Search results for "RUNS"
showing 10 items of 32 documents
Burrows-Wheeler Transform on Purely Morphic Words
2022
The study of the compressibility of repetitive sequences is an issue that is attracting great interest. We consider purely morphic words, which are highly repetitive sequences generated by iterating a morphism φ that admits a fixed point (denoted by φ^∞(a) ) starting from a given character a belonging to the finite alphabet A , i.e. φ^∞(a)=lim_{i→∞}φ^i(a) . Such morphisms are called prolongable on a . Here we focus on the compressibility via the Burrows-Wheeler Transform (BWT) of infinite families of finite sequences generated by morphisms. In particular, denoted by r(w) the number of equal-letter runs of a word w , we provide new upper bounds on r(bwt(φ^i(a))) , i.e. the number of equal-le…
Genome-wide homozygosity in Maremmana cattle
2017
The current availability of large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of patterns of genetic diversity and of genome-wide homozygosity in animal populations. The aim of this work was to estimate genetic diversity and homozygosity in the Maremmana cattle breed. We used a sample of 149 animals (males and females) geno-typed with the BovineSNP50 v2 (54K) Illumina BeadChip. After editing for call-rate >0.9 and removing SNP unassigned or on the sex chromosomes, 128 animals and 50,814 SNPs were left. We estimated the following genetic parameters: observed and expected heterozygosity (Ho and He), minor …
Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds
2021
The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furtherm…
Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data
2020
Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomi…
Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds
2020
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). I…
Genome-wide detection of signatures of selection in three Valdostana cattle populations
2020
International audience; The Valdostana is a local dual purpose cattle breed developed in Italy. Three populations are recognized within this breed, based on coat colour, production level, morphology and temperament: Valdostana Red Pied (VPR), Valdostana Black Pied (VPN) and Valdostana Chestnut (VCA). Here, we investigated putative genomic regions under selection among these three populations using the Bovine 50K SNP array by combining three different statistical methods based either on allele frequencies (F-ST) or extended haplotype homozygosity (iHS and Rsb). In total, 8, 5 and 8 chromosomes harbouring 13, 13 and 16 genomic regions potentially under selection were identified by at least tw…
Logarithmic Equal-Letter Runs for BWT of Purely Morphic Words
2022
In this paper we study the number r(bwt) of equal-letter runs produced by the Burrows-Wheeler transform (BWT) when it is applied to purely morphic finite words, which are words generated by iterating prolongable morphisms. Such a parameter r(bwt) is very significant since it provides a measure of the performances of the BWT, in terms of both compressibility and indexing. In particular, we prove that, when BWT is applied to whichever purely morphic finite word on a binary alphabet, r(bwt) is O(log n), where n is the length of the word. Moreover, we prove that r(bwt) is Theta(log n) for the binary words generated by a large class of prolongable binary morphisms. These bounds are proved by pro…
Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations.
2021
The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >
Genome-wide homozygosity and risk of four non-Hodgkin lymphoma subtypes
2021
Aim: Recessive genetic variation is thought to play a role in non-Hodgkin lymphoma (NHL) etiology. Runs of homozygosity (ROH), defined based on long, continuous segments of homozygous SNPs, can be used to estimate both measured and unmeasured recessive genetic variation. We sought to examine genome-wide homozygosity and NHL risk.Methods: We used data from eight genome-wide association studies of four common NHL subtypes: 3061 chronic lymphocytic leukemia (CLL), 3814 diffuse large B-cell lymphoma (DLBCL), 2784 follicular lymphoma (FL), and 808 marginal zone lymphoma (MZL) cases, as well as 9374 controls. We examined the effect of homozygous variation on risk by: (1) estimating the fraction o…
Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds
2018
Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly…