scholarly journals Detection of Whole Genome Selection Signatures of Pakistani Teddy Goat

2020 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Fraz Ahmed ◽  
...  
Keyword(s):  
Positive Selection ◽  
Reference Genome ◽  
Sequence Data ◽  
Body Height ◽  
Whole Genome ◽  
Selection Signatures ◽  
Genome Selection ◽  
Reference Genome Assembly ◽  
Genetic Potential ◽  
Productive Traits

Whole genome pooled sequence data of 12 Pakistani Teddy goats is analyzed for positive selection signatures as their breed defining characteristics. Selection imprints left in the Teddy genome are unveiled by genomic differentiation after the successful paired-end alignment of 635,357,043 reads with (ARS1) reference genome assembly. Pooled-heterozygosity ( ) and Tajima’s D (TD) are applied for validation and getting better hits of selection signals, while pairwise FST statistics is conducted on Teddy vs. Bezoar (wild goat ancestor) for genomic differentiation. Annotation of regions under positive selection reveals 59 genes underlying production and adaptive traits. score ≥ 5 detected six windows having highest scores on Chr. 29, 9, 25, 15 and 14 that harbor HRASLS5, LACE1 and AXIN1 genes which are candidate for embryonic development, lactation and body height. Secondly, TD value of ≤ -2.2 showed 4 windows with very strong hits on Chr.5 & 9 harbor STIM1 and ADM genes related to body mass and weight. Lastly, FST analysis generated three strong signals with threshold ≤ 0.42 on Chr.12 & 5 harbor ITGB1 gene associated with milk production & lactation traits. Other significant selection signatures encompass genes associated with wool production, prolificacy, immunity and coat colors. In brief, this study identified the genes under selection in this Pakistani goat breed that will be helpful to refining future breeding policies and converging required productive traits within and across other goat breeds and to explore full genetic potential of this valued livestock species.

scholarly journals Rapture-ready darters: choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma

2020 ◽  
Author(s):  
Brendan N. Reid ◽  
Rachel L. Moran ◽  
Christopher J. Kopack ◽  
Sarah W. Fitzpatrick
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Low Cost ◽  
Read Depth ◽  
Model Organisms ◽  
Whole Genome ◽  
Reduced Representation ◽  
Sequence Capture ◽  
Population Genomic ◽  
The Impact

AbstractResearchers studying non-model organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, are still difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

scholarly journals MUMdex: MUM-based structural variation detection

2016 ◽  
Author(s):  
Peter A. Andrews ◽  
Ivan Iossifov ◽  
Jude Kendall ◽  
Steven Marks ◽  
Lakshmi Muthuswamy ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Sequence Data ◽  
Genomic Analysis ◽  
Supplementary Information ◽  
Whole Genome ◽  
Analysis Software ◽  
Population Database ◽  
Genome Data ◽  
Split Read

AbstractMotivationStandard genome sequence alignment tools primarily designed to find one alignment per read have difficulty detecting inversion, translocation and large insertion and deletion (indel) events. Moreover, dedicated split read alignment methods that depend only upon the reference genome may misidentify or find too many potential split read alignments because of reference genome anomalies.MethodsWe introduce MUMdex, a Maximal Unique Match (MUM)-based genomic analysis software package consisting of a sequence aligner to the reference genome, a storage-indexing format and analysis software. Discordant reference alignments of MUMs are especially suitable for identifying inversion, translocation and large indel differences in unique regions. Extracted population databases are used as filters for flaws in the reference genome. We describe the concepts underlying MUM-based analysis, the software implementation and its usage.ResultsWe demonstrate via simulation that the MUMdex aligner and alignment format are able to correctly detect and record genomic events. We characterize alignment performance and output file sizes for human whole genome data and compare to Bowtie 2 and the BAM format. Preliminary results demonstrate the practicality of the analysis approach by detecting de novo mutation candidates in human whole genome DNA sequence data from 510 families. We provide a population database of events from these families for use by others.Availabilityhttp://mumdex.com/[email protected] (or [email protected])Supplementary informationSupplementary data are available online.

scholarly journals Long-Read Genome Assembly of Saccharomyces uvarum Strain CBS 7001

2022 ◽  
Author(s):  
Jingxuan Chen ◽  
David J. Garfinkel ◽  
Casey M. Bergman
Keyword(s):  
Genome Assembly ◽  
Reference Genome ◽  
Sequence Data ◽  
Sensu Stricto ◽  
Whole Genome ◽  
Saccharomyces Uvarum ◽  
Content Type ◽  
Whole Genome Shotgun Sequence ◽  
Long Read ◽  
Genome Shotgun Sequence

Here, we report a long-read genome assembly for Saccharomyces uvarum strain CBS 7001 based on PacBio whole-genome shotgun sequence data. Our assembly provides an improved reference genome for an important yeast in the Saccharomyces sensu stricto clade.

scholarly journals Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Coat Color ◽  
Body Height ◽  
Fixation Index ◽  
Whole Genome ◽  
Genetic Potential ◽  
Mapping Process ◽  
Quality Checks ◽  
Breed Improvement ◽  
Genomic Regions ◽  
Initial Process

Abstract Natural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima’s D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions with threshold (-ZHp ≥ 5, TD ≤ -2.72 & FST ≤ 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8, MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.

Detection of whole genome selection signatures of Pakistani Teddy goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Fraz Ahmad ◽  
...  
Keyword(s):  
Whole Genome ◽  
Selection Signatures ◽  
Genome Selection

scholarly journals Whole Genome Selective Sweeps Analysis in Pakistani Kamori Goat

2021 ◽  
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Tania Mahmood ◽  
Aniqa Ejaz ◽  
Saeeda Zia
Keyword(s):  
Coat Color ◽  
Body Height ◽  
Fixation Index ◽  
Whole Genome ◽  
Genetic Potential ◽  
Mapping Process ◽  
Quality Checks ◽  
Breed Improvement ◽  
Genomic Regions ◽  
Initial Process

AbstractNatural and artificial selection fix certain genomic regions of reduce heterozygosity which is an initial process in breed development. Primary goal of the current study is to identify these genomic selection signatures under positive selection and harbor genes in Pakistani Kamori goat breed. High throughput whole genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files were undergone quality checks, trimming and mapping process against ARS1 reference followed by calling variant allele frequencies. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima’s D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. Total 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions with threshold (−ZHp ≥ 5, TD ≤ −2.72 & FST ≤ 0.09) detected 60 candidate genes. The top hits harbor Chr.1, 6, 8 & 21 having genes associated with body weight (GLIS3, ASTE1), coat color (DOCK8, MIPOL1) & body height (SLC25A21). Other significant windows harbor milk production, wool production, immunity, adaptation and reproduction trait related genes. Current finding highlighted the under-selection genomic regions of Kamori breed and likely to be associated with its vested traits and further useful in breed improvement, and may be also propagated to other undefined goat breeds by adopting targeted breeding policies to improve the genetic potential of this valued species.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2

2021 ◽  
Author(s):  
Liang Cheng ◽  
Xudong Han ◽  
Zijun Zhu ◽  
Changlu Qi ◽  
Ping Wang ◽  
...  
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Purifying Selection ◽  
Virus Genome ◽  
Receptor Binding Domain ◽  
Evolutionary Trends ◽  
Synonymous Mutations ◽  
Almost All ◽  
Virus Strains ◽  
New Mutations

Abstract Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, the COVID-19 pandemic has spread rapidly worldwide. Due to the limited virus strains, few key mutations that would be very important with the evolutionary trends of virus genome were observed in early studies. Here, we downloaded 1809 sequence data of SARS-CoV-2 strains from GISAID before April 2020 to identify mutations and functional alterations caused by these mutations. Totally, we identified 1017 nonsynonymous and 512 synonymous mutations with alignment to reference genome NC_045512, none of which were observed in the receptor-binding domain (RBD) of the spike protein. On average, each of the strains could have about 1.75 new mutations each month. The current mutations may have few impacts on antibodies. Although it shows the purifying selection in whole-genome, ORF3a, ORF8 and ORF10 were under positive selection. Only 36 mutations occurred in 1% and more virus strains were further analyzed to reveal linkage disequilibrium (LD) variants and dominant mutations. As a result, we observed five dominant mutations involving three nonsynonymous mutations C28144T, C14408T and A23403G and two synonymous mutations T8782C, and C3037T. These five mutations occurred in almost all strains in April 2020. Besides, we also observed two potential dominant nonsynonymous mutations C1059T and G25563T, which occurred in most of the strains in April 2020. Further functional analysis shows that these mutations decreased protein stability largely, which could lead to a significant reduction of virus virulence. In addition, the A23403G mutation increases the spike-ACE2 interaction and finally leads to the enhancement of its infectivity. All of these proved that the evolution of SARS-CoV-2 is toward the enhancement of infectivity and reduction of virulence.

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