EGAGenomicsMichal Whalenhttps://ega-archive.org/dacs/EGAC00001000121EGAEGA DAC EGAC00001000121EGAmichael.whalen@irgb.cnr.it<h4>Background</h4>Next-Generation Sequencing methods have led to a great increase in phylogenetically useful markers within the male specific portion of the Y chromosome, but previous studies have limited themselves to the study of the X-degenerate regions.<h4>Methods</h4>DNA was extracted from peripheral blood samples of adult males whose paternal grandfathers were born in Sardinia. The DNA samples were sequenced, genotyped and subsequently analysed for variant calling for approximately 23.1 Mbp of the Y chromosome. A phylogenetic tree was built using Network 4.6 software.<h4>Results</h4>From low coverage whole genome sequencing of 1,194 Sardinian males, we extracted 20,155 phylogenetically informative single nucleotide polymorphisms from the whole euchromatic region, including the X-degenerate, X-transposed, and Ampliconic regions, along with variants in other unclassified chromosome intervals and in the readable sequences of the heterochromatic region.<h4>Conclusions</h4>The non X-degenerate classes contain a significant portion of the phylogenetic variation of the whole chromosome and their inclusion in the analysis, almost doubling the number of informative polymorphisms, refining the known molecular phylogeny of the human Y chromosome.Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample.Francalacci Paolo P, Sanna Daria D, Useli Antonella A, Berutti Riccardo R, Barbato Mario M, Whalen Michael B MB, Angius Andrea A, Sidore Carlo C, Alonso Santos S, Tofanelli Sergio S, Cucca Francesco Ffbwd4, l(2)04454, DmelCG1772, dac, CIB1, interphase chromosome, shsf3, shfm3, Decapo., E(Sev-CycE)2B, chromatid, p21[dacapo], Fbw4, FBW4, dactylin, E130112M23Rik, Dach, CDKN2B, cdi4, prophase chromosome, SHFM3, Dac, DAC, p27[Dap], Chromosome, dactylyn, dacapo/cyclin-dependent kinase interactor 4, AI182278, p21, CG1772, FBWD4, Dap, Cdi4, CDI4, CES5A1, p27, P15, fbw4, SHSF3Human, sample., human being, Man (Taxonomy), Homo sapiens, Chromosome, Modern Man, Modern, Y, Man, Y Chromosomes, human, Chromosomes, sample populationdetermination, MBP-C, Blood, adult stage, Phylogenetic Structure, MBP1, Phylogenetic Analysis, Y Chromosomes, Phylogenetic Signals, Techniques, Phylogenetic Inference, Method, Molecular Phylogenetics, Comparative Analysis, Software Engineering, Analysis, Phylogenetic Comparative Analysis, (2Z)-but-2-enedioate, adult, Computer Program, Phylogenetic Relationship, INSL3R, male, HSMBPC, Eosinophil granule major basic protein, Group, thymus nucleic acid, me75, Phylogenomic, Man (Taxonomy), Molecular, Open, Computer Programs and Programming, chromatid, procedures, Myelin membrane encephalitogenic protein, Y, Phylogenetic Networks, D17Mit170, T1, GREAT, geographical area, Methodological Studies, Phylogenetic Network, MBPD, Phylogenetic Reconstructions, Great, Pregnancy-associated major basic protein, Phylogenetic Incongruences, Double-Stranded DNA, Phylogenetic Clustering, deoxyribonucleic acids, DNAn, Relationship, Nucleotide, Phylogenetic Comparative Method, Phylogenetic Analyse, Modern, Genome Sequencing, Phylogenetic Inferences, Double-Stranded, Procedure, Tl3, Phylogenetic Analyses, Tl2, Source Softwares, results, Phylogenetic Generalized Least Squares, Software Tools, Programs, (Deoxyribonucleotide)n+m, Program, Computer Applications, mld, Complete Genome, C76307, Computer Applications Software, Computer Applications Softwares, Phylogenetic Comparative Analyses, shi, Hmbpr, Softwares, desoxyribose nucleic acid, Phylogenetic Incongruence, Adults, nucleotides, LGR8, Lgr8, Software Applications, positional polypeptide feature, Phylogenetic Tree, maleate, Source Software, Phylogenies, EMBP, Methodological, Methodological Study, human, Phylogenetic Trees, Applications, Chromosome, Comparative Method, Clustering, PBMCs, ds DNA, Phylogenetic Groups, Myelin A1 protein, Y., DNA, Community, Computer Software Applications, human being, DNS, Phylogenetic Reconstruction, Procedures, (Deoxyribonucleotide)n, region or site annotation, R75289, number, Network, Computer, Chromosomes, Deoxyribonucleic acids, Distance, Phylogenomics, Human, COLEC1, Phylogenetic Comparative Methods, Deoxyribonucleic Acid, Inference, Homo sapiens, PBMC, Relatedness, Studies, Phylogenetic Relatednesses, Low, Phylogenetic Relatedness, Technique, Man, Application, Community Phylogenetics, study, Open Source Softwares, positional, Complete, Whole Genome, Gpr106, Software Application, Complete 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Bra, Phylogenetic Relationships, assay, methodologyfalseSardinian Chromosome Y DACData Access Committee EGAC00001000121EGAC00001000121960625926048EGAS00001000532EGAD00001000618