic diversity parameters. This indicates that the 41 core germplasm resources effectively preserve the genetic diversity of the original germplasm and have been influenced by artificial selection. This study provides a scientific basis for conserving and using C. crenata germplasm resources. Full article

Diptera is one of the most ecologically significant and species-rich insect orders, but there are still unresolved phylogenetic relationships among its basal lineages, particularly within the infraorder Blephariceromorpha, due to limited molecular data. To address this gap, this study employs two parallel genomic approaches: mitochondrial genomes and nuclear genomic analysis, covering 64 families and over 100 species of Diptera and their outgroups, to elucidate these phylogenetic relationships. Our results strongly support the monophyly of each constituent family (Blephariceridae, Deuterophlebiidae, and Nymphomyiidae), yet they reject the monophyly of Blephariceromorpha. Crucially, we found that Deuterophlebiidae and Nymphomyiidae form a sister group representing the basal-most lineage of Diptera, whereas Blephariceridae is positioned within Psychodomorpha. This indicates that the similar larval habitats and morphological traits shared between Blephariceridae and the Nymphomyiidae + Deuterophlebiidae clade are the result of convergent evolution. By resolving long-standing debates on the relationships within Blephariceromorpha and the basal lineages of Diptera, this study provides new insights into the evolutionary history of Diptera, especially within the suborder Nematocera. Full article

Coastal shellfish farming areas in northern China seas face frequent starfish outbreaks, particularly from Asterias amurensis and Patiria pectinifera, leading to significant economic losses. Genomic data are key to understanding the population dynamics and adaptive traits and developing effective control measures for these species. Here, we characterized and compared the genomic information of these two starfish using a whole-genome survey approach. The genome size of A. amurensis is ~477 Mb with 1.52% heterozygosity, 53.60% repetitive sequences, and 39.94% GC content, while P. pectinifera has a ~529 Mb genome, 2.90% heterozygosity, 56.02% repetitive sequences, and 40.63% GC content. Scaffold N50 values were 1823 bp for A. amurensis and 1328 bp for P. pectinifera. We identified 161,786 microsatellite motifs in A. amurensis and 316,245 in P. pectinifera, with mononucleotide repeats being the most common. A total of 171 single-copy homologous genes were found in A. amurensis, with 94 in P. pectinifera. For both species, KEGG annotation showed functional similarities in glycan biosynthesis, translation, metabolism, catabolism, and transport. The Pairwise Sequentially Markovian Coalescent (PSMC) analysis unveiled a bottleneck effect during the Pleistocene glaciation. Additionally, phylogenetic analysis of mitochondrial genomes indicates that P. pectinifera and Patiria miniata of the same genus belong to the same branch in the evolutionary tree as sister groups with the closest genetic relationship, while A. amurensis is most closely related to Astropecten polyacanthus within the class Asteroidea. These findings provide valuable genomic insights for both species. Full article

In the past, only Oguchi disease was reported as a hereditary retinal disease from Japan. Dr. Chuuta Oguch was a Professor of Nagoya University in Japan. During the past 40 years, four new clinical entities in hereditary retinal disorders have been detected by the Miyake group from Nagoya, Japan. All disorders show essentially normal fundi, and the diagnosis was made mainly by the analysis of an electroretinogram (ERG). Gene mutations are detected in three of them. Bipolar cell (BP) dysfunction syndrome: Congenital stationary night blindness (CSNB) with negative ERG (a-wave is larger than b-wave) was named as the Schubert–Bornschein type in 1952 and considered to be an independent clinical entity. In 1986, Miyake group classified ninety patients with the Schubert–Bornschein type into two types (complete and incomplete type). The complete type of CSNB (CSNB1) showed no rod function, but the incomplete type CSNB (CSNB2) showed remaining rod function in both subjective dark adaptation and rod ERG. In order to investigate the pathogenesis, these two types of CSNB were analyzed by comparing the monkey ERGs using different glutamate analogs to the retina. The ERG analysis demonstrated that CSNB1 has a complete functional defect in the ON type BP, while CSNB2 has incomplete functional defects in the ON and OFF type BP in both rod and cone visual pathways. Evidence of several different genetic heterogeneities was reported in both diseases, indicating CSNB1 and CSNB2 are independent clinical entities. Another entity, showing total complete defect of both ON and OFF BP, was detected in 1974 and was reported by Miyake group in a brother and younger sister, showing severe photophobia, nystagmus, extremely low visual acuity, and disappearance of color vision (total color blindness). This disorder is a congenital stational condition, and subjective visual functions were severely deteriorated from birth but remained unchanged through life. This disease was termed “Total complete bipolar cell dysfunction syndrome (CSNB3)”. The relationship between BP and subjective visual function was unknown. These three kinds of BP diseases can provide information on how BP relates to subjective visual functions. Occult macular dystrophy (OMD): Occult macular dystrophy (OMD) was discovered by Miyake group in 1989. This disease shows an unusual, inherited macular dystrophy characterized by progressive decrease visual acuity due to macular dysfunction, but the fundus and fluorescein angiography are essentially normal. The full-field rod and cone ERG do not show any abnormality, but the focal macular ERG (FERG) or multifocal ERG is abnormal and the only method for diagnosis. Many pedigrees of this disorder suggest autosomal dominant heredity, showing a genetic mutation of RP1L1. This disease was termed “occult macular dystrophy”. “Occult” means “hidden from sight”. Recently, it has been called “Miyake disease”. Full article

Background: The mitochondrial genome has been used for understanding higher-level phylogenetic relationships within Coccomorpha. we sequenced and analyzed the first mitochondrial genome of Xylococcus castanopsis Wu & Huang, 2017 to elucidate its genomic features and phylogenetic position. Methods: The complete mitogenome was assembled using NOVOPlasty and annotated with MITOS. We analyzed genome organization, codon usage, and tRNA structures. Phylogenetic relationships were reconstructed using 13 protein-coding genes from 19 scale insect species with Bayesian Inference and Maximum Likelihood methods. Result: The mitochondrial genome is 16,363 bp in size and contains the typical 37 mitochondrial genes, with an A + T content of 89.2%. All protein-coding genes start with the ATN and end with TAA/TAG or a single T- residue. Sixteen tRNAs exhibit the typical cloverleaf structure, while the remaining six lack either the dihydrouridine (DHU) or TΨC (T) arm. Gene rearrangements occur only in individual tRNAs and transpositions between the gene clusters trnS2-ND1 and trnL1-rrnL-trnV-rrnS. Phylogenetic analysis consistently place Xylococcidae as a sister group to all scale insects except Matsucoccidae. Conclusions: This study provides the first complete mitogenome for Xylococcidae, revealing characteristic gene rearrangements. Phylogenetic reconstruction resolves the phylogenetic position of Xylococcidae as a distinct lineage sister to all scale insects except Matsucoccidae, providing critical evolutionary insights. Full article

Background: Asilomorpha, an infraorder of predatory Diptera (Brachycera), is of significant evolutionary interest due to their remarkable ecological diversity, broad size range, and specialized feeding behaviors. However, phylogenetic studies of this group have been limited by sampling challenges. Methods: In this study, we sequenced the complete mitochondrial genomes of two Chinese endemic species, Clephydroneura jiangxiensis (C. jiangxiensis) and Maira xizangensis (M. xizangensis), using whole-genome random sequencing. By integrating these novel data with published sequences from NCBI, we reconstructed the phylogeny of three superfamilies (Asiloidea, Empidoidea, and Nemestrinoidea). Results: Both mitochondrial genomes exhibit the typical 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs) and display pronounced AT bias. Congruent results from maximum likelihood analysis and Bayesian inference strongly supported the ideas that both new species are placed in Asilidae and that the Asilidae family is monophyletic. However, relationships among the three superfamilies remain unclear. Our results suggest that (1) although Asiloidea and Nemestrinidea are closely related, the potential positioning of Nemestrinoidea as an independent superfamily is worth investigating; and (2) Empidoidea may form a sister group to Asiloidea + Nemestrinidae, though this hypothesis requires further corroboration given the basal position of Hemipenthes hebeiensis (Bombyliidae). Conclusions: These findings highlight the need for expanded taxon sampling, particularly of underrepresented families, to resolve deep-level relationships within Asilomorpha. Clarifying the phylogenetic relationships within Asilomorpha will facilitate future investigations into their evolutionary origins and the evolution of characteristic traits. Full article

Gnathophis johnsoni sp. nov. is described on the basis of 15 specimens (138–380 mm TL) from the Emperor–Hawaiian Seamount Chain in the western and central North Pacific. The new species is most similar in morphology to G. bathytopos (Atlantic), G. cinctus (eastern Pacific), and G. smithi (Nazca and Salas-y-Gomez Seamounts in the southeastern Pacific) by the sensory pore configuration and vertebral count, but differs from these species in the following characters in combination: darkly pigmented pectoral fin, dorsal fin with black margin broadened caudally and extended onto the distal half of the caudal fin, relatively long head, jaws, gill slit and caudal fin, and on average a greater preanal distance. Although most of morphometrics overlap between the new species and its closest relatives, multivariate statistical analyses clearly discriminate this species. Molecular analysis shows sister relationships between the new species and G. cinctus, with 1.81% of genetic divergence, which significantly exceeds the differences between the haplotypes belonging to the same species (0.36 and 1.08% of divergence, usually not exceeding 0.9%) and confirms both species as close but distinct. The close relationship of G. johnsoni sp. nov. and G. cinctus represents a rare case of biogeographical relations between western and eastern Pacific demersal fish faunas. Molecular data suggest that some morphologically similar species may represent independently evolved lineages, though the group of Gnathophis possessing elevated lateral-line pores is likely monophyletic. Full article

Canna, the sole member of the Cannaceae family, is widely cultivated as an ornamental plant for its decorative flowers and foliage and is also a potential tuber crop due to its high starch content. This study sequenced, assembled, and analyzed the complete chloroplast (cp) genomes of three common Canna species with distinct leaf colors (green, purple, and variegated). The four cp genomes ranged from 164,427 to 164,509 bp in length, had a GC content of 36.23–36.25%, and exhibited identical gene content and codon preferences. Each genome contained 130 genes, including 110 unique genes (78 protein-coding genes, four of unknown function, four rRNAs, and 28 tRNAs), 18 duplicated genes located in the IR regions (six protein-coding genes, two of unknown function, four rRNAs, and eight tRNAs), and two trnM-CAU genes in the LSC region. SSR and long-repeat showed differences in long repeats numbers and distributions among the four cp genomes, highlighting potential molecular markers for Canna species identification and breeding. Comparative analysis showed high conservation across Canna cp genomes. Phylogenetic analysis confirmed a close relationship between Cannaceae and Marantaceae and supported a [Musaeceae (Cannaceae + Marantaceae)] clade as a sister group to Costaceae. The cp genome data generated in this study provide valuable insights for developing molecular markers, resolving taxonomic classifications, and advancing phylogenetic and population genetic studies in Canna species. Full article

Translation is a sine qua non process for life as we know it. Translation factors (TFs) and tRNAs are rare among viruses but are commonly found in giant viruses of the class Megaviricetes. In this study, we explored the diversity and distribution of tRNAs in giant viruses that were isolated and replicated in amoebae (phylum Amoebozoa), and investigated the evolutionary history of TFs to gain insights into their origins in these viruses. We analyzed the genomes of 77 isolated giant viruses, 52 of which contained at least 1 tRNA. In most of these viruses, tRNA sequences are dispersed throughout the genome, except in Tupanviruses and Yasmineviruses, where most tRNAs are clustered in specific genomic islands. The tRNAs in giant viruses often contain introns, with 73.1% of the genomes exhibiting at least one intronic region in these genes. Codon usage bias (CUB) analysis of various giant viruses revealed at least two distinct patterns of codon preferences among closely related viruses. We did not observe a clear correlation between the presence of tRNAs and CUB in giant viruses. Due to the limited size of these genes, we could not confidently investigate their phylogenetic relationships. However, phylogenetic analysis of TFs found in giant viruses often position these viruses as sister groups or embedded between different eukaryotic taxa with high statistical support. Overall, our findings reinforce the complexity of key components of the translation apparatus in different members of Nucleocytoviricota isolated from different regions of Earth. Full article

The family Potamanthidae is widely distributed across the Holarctic and Oriental regions, with nymphs often utilized as bioindicators for water pollution and human-induced environmental disturbances. However, limited mitochondrial genomes (mitogenomes) have been reported for this family. This study presents the first complete mitochondrial genome sequences of two Potamanthidae species, Potamanthus longitibius and Rhoenanthus youi. The mitogenome sizes were 15,430 bp and 15,232 bp, with A + T contents of 68.79% and 66.75%, respectively. The most abundant amino acids were phenylalanine (Phe), isoleucine (Ile), glycine (Gly), and alanine (Ala), with leucine (Leu2) showing the highest relative synonymous codon usage (RSCU) value. The analysis of tRNA secondary structures revealed high conservation among the tRNAs encoded on the H-strand. Phylogenetic reconstruction, incorporating 40 species from 13 families of Ephemeroptera, confirmed the monophyly of all the families and supported a sister group relationship between Potamanthidae and Ephemeridae. Additionally, the sequence previously identified as Rhoenanthus sp. JZ-2021 was reassigned to the genus Potamanthus. This study provides valuable insights into the evolutionary relationships within Potamanthidae and lays a foundation for future phylogenetic and taxonomic research. Full article