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Detection of Phylogenetically Informative Polymorphisms in the Entire Euchromatic Portion of Human Y Chromosome From a Sardinian Sample

Authors :
Genética, antropología física y fisiología animal
Genetika,antropologia fisikoa eta animalien fisiologia
Francalacci, Paolo
Sanna, Daria
Useli, Antonella
Berutti, Riccardo
Barbato, Mario
Whalen, Michael B.
Angius, Andrea
Sidore, Carlo
Alonso Alegre, Santos
Tofanelli, Sergio
Cucca, Francesco
Genética, antropología física y fisiología animal
Genetika,antropologia fisikoa eta animalien fisiologia
Francalacci, Paolo
Sanna, Daria
Useli, Antonella
Berutti, Riccardo
Barbato, Mario
Whalen, Michael B.
Angius, Andrea
Sidore, Carlo
Alonso Alegre, Santos
Tofanelli, Sergio
Cucca, Francesco
Publication Year :
2015

Abstract

BACKGROUND: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

Details

Database :
OAIster
Notes :
We thank the CRS4 HPC group for their IT support, and in particular, Lidia Leoni and Carlo Podda. This research was supported in part by the Sardinian Autonomous Region (L.R. n°7/2009) grants cRP2-597 to PF and cRP3-154 to FC, by NIH contract NO1-AG-1-2109 from the National Institute of Aging (NIA) to the IRGB institute, English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1099292703
Document Type :
Electronic Resource