7,978 results match your criteria rearrangements identified


TERT Copy Number Alterations, Promoter Mutations and Rearrangements in Adrenocortical Carcinomas.

Endocr Pathol 2021 Sep 22. Epub 2021 Sep 22.

Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.

Molecular characterization of adrenocortical carcinomas (ACC) by The Cancer Genome Atlas (TCGA) has highlighted a high prevalence of TERT alterations, which are associated with disease progression. Herein, 78 ACC were profiled using a combination of next generation sequencing (n = 76) and FISH (n = 9) to assess for TERT alterations. This data was combined with TCGA dataset (n = 91). Read More

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September 2021

Insights from the first genome assembly of Onion (Allium cepa).

G3 (Bethesda) 2021 Sep;11(9)

Plant Breeding, Wageningen University and Research Centre, 6700 AA Wageningen, The Netherlands.

Onion is an important vegetable crop with an estimated genome size of 16 Gb. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with an N50 of 464 Kb. Read More

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September 2021

Inhibition of c-Jun N-terminal kinase signaling increased apoptosis and prevented the emergence of ALK-TKI-tolerant cells in ALK-rearranged non-small cell lung cancer.

Cancer Lett 2021 Sep 15;522:119-128. Epub 2021 Sep 15.

Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kajii-cho, Kamigyo-ku, Kyoto, 602-8566, Japan.

Anaplastic lymphoma kinase-tyrosine kinase inhibitors (ALK-TKIs) have improved clinical outcomes in non-small cell lung cancer (NSCLC) harboring ALK- rearrangements. However, a small population of tumor cells survives due to adaptive resistance under drug pressure and ultimately acquires drug resistance. Thus, it is necessary to elucidate the mechanisms underlying the prevention of drug resistance to improve the prognosis of patients with ALK-rearranged NSCLC. Read More

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September 2021

Outcomes of Acute Lymphoblastic Leukemia with KMT2A (MLL) rearrangement - The MD Anderson Experience.

Blood Adv 2021 Sep 15. Epub 2021 Sep 15.

University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States.

Acute lymphoblastic leukemia (ALL) with t(4;11)(q21;q23) - KMT2A-AFF1 is associated with a poor prognosis. The impact of KMT2A rearrangements other than t(4;11) is uncertain and the benefit of allogeneic stem cell transplant (HSCT) is unclear. We reviewed adult patients with ALL treated at our institution from 1984 to 2019 and identified 50/1102 (5%) with KMT2A rearrangement: 42 (84%) with t(4;11)/KMT2A-AFF1 and 8 (16%) with other gene partners. Read More

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September 2021

Genomic and transcriptomic analyses reveal a tandem amplification unit of 11 genes and mutations in mismatch repair genes in methotrexate-resistant HT-29 cells.

Exp Mol Med 2021 Sep 14. Epub 2021 Sep 14.

Asian Genome Institute, Seoul National University Bundang Hospital, Seongnamsi, 13605, Korea.

DHFR gene amplification is commonly present in methotrexate (MTX)-resistant colon cancer cells and acute lymphoblastic leukemia. In this study, we proposed an integrative framework to characterize the amplified region by using a combination of single-molecule real-time sequencing, next-generation optical mapping, and chromosome conformation capture (Hi-C). We identified an amplification unit spanning 11 genes, from the DHFR gene to the ATP6AP1L gene position, with high adjusted interaction frequencies on chromosome 5 (~2. Read More

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September 2021

Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study.

BMC Genomics 2021 Sep 15;22(1):665. Epub 2021 Sep 15.

Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.

Background: It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. Read More

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September 2021

Detection of NTRK fusions in glioblastoma: fluorescent in situ hybridisation is more useful than pan-TRK immunohistochemistry as a screening tool prior to RNA sequencing.

Pathology 2021 Sep 10. Epub 2021 Sep 10.

CHRU Brest, Department of Pathology, Brest, France; Univ Brest, Inserm, CHU de Brest, LBAI, UMR1227, Brest, France. Electronic address:

Glioblastomas are frequent malignant brain tumours with a very poor prognosis and a need for new and efficient therapeutic strategies. With the approval of anti-TRK targeted therapies to treat patients with advanced NTRK-rearranged cancers, independent of the type of cancer, potential new treatment opportunities are available for the 0.5-5% of patients with NTRK-rearranged glioblastomas. Read More

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September 2021

Genomic characterization and outcome evaluation of kinome fusions in lung cancer revealed novel druggable fusions.

NPJ Precis Oncol 2021 Sep 10;5(1):81. Epub 2021 Sep 10.

Bone Metastasis Service, Department of Orthopaedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.

Kinase fusions represent an important type of somatic alterations that promote oncogenesis and serve as diagnostic markers in lung cancer. We aimed to identify the landscape of clinically relevant kinase fusions in Chinese lung cancer and to explore rare kinase rearrangements; thus, providing valuable evidence for therapeutic decision making. We performed genomic profiling of 425 cancer-relevant genes from tumor/plasma biopsies from a total of 17,442 Chinese lung cancer patients using next generation sequencing (NGS). Read More

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September 2021

Lungekreft behandlet med reseptortyrosin=kinasehemmer i utlandet.

Tidsskr Nor Laegeforen 2021 Sep 24;141. Epub 2021 Aug 24.

Background: Activating RET fusions are oncogenic drivers in multiple cancers and are identified in 1-2 % of non-small cell lung cancers (NSCLC). Selpercatinib and pralsetinib are tyrosine kinase inhibitors selectively targeting RET and with clinical activity in RET-positive NSCLC.

Case Presentation: A male never-smoker in his forties was diagnosed with advanced lung adenocarcinoma. Read More

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September 2021

De Novo Inverted Duplication Deletion of 4p in a 14-Week-Old Male Fetus Aborted Due to Multiple Anomalies.

J Pediatr Genet 2021 Sep 19;10(3):245-249. Epub 2020 Jun 19.

Department of Medical Genetics, AORN San Pio, PO Gaetano Rummo, Benevento, Italy.

Inverted duplications deletions are rare, complex, and nonrecurrent chromosomal rearrangements associated with a variable phenotype. In this case report, we described the phenotype and genotype of a 14-week-old male fetus, who was aborted after discovery of multiple anomalies (septal cystic hygroma, open abdominal wall, and a nonidentifiable lower limb). At autopsy, fluorescence in situ hybridization and array comparative genomic hybridization identified an inverted duplication with terminal deletion of 4p [46,XY,der(4)del(p16. Read More

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September 2021

Monogenic Syndromes with Congenital Heart Diseases in Newborns (Diagnostic Clues for Neonatologists): A Critical Analysis with Systematic Literature Review.

J Pediatr Genet 2021 Sep 10;10(3):173-193. Epub 2021 Jul 10.

Department of Clinical and Experimental Medicine, Unit of Rare Diseases of the Nervous System in Childhood, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy.

Congenital heart disease (CHD), the most common major congenital anomaly, is associated with a genetic syndrome (chromosomal anomalies, genomic disorders, or monogenic disease) in 30% of patients. The aim of this systematic review was to evaluate if, in the neonatal setting, clinical clues that orient the diagnostic path can be identified. For this purpose, we revised the most frequent dysmorphic features described in newborns with CHD, comparing those associated with monogenic syndromes (MSG) with the ones reported in newborns with genomic disorders. Read More

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September 2021

Implementation of Multigene Germline and Parallel Somatic Genetic Testing in Epithelial Ovarian Cancer: SIGNPOST Study.

Cancers (Basel) 2021 Aug 27;13(17). Epub 2021 Aug 27.

Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.

We present findings of a cancer multidisciplinary-team (MDT) coordinated mainstreaming pathway of unselected 5-panel germline and parallel somatic testing in all women with epithelial-OC and highlight the discordance between germline and somatic testing strategies across two cancer centres. Patients were counselled and consented by a cancer MDT member. The uptake of parallel multi-gene germline and somatic testing was 97. Read More

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PPARα agonist exerts protective effects in podocyte injury via inhibition of the ANGPTL3 pathway.

Exp Cell Res 2021 Sep 7;407(2):112753. Epub 2021 Sep 7.

Department of Nephrology, Children's Hospital of Fudan University, Shanghai, China; Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China. Electronic address:

Peroxisome proliferator-activated receptor α (PPARα) activation has been reported to exert protective effects on podocytes, whereas angiopoietin-like 3 (ANGPTL3) has been shown to exert significant pathogenic effects on these cells. This study aimed to investigate the link between the protective effects of PPARα activation and the pathogenic effects of ANGPTL3 in podocytes. Both PPARα and ANGPTL3 were expressed in cultured podocytes. Read More

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September 2021

A Chromosome-Level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus).

Genome Biol Evol 2021 Sep 9. Epub 2021 Sep 9.

Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway.

The reed warbler (Acrocephalus scirpaceus) is a long-distance migrant passerine with a wide distribution across Eurasia. This species has fascinated researchers for decades, especially its role as host of a brood parasite, and its capacity for rapid phenotypic change in the face of climate change. Currently, it is expanding its range northwards in Europe, and is altering its migratory behaviour in certain areas. Read More

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September 2021

Myeloid malignancies with translocation t(4;12)(q11-13;p13): molecular landscape, clonal hierarchy and clinical outcomes.

J Cell Mol Med 2021 Sep 7. Epub 2021 Sep 7.

Sorbonne Université, Service d'Hématologie Clinique, Hôpital Pitié-Salpêtrière, APHP, Paris, France.

Translocation t(4;12)(q11-13;p13) is a recurrent but very rare chromosomal aberration in acute myeloid leukaemia (AML) resulting in the non-constant expression of a CHIC2/ETV6 fusion transcript. We report clinico-biological features, molecular characteristics and outcomes of 21 cases of t(4;12) including 19 AML and two myelodysplastic syndromes (MDS). Median age at the time of t(4;12) was 78 years (range, 56-88). Read More

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September 2021

Discovery of photosynthesis genes through whole-genome sequencing of acetate-requiring mutants of Chlamydomonas reinhardtii.

PLoS Genet 2021 Sep 7;17(9):e1009725. Epub 2021 Sep 7.

Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

Large-scale mutant libraries have been indispensable for genetic studies, and the development of next-generation genome sequencing technologies has greatly advanced efforts to analyze mutants. In this work, we sequenced the genomes of 660 Chlamydomonas reinhardtii acetate-requiring mutants, part of a larger photosynthesis mutant collection previously generated by insertional mutagenesis with a linearized plasmid. We identified 554 insertion events from 509 mutants by mapping the plasmid insertion sites through paired-end sequences, in which one end aligned to the plasmid and the other to a chromosomal location. Read More

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September 2021

Riboswitch Mechanisms: New Tricks for an Old Dog.

Biochemistry (Mosc) 2021 Aug;86(8):962-975

Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.

Discovered almost twenty years ago, riboswitches turned out to be one of the most common regulatory systems in bacteria, with representatives found in eukaryotes and archaea. Unlike many other regulatory elements, riboswitches are entirely composed of RNA and capable of modulating expression of genes by direct binding of small cellular molecules. While bacterial riboswitches had been initially thought to control production of enzymes and transporters associated with small organic molecules via feedback regulatory circuits, later findings identified riboswitches directing expression of a wide range of genes and responding to various classes of molecules, including ions, signaling molecules, and others. Read More

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Distinct Clinicopathologic Features and Possible Pathogenesis of Localized ALK-positive Histiocytosis of the Breast.

Am J Surg Pathol 2021 Sep 6. Epub 2021 Sep 6.

Division of Pathology Pathology Project for Molecular Targets, Cancer Institute Department of Pathology Breast Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research Department of Pathology, Mita Hospital, International University of Health and Welfare, Tokyo Departments of Pathology Breast Surgery, Saku Central Hospital Advanced Care Center Department of Pathology, Saku Central Hospital, Saku, Nagano Prefecture, Japan.

Anaplastic lymphoma kinase (ALK)-positive histiocytosis is a rare emerging entity characterized by systemic or localized proliferation of histiocytes harboring ALK rearrangements. Breasts are reportedly affected by ALK-positive histiocytosis. Here, we evaluated 2 localized cases of breast ALK-positive histiocytosis through a comprehensive clinicopathologic, molecular, and genomic analysis to further delineate this entity and better understand its pathogenesis. Read More

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September 2021

Adult acampomelic campomelic dysplasia and disorders of sex development due to a reciprocal translocation involving chromosome 17q24.3 upstream of the SOX9 gene.

Eur J Med Genet 2021 Sep 2;64(11):104332. Epub 2021 Sep 2.

Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan. Electronic address:

Balanced chromosomal rearrangements with a breakpoint located upstream of the sex determining region Y-box 9 (SOX9) gene on chromosome 17q24.3 are associated with skeletal abnormalities, campomelic dysplasia (CMPD), or acampomelic campomelic dysplasia (ACMPD). We report on a female patient with a reciprocal translocation of t (11; 17) (p15. Read More

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September 2021

Complete characterisation of two new large Xq28 duplications involving F8 using whole genome sequencing in patients without haemophilia A.

Haemophilia 2021 Sep 4. Epub 2021 Sep 4.

Hospices Civils de Lyon, Groupe Hospitalier Est, Service de génétique, Bron, France.

Introduction: Depending on the location of insertion of the gained region, F8 duplications can have variable clinical impacts from benign impact to severe haemophilia A phenotype.

Aim: To characterize two large Xq28 duplications involving F8 incidentally detected by chromosome microarray analysis (CMA) in two patients presenting severe intellectual disability but no history of bleeding disorder.

Methods: Whole genome sequencing (WGS) was performed in order to characterize the two large Xq28 duplications at nucleotide level. Read More

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September 2021

The C-terminal loop of guanosine deaminase is essential to catalysis.

Chem Commun (Camb) 2021 Sep 3. Epub 2021 Sep 3.

MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong, 510006, People's Republic of China.

Guanosine deaminase (GSDA) in plants specifically deaminates (de)guanosine to produce xanthosine with high specificity, which is further converted to xanthine, a key intermediate in purine metabolism and nitrogen recycling. We solved GSDA's structures from in the free and ligand-bound forms at high resolutions. Unlike GDA, the enzyme employs a single-proton shuttle mechanism for catalysis and both the substrate and enzyme undergo structural rearrangements. Read More

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September 2021

Cation complexation by mucoid Pseudomonas aeruginosa extracellular polysaccharide.

PLoS One 2021 2;16(9):e0257026. Epub 2021 Sep 2.

School of Food Science & Nutrition, University of Leeds, Leeds, United Kingdom.

Mucoid Pseudomonas aeruginosa is a prevalent cystic fibrosis (CF) lung colonizer, producing an extracellular matrix (ECM) composed predominantly of the extracellular polysaccharide (EPS) alginate. The ECM limits antimicrobial penetration and, consequently, CF sufferers are prone to chronic mucoid P. aeruginosa lung infections. Read More

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September 2021

Prenatal cytogenetic diagnosis: results obtained in the specialized laboratory of Clínica Universitaria Colombia from 2013 to 2019.

J Matern Fetal Neonatal Med 2021 Sep 1:1-8. Epub 2021 Sep 1.

Science Faculty. Universidad Pedagógica y Tecnológica de Colombia, Grupo de Investigación en Ciencias Biomédicas UPTC (GICBUPTC), Tunja, Colombia.

Objective: Prenatal cytogenetic evaluation is a key tool for identifying alterations in pregnant women with high risk for fetal chromosomal abnormalities (CA). In Colombia, there are not large-scale reports about the prevalence and pattern of CA in prenatal cytogenetic analysis.

Method: A descriptive study was performed from registers of prenatal cytogenetic analysis on amniotic fluid (AF), chorionic villus biopsy (CVS), and fetal blood (FB) samples sent to the specialized laboratory of the Clínica Universitaria Colombia between 2013 and 2019. Read More

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September 2021

The histological and molecular spectrum of lipoblastoma: A case series with identification of three novel gene fusions by targeted RNA-sequencing.

Pathol Res Pract 2021 Aug 18;226:153591. Epub 2021 Aug 18.

Institute of Pathology, University of Würzburg, Würzburg, Germany; Comprehensive Cancer Center Mainfranken, University Hospital of Würzburg, Würzburg, Germany.

Lipoblastoma is a rare benign mesenchymal neoplasm that typically occurs in infancy but may also occur in older age groups and various locations. Thus, there are often numerous clinical differential diagnoses. Moreover, lipoblastomas can show a broad histologic spectrum, which can hamper the correct diagnosis, particularly in small biopsies. Read More

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Reflex ROS1 IHC Screening with FISH Confirmation for Advanced Non-Small Cell Lung Cancer-A Cost-Efficient Strategy in a Public Healthcare System.

Curr Oncol 2021 Aug 25;28(5):3268-3279. Epub 2021 Aug 25.

Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada.

rearrangements are identified in 1-2% of lung adenocarcinoma cases, and reflex testing is guideline-recommended. We developed a decision model for population-based testing from a Canadian public healthcare perspective to determine the strategy that optimized detection of true-positive (TP) cases while minimizing costs and turnaround time (TAT). Eight diagnostic strategies were compared, including reflex single gene testing via immunohistochemistry (IHC) screening, fluorescence in-situ hybridization (FISH), next-generation sequencing (NGS), and biomarker-informed ( wildtype) testing initiated by pathologists and clinician-initiated strategies. Read More

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Neuroblastoma Risk Assessment and Treatment Stratification with Hybrid Capture-Based Panel Sequencing.

J Pers Med 2021 Jul 22;11(8). Epub 2021 Jul 22.

Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.

For many years, the risk-based therapy stratification of children with neuroblastoma has relied on clinical and molecular covariates. In recent years, genome analysis has revealed further alterations defining risk, tumor biology, and therapeutic targets. The implementation of a robust and scalable method for analyzing traditional and new molecular markers in routine diagnostics is an urgent clinical need. Read More

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Balanced Chromosomal Rearrangements Associated with Hypoprolificacy in Australian Boars ().

Cells 2021 Aug 6;10(8). Epub 2021 Aug 6.

Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia.

Balanced chromosomal rearrangements, mainly reciprocal translocations, are considered to be the causative agent of several clinical conditions in farmed pigs, resulting in hypoprolificacy and economic losses. Literature suggests that reciprocal translocations are heritable and can occur de novo. The prevalence rate of these balanced structural rearrangements of chromosomes differs from country to country and varies between 0. Read More

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Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs.

Genes (Basel) 2021 Jul 26;12(8). Epub 2021 Jul 26.

Department of Ecology and Evolution, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. Read More

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SPARC-positive macrophages are the superior prognostic factor in the microenvironment of diffuse large B-cell lymphoma and independent of MYC rearrangement and double-/triple-hit status.

Ann Oncol 2021 Aug 24. Epub 2021 Aug 24.

Institute of Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.

Background: Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease with respect to outcome. Features of the tumor microenvironment (TME) are associated with prognosis when assessed by gene expression profiling. However, it is uncertain whether assessment of the microenvironment can add prognostic information to the most relevant and clinically well-established molecular subgroups when analyzed by immunohistochemistry (IHC). Read More

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A Y-linked anti-Müllerian hormone type-II receptor is the sex-determining gene in ayu, Plecoglossus altivelis.

PLoS Genet 2021 Aug 26;17(8):e1009705. Epub 2021 Aug 26.

Department of Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan.

Whole-genome duplication and genome compaction are thought to have played important roles in teleost fish evolution. Ayu (or sweetfish), Plecoglossus altivelis, belongs to the superorder Stomiati, order Osmeriformes. Stomiati is phylogenetically classified as sister taxa of Neoteleostei. Read More

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