Disequilibrium of multiple DNA markers on the human Y chromosome

We characterized four DNA polymorphisms on the Y chromosomes of 123 males from five Caucasian populations. Three markers on the male specific portion of the chromosome varied appreciably in frequency among the populations. When combined, these markers define a limited number of haplotypes compared with the maximum expected on the basis of random association. The associations found in the five groups are qualitatively similar and are thus considered to be relatively stable on an evolutionary time-scale and possibly to predate the divergence of Caucasian populations. However, the haplotype frequencies varied markedly among populations, even between weakly isolated areas such as northern vs. southern Sardinia. This may indicate rapid progression towards fixation of alternative types of Y chromosomes.
We also report data suggesting that the same associations no longer hold when examining a marker as close as 275 bp from the boundary of the pseudoautosomal region on the Y chromosome.     

A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]     

Male infertility: analysis of the markers and genes on the human Y chromosome

The long arm of the human Y chromosome is required for male fertility. Deletions in three different regions can cause severe spermatogenic defects ranging from non-obstructive azoospermia to oligozoospermia. Use of intracytoplasmic sperm injection (ICSI) may allow Y chromosome defects to be passed from father to son. Thus, numerous reports have stressed the need to offer genetic testing to infertile men who select ICSI and a number of reproductive clinics have begun to do so. The primary objectives of this review were: firstly, to discuss the characteristics of the published set of polymerase chain reaction markers and how these characteristics affect interpretation of Y chromosome deletion analysis and secondly, to summarize the recent literature pertaining to the genes on the Y chromosome.      

Y chromosome analysis reveals a sharp genetic boundary in the Carpathian region

Nine single nucleotide (SNP) or indel binary polymorphisms were used to determine the frequencies and phylogenetic relationships of 12 Y chromosomal haplogroups in 289 males from Romania and the Republic of Moldova. Our data indicated a low but not null rate of the homoplasic appearance of the DYZ3 (-) allelic state. All other markers confirmed the previously proposed phylogeny. Based on the affinities between populations in terms of haplogroup frequencies, this work identified the geographical region of the Carpathians as a break point in the gene geography of Eastern Central Europe, providing a finer definition of one of the possible sharp genetic changes between Western and Eastern Europe.     

Genetic variations on the Y chromosome in the Japanese population and implications for modern human Y chromosome lineage

A polymorphism in the coding sequence of the SRY gene was found by single-strand conformation polymorphism (SSCP) and direct sequencing analysis. The new allele of the SRY gene, which is raised by a C-to-T transition in the 155th codon, was found in 24% of Honshu, 35% of Okinawan, and 51% of Korean males respectively, whereas it was not observed among 16 Caucasian and 18 Negroid males. A haplotype analysis of the Y chromosome was carried out in Japanese, Korean, Caucasian and Negroid populations, using a combination of the polymorphisms in SRY, DXYS5Y, DYS287, and DXYS241Y loci. The results indicated that the Y chromosomes can be classified into seven haplotypes (Ia, Ib, Ic, IIa, IIb, III, IV). However, of these seven, only four (Ia, IIa, III, IV) were observed in the Japanese population. Furthermore, the presumed haplotype C, Y1, YAP, (CA)₁₄, from which haplotype III was probably derived, was not found in any populations in this study. The regional distribution of each haplotype revealed that type III is more frequently observed in Okinawa (16%) and in Korea (21%) than in Honshu (4.4%). The haplotype analysis of the Y chromosome may contribute to the exploration of the origin of Japanese and the relationship between east Asian populations. Received: February 25, 1999 / Accepted: April 5, 1999     

Y染色体的多态性遗传标记及其法医学应用

Y染色体（除拟常染区外）在减数分裂中不发生交换重组，呈单倍型传递，具有父系遗传特征，序列的变异由累积的突变所致。由于Y染色体的这些特点，使得对Y染色体上多态性遗传标记的研究不仅在人类进化学、遗传学等方面意义重大，而且在法医学、临床医学等方面亦具有重要而独特的应用价值。     

Analysis of the ORF2 of human astroviruses reveals lineage diversification,recombination and rearrangement and provides the basis for a novel sub-classification system

Canonical human astroviruses (HAstVs) are important enteric pathogens that can be classified genetically and antigenically into eight types. Sequence analysis of small diagnostic regions at either the 5′ or 3′ end of ORF2 (capsid precursor) is a good proxy for prediction of HAstV types and for distinction of intratypic genetic lineages (subtypes), although lineage diversification/classification has not been investigated systematically. Upon sequence and phylogenetic analysis of the full-length ORF2 of 86 HAstV strains selected from the databases, a detailed classification of HAstVs into lineages was established. Three main lineages could be defined in HAstV-1, four in HAstV-2, two in HAstV-3, three in HAstV-4, three in HAstV-5 and two in HAstV-6. Intratypic (inter-lineages) ORF2 recombinant strains were identified in type 1 (1b/1d) and type 2 (2c/2b) with distinct crossover points. Other potential intratypic recombinant strains were identified in type 3, type 5 and type 6. In addition, a type-1b strain with a large insertion (~600 bp) of heterologous RNA in the N-terminal region and a type-6 strain with a large RNA rearrangement in the hypervariable region were identified. The classification scheme was integrated in a novel nomenclature system suitable for designation of HAstV strains.     

Microdissection of a human marker chromosome reveals its origin and a new family of centromeric repetitive DNA.

A series of procedures including chromosome microdissection, sequence-independent PCR, Southern-blot-hybrid-selection-cloning and sequencing of microdissected DNA-library members were used to analyze DNA from a familial marker chromosome centromere and to determine the origin of the marker chromosome in the case of a live-born, tetraploid human infant. A new family of repetitive DNA, termed sn5 satellite, was sequenced and characterized by DNA hybridization. The sn5 satellite family appears to be primate-specific and shows a chromosome-specific distribution which parallels that of alpha satellite suprachromosomal family 2. This suprachromosomal classification is based on sequence similarity of centromeric alpha satellite DNA within particular groups of chromosomes. It has been postulated that the similarity of alphoid sequences within each of the three suprachromosomal families results from homologous exchanges between nonhomologous chromosomes within each family. The parallel distribution of sn5 satellite sequences at the centromeres of chromosomes of alphoid suprachromosomal family 2 suggests that homologous exchanges between non-homologous chromosomes may be the basis of simultaneous chromosome-specific sequence conservation for multiple centromeric satellite DNA families.     

Variable patterns of Y chromosome homology in Akodontini rodents (Sigmodontinae): a phylogenetic signal revealed by chromosome painting

The Akodontini is the second most speciose tribe of sigmodontine rodents, one of the most diverse groups of neotropical mammals. Molecular phylogenetic analyses are discordant regarding the interrelationships of genera, with low support for some clades. However, two clades are concordant, one (clade A) with Akodon sensu strictu (excluding Akodon serrensis), "Akodon" serrensis, Bibimys, Deltamys, Juscelinomys, Necromys, Oxymycterus, Podoxymys, Thalpomys and Thaptomys, and another (clade B) with Blarinomys, Brucepattersonius, Kunsia, Lenoxus and Scapteromys. Here, we present chromosome painting using Akodon paranaensis (APA) Y paint, after suppression of simple repetitive sequences, on ten Akodontini genera. Partial Y chromosome homology, in addition to the homology already reported on the Akodon genus, was detected on the Y chromosomes of "A." serrensis, Thaptomys, Deltamys, Necromys and Thalpomys and on Y and X chromosomes in Oxymycterus. In Blarinomys, Brucepattersonius, Scapteromys and Kunsia, no APA Y signal was observed using different hybridization conditions; APA X paint gave positive signals only on the X chromosome in all genera. The Y chromosome homology was variable in size and positioning among the species studied as follow: (1) whole acrocentric Y chromosome in Akodon and "A." serrensis, (2) Yp and pericentromeric region in submetacentric Y of Necromys and Thaptomys, (3) pericentromeric region in acrocentric Y of Deltamys, (4) distal Yq in the acrocentric Y chromosome of Thalpomys and (5) proximal Yq in the acrocentric Y and Xp in the basal clade A genus Oxymycterus. The results suggest that the homology involves pairing (pseudoautosomal) and additional regions that have undergone rearrangement during divergence. The widespread Y homology represents a phylogenetic signal in Akodontini that provides additional evidence supporting the monophyly of clade A. The findings also raise questions about the evolution of the pseudoautosomal region observed in Oxymycterus. The Y chromosomes of these closely related species seem to have undergone dynamic rearrangements, including restructuring and reduction of homologous segments. Furthermore, the changes observed may indicate progressive attrition of the Y chromosome in more distantly related species.     

A molecular method for detecting the presence of the human Y chromosome

The presence of the human Y chromosome can be inferred from the detection of a male-specific 3.4-Kb band generated by digestion with the restriction enzyme Hae III. However, direct visualization of this band is sometimes difficult owing to high background of DNA fragments common to both sexes, and Y chromosome length polymorphism. We have shown that the 3.4-Kb band can be detected by filter hybridization to a large DNA fragment (greater than 20 Kb) also generated by Hae III digestion. Since this large DNA fragment is easily isolated from either sex, it should prove useful to determine sex when chromosome analysis is impractical.     

Evolutionary history of novel genes on the tammar wallaby Y chromosome: Implications for sex chromosome evolution

We report here the isolation and sequencing of 10 Y-specific tammar wallaby (Macropus eugenii) BAC clones, revealing five hitherto undescribed tammar wallaby Y genes (in addition to the five genes already described) and several pseudogenes. Some genes on the wallaby Y display testis-specific expression, but most have low widespread expression. All have partners on the tammar X, along with homologs on the human X. Nonsynonymous and synonymous substitution ratios for nine of the tammar XY gene pairs indicate that they are each under purifying selection. All 10 were also identified as being on the Y in Tasmanian devil (Sarcophilus harrisii; a distantly related Australian marsupial); however, seven have been lost from the human Y. Maximum likelihood phylogenetic analyses of the wallaby YX genes, with respective homologs from other vertebrate representatives, revealed that three marsupial Y genes (HCFC1X/Y, MECP2X/Y, and HUWE1X/Y) were members of the ancestral therian pseudoautosomal region (PAR) at the time of the marsupial/eutherian split; three XY pairs (SOX3/SRY, RBMX/Y, and ATRX/Y) were isolated from each other before the marsupial/eutherian split, and the remaining three (RPL10X/Y, PHF6X/Y, and UBA1/UBE1Y) have a more complex evolutionary history. Thus, the small marsupial Y chromosome is surprisingly rich in ancient genes that are retained in at least Australian marsupials and evolved from testis-brain expressed genes on the X.     

6号染色体HLA区域的128个SNPs与肠炎相关性的研究

目的：为了探讨6号染色体的HLA区域与肠道性疾病(IBD)的发病和发展的关系，实验通过对某些基因的单核苷酸多态进行扫描，希望获得IBD易感基因。方法：本实验抽取了200份IBD病人血液和200份为正常对照血液，提取DNA，采用相关分析法和TaqMan技术，对6号染色体HLA-I，HLA-Ⅱ，HLA-Ⅲ区域附近的128个SNP标签进行鉴定。结果：我们得到85个真实的SNP；30个为假阳性；7个是本实验室发现的。选择其中26个单核苷酸多态在UC病人中进行SNPs扫描，获得的P值有些在统计学上有显著差异，如MOG。但是有些P值却没有统计学意义，如MICA和MICB。结论：证实了该区域的一些SNP与IBD密切相关，但是有些被认为与IBD密切相关的单核苷酸多态在本实验中统计学上没有明显差异。     

Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes

To investigate associations between genetic, linguistic, and geographic variation in Africa, we type 50 Y chromosome SNPs in 1122 individuals from 40 populations representing African geographic and linguistic diversity. We compare these patterns of variation with those that emerge from a similar analysis of published mtDNA HVS1 sequences from 1918 individuals from 39 African populations. For the Y chromosome, Mantel tests reveal a strong partial correlation between genetic and linguistic distances (r=0.33, P=0.001) and no correlation between genetic and geographic distances (r=-0.08, P>0.10). In contrast, mtDNA variation is weakly correlated with both language (r=0.16, P=0.046) and geography (r=0.17, P=0.035). AMOVA indicates that the amount of paternal among-group variation is much higher when populations are grouped by linguistics (Phi(CT)=0.21) than by geography (Phi(CT)=0.06). Levels of maternal genetic among-group variation are low for both linguistics and geography (Phi(CT)=0.03 and 0.04, respectively). When Bantu speakers are removed from these analyses, the correlation with linguistic variation disappears for the Y chromosome and strengthens for mtDNA. These data suggest that patterns of differentiation and gene flow in Africa have differed for men and women in the recent evolutionary past. We infer that sex-biased rates of admixture and/or language borrowing between expanding Bantu farmers and local hunter-gatherers played an important role in influencing patterns of genetic variation during the spread of African agriculture in the last 4000 years.     

Efficient identification of Y chromosome sequences in the human and Drosophila genomes

Notwithstanding their biological importance, Y chromosomes remain poorly known in most species. A major obstacle to their study is the identification of Y chromosome sequences; due to its high content of repetitive DNA, in most genome projects, the Y chromosome sequence is fragmented into a large number of small, unmapped scaffolds. Identification of Y-linked genes among these fragments has yielded important insights about the origin and evolution of Y chromosomes, but the process is labor intensive, restricting studies to a small number of species. Apart from these fragmentary assemblies, in a few mammalian species, the euchromatic sequence of the Y is essentially complete, owing to painstaking BAC mapping and sequencing. Here we use female short-read sequencing and k-mer comparison to identify Y-linked sequences in two very different genomes, Drosophila virilis and human. Using this method, essentially all D. virilis scaffolds were unambiguously classified as Y-linked or not Y-linked. We found 800 new scaffolds (totaling 8.5 Mbp), and four new genes in the Y chromosome of D. virilis, including JYalpha, a gene involved in hybrid male sterility. Our results also strongly support the preponderance of gene gains over gene losses in the evolution of the Drosophila Y. In the intensively studied human genome, used here as a positive control, we recovered all previously known genes or gene families, plus a small amount (283 kb) of new, unfinished sequence. Hence, this method works in large and complex genomes and can be applied to any species with sex chromosomes.Y chromosomes play a major role in sexual reproduction by harboring master sex-determination genes in many species and male fertility factors in most of them (Bull 1983; Carvalho et al. 2009; Kaiser and Bachtrog 2010; Ezaz and Graves 2012; Hughes and Rozen 2012). Analysis of their origin and evolution has revealed unexpected biological phenomena (Rozen et al. 2003; Carvalho and Clark 2005; Koerich et al. 2008; Lemos et al. 2008; Murtagh et al. 2012), as well as general principles of evolutionary genetics, including the role of recombination and sex-antagonistic genes (Rice 1996; Charlesworth and Charlesworth 2000; Zhou and Bachtrog 2012). However, despite their importance, little is known about Y chromosomes because in many species they are heterochromatic, being composed of highly repetitive DNA that cannot be fully assembled with current technologies (Carvalho et al. 2003; Hoskins et al. 2007). The same issues apply to W chromosomes in ZZ/ZW sex-determination systems (Bull 1983; International Chicken Genome Sequencing Consortium 2004). Mammalian Y chromosomes contain a large euchromatic portion that nonetheless is also very repetitive; in a few species (human, chimp, and macaque), its sequence is nearly complete, owing to painstaking BAC mapping and sequencing (Skaletsky et al. 2003; Hughes and Rozen 2012). These formidable achievements demanded a huge investment of time and resources and placed these Y chromosomes apart (in all other species, only fragmentary assemblies are available, at best). A similar effort successfully assembled the less repetitive portion of the D. melanogaster heterochromatin (Hoskins et al. 2007). It is telling that even in the finished human genome most heterochromatic regions remain unassembled (International Human Genome Sequencing Consortium 2004).Although it is not possible to fully assemble heterochromatic Y chromosomes, Y-linked genes can nonetheless be assembled even if they are deeply buried within repetitive DNA, and this partial genomic data is very informative (Carvalho et al. 2000; Carvalho and Clark 2005; Koerich et al. 2008; Murtagh et al. 2012). In “whole genome shotgun” projects (WGS), which comprise the majority of recent genome projects, the euchromatic portion of chromosomes assemble into large and easily studied scaffolds, whereas heterochromatic regions are represented by thousands of small unmapped scaffolds (International Chicken Genome Sequencing Consortium 2004; Hoskins et al. 2007; Levy et al. 2007). Exons of heterochromatic genes and other islands of unique sequence are faithfully assembled but appear as isolated scaffolds because the repeat-laden introns and intergenic regions cannot be assembled. Further assembly fragmentation in the Y-chromosome is caused by its low coverage (compared to the autosomes) (Carvalho et al. 2003), a consequence of its hemizygosity. A major obstacle to the study of the Y chromosome is to identify among the many unmapped scaffolds those that are Y-linked. This has been done by a combination of computational methods that suggest candidates and a PCR test to confirm Y-linkage (Carvalho et al. 2000; Carvalho and Clark 2005; Koerich et al. 2008; see Chen et al. 2012 for W-linkage). The experimental verification is labor intensive when applied to hundreds of scaffolds but is necessary owing to the high rate of false positives of current computational methods. Nearly all known Drosophila Y-linked genes were identified using this approach (Carvalho et al. 2000; Carvalho and Clark 2005; Carvalho et al. 2009; Krsticevic et al. 2010). When technically feasible, Y-linked scaffolds can be identified by the preparation of separate male and female DNA libraries before WGS sequencing, as these scaffolds would contain only male reads (Krzywinski et al. 2004). This approach is not possible for the majority of the available genome sequences because they employed mixed-sex libraries (also, in mammals, sequencing of a single homogametic female is common practice).Here we show that Y chromosome sequences can be identified with a simple, efficient, and inexpensive method (Y chromosome Genome Scan or YGS) (Fig. 1) suitable for all genome projects that include the heterogametic sex, and apply it to Drosophila and humans.Open in a separate windowFigure 1.Outline of the YGS (Y chromosome Genome Scan) method. Y-linked sequences can be efficiently identified by a comparison of the assembled genome with inexpensive short-reads obtained from female DNA: The Y-linked sequences should get no match, whereas autosomal and X-linked sequences should be nearly completely matched. Efficient removal of all types of repetitive sequences is critical because they are shared between the Y chromosome and the female DNA, and was accomplished by a straight comparison of the short DNA words (k-mers) present in the assembled genome and female short-reads. We successfully applied the YGS method to two very different genomes, D. virilis and human.     

Use of a biotinylated DNA probe specific for the human Y chromosome for rapid antenatal sex determination

We have cloned a male-specific 3.4 kb human DNA sequence which showed only little crosshybridisation to autosomal sequences. To further enhance the specificity of the probe, we subcloned an internal TaqI-fragment resulting in clone pH343T33. This clone was used to determine the presence of Y-chromosomal sequences in DNA extracted from amniotic cells and from chorionic villi by Southern and dot hybridisation assays, respectively. Using this clone, we correctly predicted fetal sex in all of 148 cases analysed. To facilitate the use of this clone in clinical practice, we simplified the dot hybridisation procedure so that it can be performed in less than 48 h. The procedure with 32P-labeled DNA probes requires less than 0.5 mL of amniotic fluid; when biotinylated DNA probes are used, 3-5 mL of amniotic fluid usually suffice. We have used this probe in genetic counseling of families at risk for X-linked disorders.     

Ca3 fingerprinting of Candida albicans isolates from human immunodeficiency virus-positive and healthy individuals reveals a new clade in South Africa

To examine the question of strain specificity in oropharyngeal candidiasis associated with human immunodeficiency virus (HIV) infection, oral samples were collected from 1,196 HIV-positive black South Africans visiting three clinics and 249 Candida albicans isolates were selected for DNA fingerprinting with the complex DNA fingerprinting probe Ca3. A total of 66 C. albicans isolates from healthy black South Africans and 46 from healthy white South Africans were also DNA fingerprinted as controls. Using DENDRON software, a cluster analysis was performed and the identified groups were compared to a test set of isolates from the United States in which three genetic groups (I, II, and III) were previously identified by a variety of genetic fingerprinting methods. All of the characterized South African collections (three from HIV-positive black persons, two from healthy black persons, and one from healthy white persons) included group I, II, and III isolates. In addition, all South African collections included a fourth group (group SA) completely absent in the U.S. collection. The proportion of group SA isolates in HIV-positive and healthy black South Africans was 53% in both cases. The proportion in healthy white South Africans was 33%. In a comparison of HIV-positive patients with and without oropharyngeal symptoms of infection, the same proportions of group I, II, III, and SA isolates were obtained, indicating no shift to a particular group on infection. However, by virtue of its predominance as a commensal and in infections, group SA must be considered the most successful in South Africa. Why group SA isolates represent 53 and 33% of colonizing strains in black and white South Africans and are absent in the U.S. collection represents an interesting epidemiological question.