Y chromosome sequence variation of common forensic STR markers and their flanking regions among Polish population

This paper presents a comprehensive Y-chromosomal STR haplotype analysis in the Lithuanian population in order to evaluate Lithuanians’ Y chromosome diversity, to infer genetic relations between Lithuanian and other European neighbouring populations and to introduce population reference data for generation of reliable Y-STR haplotype frequency estimates to be used in the quantitative assessment of Y-STR haplotype match in the forensic casework. Data were collected from the peripheral blood samples of 194 unrelated males throughout various regions of Lithuania. The amplification of 17 Y-STRs was carried out in one multiplex PCR using an AmpFlSTR® Yfiler<sup>TM</sup> PCR Amplication Kit according to the supplier’s protocol. The results indicated that the Y-chromosomal haplotype diversity in the Lithuanian population rises as the number of the analyzed Y-STRs is increased. However, all additional Y-STR loci are not hypervariable and only their whole makes a large diversity of Y-STR haplotypes in Lithuanian males. The analysis of molecular variance revealed low but significant interpopulation differences except the pair of Lithuanian and Latvian populations. The phylogenetic analysis showed that the clustered Y chromosome gene pool of Lithuanians and Latvians has a closer phylogenetic relation to Russian and Estonian populations and is less genetically related to other neighbouring populations of Belarus and Poland. Yet Y-STRs alleles and haplotypes differentiate effectively inside the Lithuanian population and between Lithuanians and its geographical neighbours excluding the Latvian population. Comparison of the Y-STR data suggests that Lithuanian and Latvian populations are closely related not only by geography and language but also by the Y chromosome gene pool represented by forensic Y-STR markers. Consequently, more forensic Y-STR markers should be included in the Y-STR haplotype in order to achieve a resolution between the Y chromosomes of Lithuanian and Latvian males. Lithuanian Y-STR haplotype data were submitted to the 34th release of the Y-STR Haplotype Reference Database 3.0 for match probability calculations in the forensic casework.

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Human retroviral sequences on the Y chromosome

Molecular and Cellular Biology ◽

10.1128/mcb.7.4.1559-1562.1987 ◽

1987 ◽

Vol 7 (4) ◽

pp. 1559-1562

Author(s):

J Silver ◽

A Rabson ◽

T Bryan ◽

R Willey ◽

M A Martin

Keyword(s):

Gene Duplication ◽

Long Terminal Repeat ◽

Y Chromosome ◽

Full Length ◽

Terminal Repeat ◽

Male And Female ◽

Southern Blots ◽

Repeat Sequences ◽

Flanking Regions ◽

Human Retrovirus

Novel endogenous human retroviral sequences were cloned by low-stringency hybridization, using the pol gene of endogenous human retrovirus 51-1. One clone, lambda NP-2, contained gag, pol, env, and long terminal repeat sequences related to the corresponding portions of clone 51-1 and the closely related full-length endogenous human retrovirus 4-1. The sequence of the env gene of NP-2 was 73% homologous to that of 4-1. Genomic Southern blots of male and female DNAs showed that NP-2 is located on the Y chromosome and that the Y chromosome also contains one other sequence closely related to the env and 3' flanking regions of NP-2. Conservation of flanking DNA suggests that the second Y chromosome copy of the NP-2 env sequence arose by gene duplication rather than provirus insertion.

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Amplification of Y Chromosome STR Markers by Multiplex PCR

Springer Protocols Handbooks - Principles and Practices of DNA Analysis: A Laboratory Manual for Forensic DNA Typing ◽

10.1007/978-1-0716-0274-4_20 ◽

2020 ◽

pp. 165-171

Author(s):

Hirak Ranjan Dash ◽

Pankaj Shrivastava ◽

Surajit Das

Keyword(s):

Multiplex Pcr ◽

Y Chromosome ◽

Str Markers ◽

Y Chromosome Str

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263 LABELING BOVINE SPERM Y-CHROMOSOME SEQUENCE USING DNA MIMICS

Reproduction Fertility and Development ◽

10.1071/rdv21n1ab263 ◽

2009 ◽

Vol 21 (1) ◽

pp. 229 ◽

Cited By ~ 3

Author(s):

B. A. Didion ◽

R. Bleher

Keyword(s):

Y Chromosome ◽

Somatic Cells ◽

Cell Nuclei ◽

Metaphase Chromosomes ◽

Synthetic Dna ◽

Bovine Sperm ◽

Hybridization Probes ◽

Y Chromosomes ◽

Chromosome Sequence ◽

In Situ Detection

Flow cytometric separation of X- and Y-chromosome bearing bovine sperm is an accepted technology for use at the commercial level. Nevertheless it is important to continue researching the area of gender-preselected sperm for improved efficiencies. We used a synthetic DNA mimic conjugated to a fluorescent dye for in situ detection of Y chromosomes in metaphase preparations of bovine somatic cells and spermatozoa. Peptide nucleic acids (PNA) are a type of DNA mimic having a higher affinity and stability than conventional DNA probes and are used as hybridization probes to complementary DNA. Using male bovine somatic cells and the Y-chromosome as a template, we arranged for the synthesis of a CY3-conjugated PNA to bind 13 to 15 base pairs of unique, Y-chromosome sequence. By testing different labeling conditions, we found that brief incubation (~1 h) of metaphase chromosomes with the PNA produced a localized signal on the Y-chromosome. No signals were observed when chromosomes of female bovine somatic cells were incubated with the same PNA probe. Because chromosomes occupy non-random territories in all cell nuclei, including sperm, we proposed to find centrally-located signals in 50% of fixed bovine sperm when treated with the same PNA as used for the somatic cells. As expected, we found the PNA signals present in 50% sperm (23/43) existing as a single, centrally-located, round fluorescent dot in the sperm head. Validation studies were also conducted using bovine sperm previously flow sorted into X or Y populations, and we found the signals in accordance to an expected signal present using the PNA (146/165 or 88.5% with PNA signal in presorted Y sperm heads and 13/174 or 7.5% with PNA signal in presorted X sperm heads).

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Human retroviral sequences on the Y chromosome.

Molecular and Cellular Biology ◽

10.1128/mcb.7.4.1559 ◽

1987 ◽

Vol 7 (4) ◽

pp. 1559-1562 ◽

Cited By ~ 26

Author(s):

J Silver ◽

A Rabson ◽

T Bryan ◽

R Willey ◽

M A Martin

Keyword(s):

Gene Duplication ◽

Long Terminal Repeat ◽

Y Chromosome ◽

Full Length ◽

Terminal Repeat ◽

Male And Female ◽

Southern Blots ◽

Repeat Sequences ◽

Flanking Regions ◽

Human Retrovirus

Novel endogenous human retroviral sequences were cloned by low-stringency hybridization, using the pol gene of endogenous human retrovirus 51-1. One clone, lambda NP-2, contained gag, pol, env, and long terminal repeat sequences related to the corresponding portions of clone 51-1 and the closely related full-length endogenous human retrovirus 4-1. The sequence of the env gene of NP-2 was 73% homologous to that of 4-1. Genomic Southern blots of male and female DNAs showed that NP-2 is located on the Y chromosome and that the Y chromosome also contains one other sequence closely related to the env and 3' flanking regions of NP-2. Conservation of flanking DNA suggests that the second Y chromosome copy of the NP-2 env sequence arose by gene duplication rather than provirus insertion.

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Gene discovery and comparative analysis of X-degenerate genes from the domestic cat Y chromosome☆☆Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession No. EU879967-EU879988.

Genomics ◽

10.1016/j.ygeno.2008.06.012 ◽

2008 ◽

Vol 92 (5) ◽

pp. 329-338 ◽

Cited By ~ 36

Author(s):

Alison J. Pearks Wilkerson ◽

Terje Raudsepp ◽

Tina Graves ◽

Derek Albracht ◽

Wesley Warren ◽

...

Keyword(s):

Comparative Analysis ◽

Y Chromosome ◽

Sequence Data ◽

Gene Discovery ◽

Domestic Cat ◽

Chromosome Sequence ◽

Data Libraries

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The Red Fox Y-Chromosome in Comparative Context

Genes ◽

10.3390/genes10060409 ◽

2019 ◽

Vol 10 (6) ◽

pp. 409 ◽

Cited By ~ 1

Author(s):

Halie M. Rando ◽

William H. Wadlington ◽

Jennifer L. Johnson ◽

Jeremy T. Stutchman ◽

Lyudmila N. Trut ◽

...

Keyword(s):

Y Chromosome ◽

Canis Lupus ◽

Related Species ◽

Red Fox ◽

Draft Genome ◽

Canis Lupus Familiaris ◽

Short Read ◽

Repeat Content ◽

Y Chromosomes ◽

Chromosome Sequence

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Felis catus), dog (Canis lupus familiaris), and grey wolf (Canis lupus lupus), providing the opportunity to examine the red fox (Vulpes vulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.

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