RESUMEN
The novel allele, HLA-DQB1*03:517, differs by a single nucleotide substitution in exon 3 to HLA-DQB1*03:02:01:02.
Asunto(s)
Alelos , Exones , Cadenas beta de HLA-DQ , Prueba de Histocompatibilidad , Humanos , Cadenas beta de HLA-DQ/genética , Arabia Saudita , Secuencia de Bases , Análisis de Secuencia de ADN , Polimorfismo de Nucleótido Simple , Alineación de Secuencia , CodónRESUMEN
HLA-DRB1*08:126 differs from HLA-DRB1*08:04:01:01 by one nucleotide substitution in codon 152 in exon 3.
Asunto(s)
Alelos , Secuencia de Bases , Exones , Cadenas HLA-DRB1 , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Cadenas HLA-DRB1/genética , Prueba de Histocompatibilidad/métodos , Análisis de Secuencia de ADN/métodos , Codón , Alineación de SecuenciaRESUMEN
HLA-B*15:689, HLA-B*35:603 and HLA-B*49:01:25, three novel HLA class I alleles detected by next-generation sequencing.
Asunto(s)
Alelos , Exones , Secuenciación de Nucleótidos de Alto Rendimiento , Prueba de Histocompatibilidad , Humanos , Antígeno HLA-B35/genética , Antígeno HLA-B15/genética , Antígeno HLA-B15/inmunología , Antígenos HLA-B/genética , Análisis de Secuencia de ADN , Codón , Secuencia de Bases , Antígeno HLA-B39/genética , Antígeno HLA-B39/inmunología , Donantes de TejidosRESUMEN
The novel HLA-DPB1*14:01:15 allele differs from DPB1*14:01:01:01 by change of C > T in exon 3.
Asunto(s)
Alelos , Secuencia de Bases , Exones , Cadenas beta de HLA-DP , Prueba de Histocompatibilidad , Donantes de Tejidos , Humanos , Cadenas beta de HLA-DP/genética , Brasil , Análisis de Secuencia de ADN/métodos , Médula Ósea , Alineación de Secuencia , Codón , Trasplante de Médula ÓseaRESUMEN
Two novel HLA-DQB1 alleles, HLA-DQB1*05:01:50 and HLA-DQB1*06:486, characterised in bone marrow volunteers.
Asunto(s)
Alelos , Exones , Cadenas beta de HLA-DQ , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Cadenas beta de HLA-DQ/genética , Prueba de Histocompatibilidad/métodos , Secuencia de Bases , Análisis de Secuencia de ADN/métodos , Codón , Médula ÓseaRESUMEN
HLA-C*07:02:151 differs from HLA-C*07:02:01:01 by one nucleotide substitution in codon 166 in exon 3.
Asunto(s)
Alelos , Secuencia de Bases , Codón , Exones , Antígenos HLA-C , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Antígenos HLA-C/genética , Prueba de Histocompatibilidad/métodos , Análisis de Secuencia de ADN/métodos , Alineación de SecuenciaRESUMEN
The novel HLA-C*15:279 allele differs from HLA-C*15:02:01:01 by five nucleotide substitutions in exons 4 and 5.
Asunto(s)
Alelos , Pueblo Asiatico , Secuencia de Bases , Exones , Antígenos HLA-C , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Antígenos HLA-C/genética , Pueblo Asiatico/genética , Análisis de Secuencia de ADN/métodos , Prueba de Histocompatibilidad/métodos , Alineación de Secuencia , Codón , Pueblos del Este de AsiaRESUMEN
Scrapie is a transmissible spongiform encephalopathy affecting sheep and goats. The prion protein-encoding gene (PRNP) plays a crucial role in determining susceptibility and resistance to scrapie. At the European level, surveillance of scrapie is essential to prevent the spread of the disease to livestock. According to the Regulation EU 2020/772 polymorphisms K222, D/S146 could function as resistance alleles in the genetic management of disease prevention. In Italy, a breeding plan for scrapie eradication has not been implemented for goats. However, surveillance plans based on the PRNP genotype have been developed as a preventive measure for scrapie. This research aimed to describe the polymorphisms at 7 positions within the PRNP gene in 956 goats of the Alpine, Saanen and mixed populations farmed in the Lombardy Region in Italy. PRNP polymorphisms were detected using single nucleotide polymorphism markers included in the Neogen GGP Goat 70 k chip. The K222 allele occurred in all populations, with frequencies ranging from 2.1 to 12.7%. No animals carried the S/D146 resistance allele. However, it has been demonstrated that polymorphisms in the other positions analysed could influence resistance or susceptibility to scrapie outbreaks in different ways. Ten potentially distinct haplotypes were found, and the most prevalent of the three populations was H2, which differed from the wild type (H1) in terms of mutation (S vs P) at codon 240. This study provided additional information on the genetic variability of the PRNP gene in these populations in the Lombardy region of Italy, contributing to the development of genetic control measures for disease prevention.
Asunto(s)
Enfermedades de las Cabras , Cabras , Proteínas Priónicas , Scrapie , Animales , Italia/epidemiología , Cabras/genética , Enfermedades de las Cabras/genética , Enfermedades de las Cabras/epidemiología , Proteínas Priónicas/genética , Scrapie/genética , Scrapie/epidemiología , Codón/genética , Variación Genética , Polimorfismo de Nucleótido SimpleRESUMEN
HLA-A*24:617 differs from HLA-A*24:02:01:01 by one nucleotide in exon 4.
Asunto(s)
Alelos , Pueblo Asiatico , Secuencia de Bases , Exones , Antígeno HLA-A24 , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Antígeno HLA-A24/genética , Pueblo Asiatico/genética , Análisis de Secuencia de ADN/métodos , Alineación de Secuencia , Codón , Polimorfismo de Nucleótido Simple , Pueblos del Este de AsiaRESUMEN
The new HLA-DRB3*03:69 allele differs from DRB3*03:01:01:03 by change of C â G in exon 3.
Asunto(s)
Alelos , Exones , Cadenas HLA-DRB3 , Secuenciación de Nucleótidos de Alto Rendimiento , Prueba de Histocompatibilidad , Humanos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Cadenas HLA-DRB3/genética , Prueba de Histocompatibilidad/métodos , Secuencia de Bases , Análisis de Secuencia de ADN/métodos , Alineación de Secuencia , CodónRESUMEN
A missense nucleotide substitution at codon 95 of HLA-C*18:01:01:01 creates a novel allele HLA-C*18:20.
Asunto(s)
Alelos , Exones , Antígenos HLA-C , Secuenciación de Nucleótidos de Alto Rendimiento , Prueba de Histocompatibilidad , Humanos , Antígenos HLA-C/genética , Prueba de Histocompatibilidad/métodos , Codón , Mutación Missense , Secuencia de Bases , Análisis de Secuencia de ADN/métodos , Donantes de TejidosRESUMEN
HLA-A*24:630 differs from HLA-A*24:20:01:01 by one nucleotide substitution in codon 131 in exon 3.
Asunto(s)
Alelos , Secuencia de Bases , Exones , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Prueba de Histocompatibilidad/métodos , Análisis de Secuencia de ADN/métodos , Codón , Antígeno HLA-A24/genética , Antígeno HLA-A24/inmunología , Alineación de Secuencia , Polimorfismo de Nucleótido SimpleRESUMEN
The coding sequence of HLA-B*40:540N differs from HLA-B*40:02:01:01 by a non-synonymous nucleotide substitution in exon 3.
Asunto(s)
Alelos , Secuencia de Bases , Exones , Humanos , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Antígeno HLA-B40/genética , Antígenos HLA-B/genética , Donantes de Tejidos , Alineación de Secuencia , CodónRESUMEN
HLA-A*02:1146 differs from HLA-A*02:01:01:01 by one nucleotide in exon 1.
Asunto(s)
Alelos , Pueblo Asiatico , Secuencia de Bases , Exones , Antígeno HLA-A2 , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Humanos , Pueblo Asiatico/genética , Análisis de Secuencia de ADN/métodos , Antígeno HLA-A2/genética , Alineación de Secuencia , Codón , Pueblos del Este de AsiaRESUMEN
Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.
Asunto(s)
Genoma del Cloroplasto , Filogenia , Vitaceae , Genoma del Cloroplasto/genética , Vitaceae/genética , Vitaceae/clasificación , Evolución Molecular , Repeticiones de Microsatélite/genética , Uso de Codones , Selección Genética , Composición de Base/genética , Codón/genética , Variación GenéticaRESUMEN
The codon usage bias (CUB) of genes encoded by different species' genomes varies greatly. The analysis of codon usage patterns enriches our comprehension of genetic and evolutionary characteristics across diverse species. In this study, we performed a genome-wide analysis of CUB and its influencing factors in six sequenced Eimeria species that cause coccidiosis in poultry: Eimeria acervulina, Eimeria necatrix, Eimeria brunetti, Eimeria tenella, Eimeria praecox, and Eimeria maxima. The GC content of protein-coding genes varies between 52.67% and 58.24% among the six Eimeria species. The distribution trend of GC content at different codon positions follows GC1 > GC3 > GC2. Most high-frequency codons tend to end with C/G, except in E. maxima. Additionally, there is a positive correlation between GC3 content and GC3s/C3s, but a significantly negative correlation with A3s. Analysis of the ENC-Plot, neutrality plot, and PR2-bias plot suggests that selection pressure has a stronger influence than mutational pressure on CUB in the six Eimeria genomes. Finally, we identified from 11 to 15 optimal codons, with GCA, CAG, and AGC being the most commonly used optimal codons across these species. This study offers a thorough exploration of the relationships between CUB and selection pressures within the protein-coding genes of Eimeria species. Genetic evolution in these species appears to be influenced by mutations and selection pressures. Additionally, the findings shed light on unique characteristics and evolutionary traits specific to the six Eimeria species.
Asunto(s)
Composición de Base , Uso de Codones , Eimeria , Eimeria/genética , Composición de Base/genética , Animales , Genoma de Protozoos , Coccidiosis/veterinaria , Coccidiosis/parasitología , Coccidiosis/genética , Evolución Molecular , Codón/genéticaRESUMEN
MICB*002:06 differs from MICB*002:01:01 by one nucleotide change at nucleotide 33 in exon 1 from C to T.
Asunto(s)
Exones , Antígenos de Histocompatibilidad Clase I , Humanos , Antígenos de Histocompatibilidad Clase I/genética , Antígenos de Histocompatibilidad Clase I/inmunología , Alelos , Secuencia de Bases , Análisis de Secuencia de ADN/métodos , Prueba de Histocompatibilidad , Alineación de Secuencia , CodónRESUMEN
HLA-C*17:78 differs from HLA-C*17:03:01:03 by one nucleotide change C>T in exon 3 (GCG>GTG).
Asunto(s)
Alelos , Secuencia de Bases , Exones , Antígenos HLA-C , Humanos , Antígenos HLA-C/genética , India , Prueba de Histocompatibilidad , Análisis de Secuencia de ADN , Alineación de Secuencia , Polimorfismo de Nucleótido Simple , CodónAsunto(s)
Alelos , Pueblo Asiatico , Exones , Humanos , Pueblo Asiatico/genética , Ciudad de Nueva York , Prueba de Histocompatibilidad , Antígeno HLA-A2/genética , Antígeno HLA-A2/inmunología , Secuencia de Bases , Análisis de Secuencia de ADN/métodos , Alineación de Secuencia , Codón , Pueblos del Este de AsiaRESUMEN
HLA-DQB1*02:211 allele differs from DQB1*02:02:01:02 by change of C â A in exon 2.