Journal of Genetics最新文献_第3页

Efficient assembly of a synthetic attenuated SARS-CoV-2 genome in Saccharomyces cerevisiae using multi-copy yeast vectors 利用多拷贝酵母载体在酿酒酵母中高效组装合成减毒 SARS-CoV-2 基因组

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-02-01 DOI: 10.1007/s12041-023-01455-5

{"title":"Efficient assembly of a synthetic attenuated SARS-CoV-2 genome in Saccharomyces cerevisiae using multi-copy yeast vectors","authors":"","doi":"10.1007/s12041-023-01455-5","DOIUrl":"https://doi.org/10.1007/s12041-023-01455-5","url":null,"abstract":"<h3>Abstract</h3> Saccharomyces cerevisiae has been demonstrated to be an excellent platform for the multi-fragment assembly of large DNA constructs through its powerful homologous recombination ability. These assemblies have invariably used the stable centromeric single copy vectors. However, many applications of these assembled genomes would benefit from assembly in a higher copy number vector for improved downstream extraction of intact genomes from the yeast. A review of the literature revealed that large multi-fragment assemblies did not appear to have been attempted in multicopy vectors. Therefore, we devised a toolkit that would enable one to seamlessly transition with the same assembling fragments between a single copy and a multicopy vector. We evaluated the assembly of a 28 kb attenuated SARS-CoV-2 genome (lacking the N gene) from 10 fragments in both single copy and multicopy vector systems. Our results reveal that assembly was comparably efficient in the two vector systems. The findings should add to the synthetic biology toolkit of S. cerevisiae and should enable researchers to utilize any of these vector systems depending on their downstream applications.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"1 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139661798","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

Role of VDR gene polymorphisms and vitamin D levels in normal and overweight patients with PCOS 多囊卵巢综合征正常和超重患者体内 VDR 基因多态性和维生素 D 水平的作用

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-17 DOI: 10.1007/s12041-023-01461-7

{"title":"Role of VDR gene polymorphisms and vitamin D levels in normal and overweight patients with PCOS","authors":"","doi":"10.1007/s12041-023-01461-7","DOIUrl":"https://doi.org/10.1007/s12041-023-01461-7","url":null,"abstract":"<h3>Abstract</h3> Polycystic ovary syndrome (PCOS) is one of the most common endocrine diseases in women. In recent years, the effects of vitamin D receptor (VDR) gene variants and VitD3 levels on clinical features of PCOS have been frequently described. In this study, we aimed to determine the relationship between VDR ApaI, TaqI and Cdx2 gene variants and VitD3 levels in PCOS patients. Patients were divided into two groups: BMI<25 and BMI≥25. VDR genotypes were determined by real-time polymerase chain reaction (PCR) and serum VitD3 levels were examined by ELISA. We observed that frequencies of the Apa1 AC genotype, C allele and Cdx2 T allele are increased in the BMI≥25 group compared to BMI<25 group. Also, the ApaI C allele, Taq1 AA genotype and A allele, Cdx2 CC genotype and C allele are associated with increased triglyceride, total cholesterol, LDL-cholesterol levels in patients with BMI≥25. When examining the relationship between VitD3 levels and clinical profiles in all PCOS patients, regardless of BMI distinction, it is determined that there is a positive correlation between LDL-cholesterol and ftestosterone levels. The present findings suggest that VDR variants are one of the most important risk factors for PCOS, especially for patients with BMI≥25.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"23 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139496554","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以广泛的多义性为特征

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-17 DOI: 10.1007/s12041-023-01460-8

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":"10.1007/s12041-023-01460-8","DOIUrl":"https://doi.org/10.1007/s12041-023-01460-8","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":"22 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139496267","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

Transferability of Nikita and Sukkula retrotransposons in domestic goose (Anser anser domesticus) genome 家鹅（Anser anser domesticus）基因组中尼基塔（Nikita）和苏库拉（Sukkula）反转座子的可转移性

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-12 DOI: 10.1007/s12041-023-01454-6

{"title":"Transferability of Nikita and Sukkula retrotransposons in domestic goose (Anser anser domesticus) genome","authors":"","doi":"10.1007/s12041-023-01454-6","DOIUrl":"https://doi.org/10.1007/s12041-023-01454-6","url":null,"abstract":"<h3>Abstract</h3> This article aimed to detect the existence of barley-specific Nikita and Sukkula retrotransposons in domestic geese samples and to evaluate the evolutionary relationships between these and other transposons belonging to the family Anatidae. Inter-retrotransposon-amplified polymorphism-polymerase chain reaction (IRAP-PCR) method was performed for these retrotransposons movements in three diverse domestic goose populations (Chinese × Embden crossbred, Turkish White, and Turkish Multicolor). Polymorphism ratios were between 0 and 33% in all samples for Nikita and 0–73% in all samples for Sukkula. In addition, intrapopulation genetic polymorphism rates were also 0–15% in Chinese × Embden crossbred, 0–25% in Turkish White, 0–25% in Turkish Multicolor for Nikita; while 0–27% in Chinese × Embden, and 0–50% in Turkish Multicolor for Sukkula. There was no polymorphism for Sukkula among Turkish White samples. Moreover, the neighbour-joining method was used for phylogenetic tree construction using 38 sequences of different ducks, geese, and swans. In silico analyses supported the transitions of retrotransposons in the family Anatidae. It is concluded that transposon mobility among the phylogenetically distant species may lead to understanding evolutionary relationships. This report is one of the first studies investigating retrotransposon movements in domestic geese, revealing a new perspective on the goose genome regarding mobile genetic elements.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"123 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139461844","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

Two novel heterozygous ADCY10 variants identified in Chinese pediatric patients with absorptive hypercalciuria: case report and literature review 在中国儿童吸收性高钙尿症患者中发现的两个新型杂合子ADCY10变异：病例报告和文献综述

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-10 DOI: 10.1007/s12041-023-01458-2

Yucheng Ge, Yukun Liu, Ruichao Zhan, Zhenqiang Zhao, Wenying Wang, Ye Tian

{"title":"Two novel heterozygous ADCY10 variants identified in Chinese pediatric patients with absorptive hypercalciuria: case report and literature review","authors":"Yucheng Ge, Yukun Liu, Ruichao Zhan, Zhenqiang Zhao, Wenying Wang, Ye Tian","doi":"10.1007/s12041-023-01458-2","DOIUrl":"https://doi.org/10.1007/s12041-023-01458-2","url":null,"abstract":"Absorptive hypercalciuria (AH) is a prevalent cause of kidney stones, and the adenylate cyclase 10 (ADCY10) gene is a rare causative gene of AH. This study aims to investigate the genotypic and phenotypic characteristics of patients with AH caused by ADCY10 gene mutations. Whole-exome sequencing and Sanger sequencing were performed on the probands and their family members, respectively. Clinical and genetic data of patients with AH caused by ADCY10 gene mutations were collected and analysed retrospectively from the present study and published literature. Two female patients (6 years old and 1 year old) with multiple bilateral kidney stones were found to have a heterozygous c.3304T>C mutation and a heterozygous c.1726C>T mutation in the ADCY10 gene. Urinary metabolite analysis revealed that urine calcium / creatinine ratios were 0.95 mmol/mmol and 1.61 mmol/mmol, respectively. Both patients underwent thiazide intake postoperatively, and upon reexamination, urine calcium decreased to within the normal range. A total of 61 patients with AH were reported from previous and present studies. The sex ratio was 7:5 for males to females, and the mean age of onset was 23.61±20.08 years. A total of 16 ADCY10 gene mutations were identified, including seven missense (43.75%), five splicing (31.25%), two frameshift (12.50%) and two nonsense mutations (12.50%). Only two cases were identified as homozygous mutations (c.1205_1206del), and the others were heterozygous mutations. In summary, we identified two novel ADCY10 gene candidate pathogenic variants in Chinese pediatric patients, which expands the mutational spectrum of the ADCY10 gene and provides a potential diagnostic and therapeutic target.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"119 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139424093","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

FSTest: an efficient tool for cross-population fixation index estimation on variant call format files FSTest：对变异调用格式文件进行跨种群固定指数估算的高效工具

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-05 DOI: 10.1007/s12041-023-01459-1

{"title":"FSTest: an efficient tool for cross-population fixation index estimation on variant call format files","authors":"","doi":"10.1007/s12041-023-01459-1","DOIUrl":"https://doi.org/10.1007/s12041-023-01459-1","url":null,"abstract":"<h3>Abstract</h3> Fixation index (Fst) statistics provide critical insights into evolutionary processes affecting the structure of genetic variation within and among populations. Fst statistics have been widely applied in population and evolutionary genetics to identify genomic regions targeted by selection pressures. The FSTest 1.3 software was developed to estimate four Fst statistics of Hudson, Weir and Cockerham, Nei, and Wright using high-throughput genotyping or sequencing data. Here, we introduced FSTest 1.3 and compared its performance with two widely used software VCFtools 0.1.16 and PLINK 2.0. Chromosome 1 of 1000 Genomes Phase III variant data belonging to South Asian (n = 211) and African (n = 274) populations were included as an example case in this study. Different Fst estimates were calculated for each single-nucleotide polymorphism (SNP) in a pairwise comparison of South Asian against African populations, and the results of FSTest 1.3 were confirmed by VCFtools 0.1.16 and PLINK 2.0. Two different sliding window approaches, one based on a fixed number of SNPs and another based on a fixed number of base pair (bp) were conducted using FSTest 1.3 and VCFtools 0.1.16. Our results showed that regions with low coverage genotypic data could lead to an overestimation of Fst in sliding window analysis using a fixed number of bp. FSTest 1.3 could mitigate this challenge by estimating the average of consecutive SNPs along the chromosome. FSTest 1.3 allows direct analysis of VCF files with a small amount of code and can calculate Fst estimates on a desktop computer for more than a million SNPs in a few minutes. FSTest 1.3 is freely available at https://github.com/similab/FSTest.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"208 4 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139104635","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

Molecular data reveals a new genus of blindsnakes within Asiatyphlopinae from India 分子数据揭示了印度亚洲百步蛇科的一个新属

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-02 DOI: 10.1007/s12041-023-01457-3

Chinta Sidharthan, Pragyadeep Roy, K. Praveen Karanth

{"title":"Molecular data reveals a new genus of blindsnakes within Asiatyphlopinae from India","authors":"Chinta Sidharthan, Pragyadeep Roy, K. Praveen Karanth","doi":"10.1007/s12041-023-01457-3","DOIUrl":"https://doi.org/10.1007/s12041-023-01457-3","url":null,"abstract":"The genus Indotyphlops has a widespread distribution in the Indian landmass and Southeast Asia, with 20 reported species. The current classification within the genus is based on morphology. In this study, we sampled all the reported Indotyphlops species from subcontinental India, to resolve relationships within this genus and to understand biogeographic patterns that resulted in the widespread distribution. We generated sequences for five nuclear markers which were used in the global typhlopoid phylogeny and built phylogenetic trees of the superfamily Typhlopoidea. We also carried out divergence time analysis and biogeographic analysis to understand the time and modes of dispersal and diversification of these species. The results show Indotyphlops sensu lato to be polyphyletic, with the clade consisting of I. porrectus and I. exiguus sister to a clade consisting of the southeast Asian typhlopid genera Ramphotyphlops, Anilios, Malayotyphlops, Acutotyphlops, Sundatyphlops, and Indotyphlops sensu stricto. The other clade consists of I. pammeces and I. braminus from the Indian subcontinent and I. albiceps from Southeast Asia. Biogeographical analysis suggests two dispersals from Asia to the Indian landmass—an earlier dispersal from Eurasia into India led to the lineage consisting of I. porrectus and I. exiguus, followed by a later dispersal that evolved into I. pammeces and I. braminus. These results necessitate a taxonomic revision. We propose the genus Pseudoindotyphlops gen. nov. for the clade currently consisting of the most recent common ancestor (MRCA) of I. porrectus and I. exiguus, and all descendants thereof.","PeriodicalId":15907,"journal":{"name":"Journal of Genetics","volume":"34 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139080128","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

Two novel heterozygous ADCY10 variants identified in Chinese pediatric patients with absorptive hypercalciuria: case report and literature review. 在中国儿童吸收性高钙尿症患者中发现的两个新型杂合ADCY10变体：病例报告和文献综述。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Yucheng Ge, Yukun Liu, Ruichao Zhan, Zhenqiang Zhao, Wenying Wang, Ye Tian

{"title":"Two novel heterozygous ADCY10 variants identified in Chinese pediatric patients with absorptive hypercalciuria: case report and literature review.","authors":"Yucheng Ge, Yukun Liu, Ruichao Zhan, Zhenqiang Zhao, Wenying Wang, Ye Tian","doi":"","DOIUrl":"","url":null,"abstract":"Absorptive hypercalciuria (AH) is a prevalent cause of kidney stones, and the adenylate cyclase 10 (ADCY10) gene is a rare causative gene of AH. This study aims to investigate the genotypic and phenotypic characteristics of patients with AH caused by ADCY10 gene mutations. Whole-exome sequencing and Sanger sequencing were performed on the probands and their family members, respectively. Clinical and genetic data of patients with AH caused by ADCY10 gene mutations were collected and analysed retrospectively from the present study and published literature. Two female patients (6 years old and 1 year old) with multiple bilateral kidney stones were found to have a heterozygous c.3304T>C mutation and a heterozygous c.1726C>T mutation in the ADCY10 gene. Urinary metabolite analysis revealed that urine calcium / creatinine ratios were 0.95 mmol/mmol and 1.61 mmol/mmol, respectively. Both patients underwent thiazide intake postoperatively, and upon reexamination, urine calcium decreased to within the normal range. A total of 61 patients with AH were reported from previous and present studies. The sex ratio was 7:5 for males to females, and the mean age of onset was 23.61±20.08 years. A total of 16 ADCY10 gene mutations were identified, including seven missense (43.75%), five splicing (31.25%), two frameshift (12.50%) and two nonsense mutations (12.50%). Only two cases were identified as homozygous mutations (c.1205_1206del), and the others were heterozygous mutations. In summary, we identified two novel ADCY10 gene candidate pathogenic variants in Chinese pediatric patients, which expands the mutational spectrum of the ADCY10 gene and provides a potential diagnostic and therapeutic target.","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":"139521124","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

COQ7 splice site variant causing a spastic paraparesis phenotype in siblings. COQ7 剪接位点变异导致同胞出现痉挛性截瘫表型。

IF 2.9 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Haseena Sait, Manmohan Pandey, Shubha R Phadke

{"title":"COQ7 splice site variant causing a spastic paraparesis phenotype in siblings.","authors":"Haseena Sait, Manmohan Pandey, Shubha R Phadke","doi":"","DOIUrl":"","url":null,"abstract":"The COQ7 gene is one of the causative genes for primary COQ10 deficiency-related disorders. OMIM-related phenotypes include severe encephalo-myo-nephrocardiopathy and distal hereditary motor neuronopathy. In the present study, we performed the exome sequencing analysis on the proband of a single family with two siblings affected by hereditary spastic paraparesis (HSP). Segregation analysis was conducted on the affected siblings and parents using the Sanger sequencing. In silico secondary and tertiary pre-mRNA structure analysis and protein modelling were carried out. Exome sequencing identified a homozygous splice site variant in the COQ7 gene (NM_016138.5: c.367+G>A) in the proband. Sanger sequencing confirmed the homozygous status in the affected sibling and heterozygous status in both parents, consistent with autosomal recessive inheritance. In silico secondary and tertiary premRNA structure analysis and protein modelling predicted the deleterious nature of the variant. This case highlights a distinct intermediate phenotype of COQ7 related disorders comprising early-onset spastic paraparesis due to a novel splice site variant in the COQ7 gene. This expands the spectrum of clinical manifestations associated with COQ7 deficiency and underscores the importance of considering COQ7 gene mutations in the differential diagnosis of HSP.","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":"141855713","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

FSTest: an efficient tool for cross-population fixation index estimation on variant call format files. FSTest：对变异调用格式文件进行跨种群固定指数估算的高效工具。

IF 1.5 4区生物学

Journal of Genetics Pub Date : 2024-01-01

Seyed Milad Vahedi, Siavash Salek Ardestani

{"title":"FSTest: an efficient tool for cross-population fixation index estimation on variant call format files.","authors":"Seyed Milad Vahedi, Siavash Salek Ardestani","doi":"","DOIUrl":"","url":null,"abstract":"Fixation index (Fst) statistics provide critical insights into evolutionary processes affecting the structure of genetic variation within and among populations. Fst statistics have been widely applied in population and evolutionary genetics to identify genomic regions targeted by selection pressures. The FSTest 1.3 software was developed to estimate four Fst statistics of Hudson, Weir and Cockerham, Nei, and Wright using high-throughput genotyping or sequencing data. Here, we introduced FSTest 1.3 and compared its performance with two widely used software VCFtools 0.1.16 and PLINK 2.0. Chromosome 1 of 1000 Genomes Phase III variant data belonging to South Asian (n = 211) and African (n = 274) populations were included as an example case in this study. Different Fst estimates were calculated for each single-nucleotide polymorphism (SNP) in a pairwise comparison of South Asian against African populations, and the results of FSTest 1.3 were confirmed by VCFtools 0.1.16 and PLINK 2.0. Two different sliding window approaches, one based on a fixed number of SNPs and another based on a fixed number of base pair (bp) were conducted using FSTest 1.3 and VCFtools 0.1.16. Our results showed that regions with low coverage genotypic data could lead to an overestimation of Fst in sliding window analysis using a fixed number of bp. FSTest 1.3 could mitigate this challenge by estimating the average of consecutive SNPs along the chromosome. FSTest 1.3 allows direct analysis of VCF files with a small amount of code and can calculate Fst estimates on a desktop computer for more than a million SNPs in a few minutes. FSTest 1.3 is freely available at https://github.com/similab/FSTest.","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":"139521093","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