Journal of Genetics最新文献_第6页

Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales). 红藻角叉菜（红藻门，Halymeniales）的有丝分裂基因组特征和系统发育分析。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Maheshkumar Prakash Patil, Young-Ryun Kim, Shinya Nakashita, Jong-Oh Kim, Kyunghoi Kim

{"title":"Mitogenome features and phylogenetic analysis of red algae, Grateloupia cornea (Rhodophyta, Halymeniales).","authors":"Maheshkumar Prakash Patil, Young-Ryun Kim, Shinya Nakashita, Jong-Oh Kim, Kyunghoi Kim","doi":"","DOIUrl":"","url":null,"abstract":"The mitogenome is an important tool for taxonomic and evolutionary investigation. Here, a few complete mitogenomes of red algae have been reported. We have reported the complete mitogenome sequences of Grateloupia cornea Okamura, 1913 (Rhodophyta, Halymeniales). The genome is 30,595 bp in circumference, and has a strongly biased [AT] = 66.9%. Like most other Grateloupia species, it has a group II intron in the cox1 gene. Maximum likelihood and maximum parsimony analyses showed that G. cornea is more closely related to G. asiatica. This shows that the group II intron in the cox1 ORF present in most species of Grateloupia was present in their common ancestor, and uniquely lost in G. asiatica. The seven Grateloupia species with known mitogenome sequences remain monophyletic, with the genus Polyopes as sister taxon. The complete mitochondrial genome data will be valuable for future research on comparative mitochondrial genome analysis, an extensive understanding of gene content and organization, evolution of the cox1 intron in Rhodophyta as well as phylogenetic analysis.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141237472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A global evaluation of mitochondrial DNA diversity and distribution of dromedary, Camelus dromedarius from north-central Saudi Arabia. 沙特阿拉伯中北部单峰驼线粒体 DNA 多样性和分布的全球评估。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Fevzi Bardakci, Abdelmuhsin Abdelgadir, Md Jahoor Alam, Haci Halil Biyik, Arif Jamal Siddiqui, Riadh Badraoui, Mohd Adnan, Mousa Alreshidi, Atakan Koc, Mejdi Snoussi

{"title":"A global evaluation of mitochondrial DNA diversity and distribution of dromedary, Camelus dromedarius from north-central Saudi Arabia.","authors":"Fevzi Bardakci, Abdelmuhsin Abdelgadir, Md Jahoor Alam, Haci Halil Biyik, Arif Jamal Siddiqui, Riadh Badraoui, Mohd Adnan, Mousa Alreshidi, Atakan Koc, Mejdi Snoussi","doi":"","DOIUrl":"","url":null,"abstract":"Knowledge of genetic variability within and among types and breeds of dromedary (Camelus dromedarius L.) can be a valuable asset in selective breeding of desirable characteristics and will shed light on their origin, dynamics of domestication, and dispersion. Variability in an 809 bp segment of the mtDNA genome was measured within and among dromedaries from eight indigenous and one exogenous breed from Ha'il in north-central Saudi Arabia. Sixteen mtDNA haplotypes were identified among 47 camels. Haplotypic diversity among breeds is high (Hd = 0.817); most of the AMOVA variance (55.05%) occurs within breeds. Phylogenetic comparison of these haplotypes with those obtained across their geographic range showed that most haplotypes were placed within the same cluster with ancient wild dromedaries and the two newly identified haplotypes in this study. The most prevalent haplotypes found in dromedaries from this area appear to be ancestral to most other dromedaries and differ from each other by only one SNP. These results support the hypothesis that the Arabian Peninsula is a hub of diversification for dromedaries.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association of polymorphisms of HSD11B1 and ACE genes with trachoma disease. HSD11B1 和 ACE 基因的多态性与沙眼疾病的关系。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Laura L Valdez-Velazquez, Héctor Ochoa-Díaz-López, Iván Delgado-Enciso, Héctor Rangel-Villalobos, Irám P Rodríguez-Sánchez, Rosario García-Miranda, Doireyner Daniel Velázquez-Ramírez, Nancy A Reyes-Méndez, Carlos Eduardo Barajas-Saucedo, Margarita L Martínez-Fierro

{"title":"Association of polymorphisms of HSD11B1 and ACE genes with trachoma disease.","authors":"Laura L Valdez-Velazquez, Héctor Ochoa-Díaz-López, Iván Delgado-Enciso, Héctor Rangel-Villalobos, Irám P Rodríguez-Sánchez, Rosario García-Miranda, Doireyner Daniel Velázquez-Ramírez, Nancy A Reyes-Méndez, Carlos Eduardo Barajas-Saucedo, Margarita L Martínez-Fierro","doi":"","DOIUrl":"","url":null,"abstract":"Trachoma, caused by Chlamydia trachomatis, is the most common infectious blindness in the world and is present in indigenous Mayan from Chiapas (Mexico). Inflammatory genes are activated when suffering from trachoma, thus some polymorphisms could increase the susceptibility to develop irreversible blindness. This study aimed to evaluate the genetic risk of developing late-stage trachoma in Mayan ethnic groups. In a case-control study (n = 51 vs n = 102, respectively), the following single-nucleotide polymorphisms (SNPs) in genes related to inflammation were analysed: HSD11B1 (rs11807619), HSD11B1 (rs932335), ABCG2 (rs2231142), SLCO1B1 (rs4149056), IL-10 (rs1800890), TNF (rs1800629), MMP2 (rs243865) and ACE. Three SNPs were associated with late-stage trachoma risk: (i) the T allele of rs11807619, (ii) the C allele of rs932335, which are linked to the HSD11B1 gene (OR = 22.5-27.3), particularly in men when adjusts for gender (OR = 16-16.7); and (iii) D allele of rs4340 in the ACE gene (OR = 5.2-5.3). In fact, significant linkage disequilibrium demonstrated association between ACE gene and HSD11B1 SNPs (r = 0.17-0.179; P = 0.0048-0.0073). Two SNPs HSD11B1 gene (P = 0.013 vs 0.0039) and HSD11B1-ACE haplotypes showed association with late-stage trachoma in Mayan ethnic groups.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141759166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomewide architecture of adaptation in experimentally evolved Drosophila characterized by widespread pleiotropy. 实验进化果蝇适应性的全基因组结构具有广泛的多义性。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Zachary S Greenspan, Thomas T Barter, Mark A Phillips, José M Ranz, Michael R Rose, Laurence D Mueller

{"title":"Genomewide architecture of adaptation in experimentally evolved Drosophila characterized by widespread pleiotropy.","authors":"Zachary S Greenspan, Thomas T Barter, Mark A Phillips, José M Ranz, Michael R Rose, Laurence D Mueller","doi":"","DOIUrl":"","url":null,"abstract":"Dissecting the molecular basis of adaptation remains elusive despite our ability to sequence genomes and transcriptomes. At present, most genomic research on selection focusses on signatures of selective sweeps in patterns of heterozygosity. Other research has studied changes in patterns of gene expression in evolving populations but has not usually identified the genetic changes causing these shifts in expression. Here we attempt to go beyond these approaches by using machine learning tools to explore interactions between the genome, transcriptome, and life-history phenotypes in two groups of 10 experimentally evolved Drosophila populations subjected to selection for opposing life history patterns. Our findings indicate that genomic and transcriptomic data have comparable power for predicting phenotypic characters. Looking at the relationships between the genome and the transcriptome, we find that the expression of individual transcripts is influenced by many sites across the genome that are differentiated between the two types of populations. We find that single-nucleotide polymorphisms (SNPs), transposable elements, and indels are powerful predictors of gene expression. Collectively, our results suggest that the genomic architecture of adaptation is highly polygenic with extensive pleiotropy.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139521095","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic determinants of antibody response to a typhoid vaccine in Indian recipients. 印度接种者伤寒疫苗抗体反应的基因组决定因素。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Vijay Laxmi Roy, Partha Pratim Majumder

{"title":"Genomic determinants of antibody response to a typhoid vaccine in Indian recipients.","authors":"Vijay Laxmi Roy, Partha Pratim Majumder","doi":"","DOIUrl":"","url":null,"abstract":"Typhoid is endemic in India and has high global incidence. There were large outbreaks of typhoid in India between 1990 and 2018. Available typhoid vaccines induce variable levels of protective antibodies among recipients; thus, there is variability in response to the vaccine. Interindividual genomic differences is hypothesized to be a determinant of the variability in response. We studied the antibody response of ~1000 recipients of the Vi-polysaccharide typhoid vaccine from Kolkata, India, who showed considerable variability of antibody response, i.e., anti-Vi-polysaccharide antibody level 28 days postvaccination relative to prevaccination. For each vaccinee, wholegenome genotyping was performed using the Infinium Global Screening Array (Illumina). We identified 39 SNPs that mapped to 13 chromosomal regions to be associated with antibody response to the vaccine; these included SNPs on genes LRRC28 (15q26.3), RGS7 (1q43), PTPRD (9p23), CERKL (2q31.3), DGKB (7p21.2), and TCF4 (18q21.2). Many of these loci are known to be associated with various blood cell traits, autoimmune traits and responses to other vaccines; these genes are involved in immune related functions, including TLR response, JAK-STAT signalling, phagocytosis and immune homeostasis.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genetic analysis of a child with severe intellectual disability caused by a novel variant in the FERM domain of the FRMPD4 protein. 对一名因 FRMPD4 蛋白 FERM 结构域的新型变异而导致严重智力障碍的儿童的遗传分析。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Hua Pan, Feng Zhu, Kun Chen, Yin Zhang

{"title":"Genetic analysis of a child with severe intellectual disability caused by a novel variant in the FERM domain of the FRMPD4 protein.","authors":"Hua Pan, Feng Zhu, Kun Chen, Yin Zhang","doi":"","DOIUrl":"","url":null,"abstract":"Intellectual developmental disorder, X-linked 104 (XLID104), caused by the FRMPD4 gene variant, is a rare X-linked genetic disease that primarily manifests as intellectual disability (ID) and language delay, and may be accompanied by behavioural abnormalities. Currently, only 11 patients from four families have been reported to carry FRMPD4 gene variants. Here, we report a rare case of a Chinese patient with XLID104 who was presented with severe ID and language impairment. Genetic testing results showed that the patient had a novel hemizygous variant on FRMPD4 inherited from the heterozygous variant NM_001368397: c.1772A>C (p.Glu591Ala) carried by his mother. To our knowledge, this variant has not been reported previously. Western blot results for the recombinant plasmid constructed in vitro indicated that the expression of the mutant protein may be reduced. Using molecular dynamics simulations, we predicted that the mutant protein may affect the interaction of the FRMPD4 protein with DLG4. In this study, we expand the spectrum of FRMPD4 variants and suggest that the clinical awareness of the genetic diagnosis of nonsyndromic ID should be strengthened.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140335936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Association study of common KLF1 variants with Hb F and Hb A₂ levels in β-thalassaemia carriers of Portuguese ancestry. 葡萄牙血统的β-地中海贫血症携带者中常见 KLF1 变体与血红蛋白 F 和血红蛋白 A2 水平的关联研究。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Licínio Manco, Celeste Bento, Luís Relvas, Tabita Maia, Letícia Ribeiro

{"title":"Association study of common KLF1 variants with Hb F and Hb A2 levels in β-thalassaemia carriers of Portuguese ancestry.","authors":"Licínio Manco, Celeste Bento, Luís Relvas, Tabita Maia, Letícia Ribeiro","doi":"","DOIUrl":"","url":null,"abstract":"Kruppel-like factor 1 (KLF1) is an essential erythroid-specific transcription factor. Several reports have shown that KLF1 gene mutations are associated with increased levels of Hb F and Hb A2. However, scarce population studies have analysed common KLF1 variations. This study examines the potential association with Hb F and Hb A2 levels in β-thalassemia (β-thal) carriers of Portugueseancestry of the four common KLF1 gene variants: -251C>G (rs3817621) and -148G>A (rs79334031), in the promoter region; and c.115A>C (p.Met39Leu) (rs112631212) and c.304T>C (p.Ser102Pro) (rs2072597), in exon 2. Ninety-two Portuguese β-thal carriers (43 males and 49 females) aged 2 to 77 years old (mean 32.55 years) were engaged in the study. Hb F levels range from 0.2 to 12.5% and Hb A2 was above the normal level, ranging from 3.6 to 6%. The Hb A2 and Hb F levels were determined by high-performance liquid chromatography. Single-nucleotide polymorphisms were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Minor allele frequencies for SNPs rs3817621 (G), rs79334031 (A), rs112631212 (C) and rs2072597 (C) were 0.196, 0.016, 0.011 and 0.169, respectively. Basic simple linear regression in the total population showed no significant associations with the levels of Hb F (P>0.05). For the low-frequency variant -148A, a statistically significant association was found with increased levels of Hb A2 (β = 0.855; P = 0.017). In conclusion, an association signal with Hb A2 levels was observed for the variant -148A>G (rs79334031). The complex pattern of SNP interactions related to their influence on the KLF1 transcriptional activity mayexplain the absence of association with Hb F levels.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142501967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The complete mitochondrial genome of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila: leveraging 'waste' in metagenomic data. 深海产甲烷海绵Hymedesmia methanophila和Iophon methanophila的完整线粒体基因组：利用元基因组数据中的“废物”。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Dora de Moura Barbosa Leite, Thiago Silva de Paula, Eduardo Hajdu

{"title":"The complete mitochondrial genome of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila: leveraging 'waste' in metagenomic data.","authors":"Dora de Moura Barbosa Leite, Thiago Silva de Paula, Eduardo Hajdu","doi":"","DOIUrl":"","url":null,"abstract":"A significant proportion of next-generation sequencing (NGS) data ends up not being used since they comprise information out-of-scope of the primary studies. This 'waste' of potential can be harnessed to explore organellar genomes, such as the mitochondrial DNA, and be used for evolutionary, conservation and biodiversity research. We present the complete mitochondrial genomes of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila (Demospongiae, Poecilosclerida) retrieved from previously published whole metagenome sequencing data. The predicted mitogenome of H. methanophila (18,657 bp) and I. methanophila (18,718 bp) present the characteristic arrangement observed among Poecilosclerida sponges. These mtDNAs encode the usual set of 14 proteins, two ribosomal RNA, and 24 or 23 transfer RNA genes, respectively, with intergenic regions amounting ~5% of their total length. The overall similarity of these mitogenomes to those of phylogenetic relatives, both in organization and divergence, suggests that neither their extremophilic habitat in asphalt seeps within the deep sea nor their symbiotic association with methaneoxidizing bacteria imposed a major influence on the evolution of their mitochondrial genome. This research shows how metagenomic data can be leveraged to extract additional genetic knowledge from primary metagenome sources, and by exploiting previously unexplored sequencing data, valuable information can be unlocked to shed light on the evolutionary dynamics of diverse organisms inhabiting extreme environments.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142914964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel missense variant in PNLDC1 associated with nonobstructive azoospermia. 与非梗阻性无精子症相关的新型 PNLDC1 错义变异。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Mouness Rahimian, Masomeh Askari, Najmeh Salehi, Mojtaba Jaafarinia, Mohsen Forouzanfar, Navid Almadani, Andrea Riccio, Mehdi Totonchi

{"title":"A novel missense variant in PNLDC1 associated with nonobstructive azoospermia.","authors":"Mouness Rahimian, Masomeh Askari, Najmeh Salehi, Mojtaba Jaafarinia, Mohsen Forouzanfar, Navid Almadani, Andrea Riccio, Mehdi Totonchi","doi":"","DOIUrl":"","url":null,"abstract":"The most severe type of male infertility is nonobstructive azoospermia (NOA), where there is no sperm in the ejaculate due to failure of spermatogenesis. The predictable frequency of NOA in the general population is one in 100 men. Genetic studies have recognized dozens of NOA genes. Most NOA aetiologies remain idiopathic. Monogenic mutations can be a reason for a part of idiopathic NOA cases. To address this, we studied the pedigree of a consanguineous family with three NOAs by a family-based exome sequencing. Our goal was to pinpoint the genetic variants responsible for idiopathic NOA to aid future clinical genetic diagnostics and treatment strategies. Bioinformatics analysis followed by Sanger sequencing revealed that NOA patients were homozygous for a rare novel missense variant in PNLDC1(NM_173516:exon9:c.710G>A;p.Gly237Asp). In silico, single-cell RNA sequencing data analysis and protein modelling demonstrated that PNLDC1, Gly237Asp resided in the conserved region of the CAF1 domain which could lead to local instability in the structure and alteration of protein phosphorylation site. We conclude that the novel missense PNLDC1 variant may affect meiosis and spermatogenesis, leading to NOA and the genetic cause of this idiopathic NOA family. Our result helps genetic counselling for idiopathic NOA cases and provides the occasion for more efficient diagnosis in the clinical setting.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"103 ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142120012","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Estimation of genetic diversity of the exotic Indian trout populations by using microsatellite markers. 利用微卫星标记估算外来印度鳟鱼种群的遗传多样性。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Walter Devaa, Vimal Panneerselvam, Ramesh Uthandakalaipandian

引用次数: 0