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Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample

Francalacci, Paolo and Sanna, Daria and Useli, Antonella and Berutti, Riccardo and Barbato, Mario and Whalen, Michael B. and Angius, Andrea and Sidore, Carlo and Alonso, Santos and Tofanelli, Sergio and Cucca, Francesco (2015) Detection of phylogenetically informative polymorphisms in the entire euchromatic portion of human Y chromosome from a Sardinian sample. BMC Research Notes, Vol. 8 (174), p. 13. ISSN 1756-0500. Article.

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DOI: 10.1186/s13104-015-1130-z

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.

Item Type:Article
ID Code:10979
Status:Published
Refereed:Yes
Uncontrolled Keywords:Human evolutionary genetics, single nucleotide polymorphisms, molecular phylogeny, Next Generation Sequencing
Subjects:Area 06 - Scienze mediche > MED/03 Genetica medica
Area 05 - Scienze biologiche > BIO/18 Genetica
Divisions:001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze della Natura e del Territorio
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
Publisher:BioMed Central
ISSN:1756-0500
Copyright Holders:© 2015 Francalacci et al.
Deposited On:12 Jun 2015 08:30

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