A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes

Background

Knowing the phase of marker genotype data can be useful in genome-wide association studies, because it makes it possible to use analysis frameworks that account for identity by descent or parent of origin of alleles and it can lead to a large increase in data quantities via genotype or sequence imputation. Long-range phasing and haplotype library imputation constitute a fast and accurate method to impute phase for SNP data.

Methods

A long-range phasing and haplotype library imputation algorithm was developed. It combines information from surrogate parents and long haplotypes to resolve phase in a manner that is not dependent on the family structure of a dataset or on the presence of pedigree information.

Results

The algorithm performed well in both simulated and real livestock and human datasets in terms of both phasing accuracy and computation efficiency. The percentage of alleles that could be phased in both simulated and real datasets of varying size generally exceeded 98% while the percentage of alleles incorrectly phased in simulated data was generally less than 0.5%. The accuracy of phasing was affected by dataset size, with lower accuracy for dataset sizes less than 1000, but was not affected by effective population size, family data structure, presence or absence of pedigree information, and SNP density. The method was computationally fast. In comparison to a commonly used statistical method (fastPHASE), the current method made about 8% less phasing mistakes and ran about 26 times faster for a small dataset. For larger datasets, the differences in computational time are expected to be even greater. A computer program implementing these methods has been made available.

Conclusions

The algorithm and software developed in this study make feasible the routine phasing of high-density SNP chips in large datasets.     

Imputation of missing genotypes from sparse to high density using long-range phasing

Related individuals share potentially long chromosome segments that trace to a common ancestor. We describe a phasing algorithm (ChromoPhase) that utilizes this characteristic of finite populations to phase large sections of a chromosome. In addition to phasing, our method imputes missing genotypes in individuals genotyped at lower marker density when more densely genotyped relatives are available. ChromoPhase uses a pedigree to collect an individual's (the proband) surrogate parents and offspring and uses genotypic similarity to identify its genomic surrogates. The algorithm then cycles through the relatives and genomic surrogates one at a time to find shared chromosome segments. Once a segment has been identified, any missing information in the proband is filled in with information from the relative. We tested ChromoPhase in a simulated population consisting of 400 individuals at a marker density of 1500/M, which is approximately equivalent to a 50K bovine single nucleotide polymorphism chip. In simulated data, 99.9% loci were correctly phased and, when imputing from 100 to 1500 markers, more than 87% of missing genotypes were correctly imputed. Performance increased when the number of generations available in the pedigree increased, but was reduced when the sparse genotype contained fewer loci. However, in simulated data, ChromoPhase correctly imputed at least 12% more genotypes than fastPHASE, depending on sparse marker density. We also tested the algorithm in a real Holstein cattle data set to impute 50K genotypes in animals with a sparse 3K genotype. In these data 92% of genotypes were correctly imputed in animals with a genotyped sire. We evaluated the accuracy of genomic predictions with the dense, sparse, and imputed simulated data sets and show that the reduction in genomic evaluation accuracy is modest even with imperfectly imputed genotype data. Our results demonstrate that imputation of missing genotypes, and potentially full genome sequence, using long-range phasing is feasible.     

Detection of recombination events,haplotype reconstruction and imputation of sires using half-sib SNP genotypes

Background

Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring’s sequence based on sequence data of the sire.

Methods

The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire’s genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R²) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs – AlphaPhase, BEAGLE and PedPhase 3.

Results

Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE.

Conclusions

In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).     

精子性染色体相关基因转录本及检测方法研究进展

精子形成过程中,基因表达经历了减数分裂性染色体失活,但有很多基因在减数分裂后期转录又重新被激活。转录产物研究表明,X和Y染色体特异基因在不同物种精子中都发生了不同程度的转录,并且对转录产物的研究方法也取得了巨大进展,产生了微阵列、SAGE及抑制消减杂交等先进的技术手段,随着这些技术的日益成熟和完善,通过深入研究,精子中性别相关基因转录表达调控机理将越来越清晰,并推动性别特异蛋白的研究取得更大进展。     

How to identify sex chromosomes and their turnover

Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non‐model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.     

Haploinsufficiency and the sex chromosomes from yeasts to humans

Background  

Haploinsufficient (HI) genes are those for which a reduction in copy number in a diploid from two to one results in significantly reduced fitness. Haploinsufficiency is increasingly implicated in human disease, and so predicting this phenotype could provide insights into the genetic mechanisms behind many human diseases, including some cancers.     

性染色体与精子功能研究进展

最新研究表明：Y染色体上男性特有序列(MSY)是一个包含不同DNA序列的嵌合体,包含多个回文序列。回文序列上经常发生臂间基因交换,使Y染色体具有自我保护能力。女性失活X染色体上有15%的基因逃离失活进行表达,可能在男女性别不同和女性个体间差异中起决定作用。精子在受精时,是一个综合运输体,不仅仅只向卵子转移DNA,还有RNA和蛋白质。     

Causes and consequences of reciprocal translocations on sex chromosomes

Under XY sex determination, the Y chromosome is only inherited via males, whereas the X chromosome is predominantly found in females. Thus, it is favourable when alleles with high male fitness become associated with the Y chromosome and when alleles with high female fitness become associated with the X chromosome. These favourable associations can be strengthened through linkage. Rearrangements, such as inversions and sex chromosome–autosome fusions, can increase linkage and thereby become favoured (Charlesworth, 2017). In a From the Cover article in this issue of Molecular Ecology, Toups, Rodrigues, Perrin, and Kirkpatrick (2019) present the first genomic analysis of a sex chromosome reciprocal translocation, a particularly dramatic chromosomal rearrangement that modifies linkage with the sex chromosome. As a result of reciprocal translocation, one studied population of the common frog (Rana temporaria, Figure 1) displays a remarkable sex‐determining system in which there are two physically unlinked sex chromosomes that are exclusively cotransmitted (Figure 2a).     

Sex from W to Z: evolution of vertebrate sex chromosomes and sex determining genes

Sex determination in major vertebrate groups appears to be very variable, including systems of male heterogamety, female heterogamety and a variety of genetic and environmental sex determining systems. Yet comparative studies of sex chromosomes and sex determining genes now suggest that these differences are more apparent than real. The sex chromosomes of even widely divergent groups now appear to have changed very little over the last 300+ million years, and even independently derived sex chromosomes seem to have followed the same set of evolutionary rules. The sex determining pathway seems to be extremely conserved, although the control of the genes in this pathway is vested in different elements. We present a scenario for the independent evolution of XY male heterogamety in mammals and ZW female heterogamety in birds and some reptiles. We suggest that sex determining genes can be made redundant, and replaced by control at another step of a conserved sex determining pathway, and how choice of a gene as a sex switch has led to the evolution of new sex chromosome systems. J. Exp. Zool. 290:449-462, 2001.     

Studies on the chromosomes and sex chromatin in the horse

This study provides accumulated data to assist the definition of karyotypes from normal and infertile horses. The normal karyotype of the horse (2n = 64) was characterized following Giemsa staining and C- banding, and 23% aneuploidy was found among chromosome counts of cells prepared from 44 clinically normal horses and 24 equine embryos. These expected variations in chromosome counts are especially important in the evaluation of potential mosaicism. Centromere staining was shown to be a valuable aid for the identification of specific chromosomes, in particular the sex chromosomes. Sex chromatin studies were applied to nerve tissue and polymorphonuclear neutrophils obtained from three horses. Distinctive sex chromatin bodies were detected in 70% of neurones from a normal mare. The sex chromatin was most frequently located adjacent to the nucleolus. Nuclear appendages ("drumsticks") were present in 4% of polymorphonuclear neutrophils from a normal mare. Small numbers of similar structures were noted in the neutrophils from each animal examined.     

Human and mouse amelogenin gene loci are on the sex chromosomes

Enamel is the outermost covering of teeth and is the hardest tissue in the vertebrate body. The enamel matrix is composed of enamelin and amelogenin classes of protein. We have determined the chromosomal locations for the human and mouse amelogenin (AMEL) loci using Southern blot analyses of DNA from human, mouse, or somatic cell hybrids by hybridization to a characterized mouse amelogenin cDNA. We have determined that human AMEL sequences are located on the distal short arm of the X chromosome in the p22.1----p22.3 region and near the centromere on the Y chromosome, possibly at the proximal long arm (Yq11) region. These chromosomal assignments are consistent with the hypothesis that perturbation of the amelogenin gene is involved in X-linked types of amelogenesis imperfecta, as well as with the Y-chromosomal locations for genes that participate in regulating tooth size and shape. Unlike the locus in humans, the mouse AMEL locus appears to be assigned solely to the X chromosome. Finally, together with the data on other X and Y chromosome sequences, these data for AMEL mapping support the notion of a pericentric inversion occurring in the human Y chromosome during primate evolution.     

Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing

Background

Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets.

Results

We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly.

Conclusion

Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0682-1) contains supplementary material, which is available to authorized users.     

Z and W chromosomes of chickens: studies on their gene functions in sex determination and sex differentiation

Since the discovery of SRY/SRY as a testis-determining gene on the mammalian Y chromosome in 1990, extensive studies have been carried out on the immediate target of SRY/SRY and genes functioning in the course of testis development. Comparative studies in non-mammalian vertebrates including birds have failed to find a gene equivalent to SRY/SRY, whereas they have suggested that most of the downstream factors found in mammals including SOX9 are also involved in the process of gonadal differentiation. Although a gene whose function is to trigger the cascade of gene expression toward gonadal differentiation has not been identified yet on either W or Z chromosomes of birds, a few interesting genes have been found recently on the sex chromosomes of chickens and their possible roles in sex determination or sex differentiation are being investigated. It is the purpose of this review to summarize the present knowledge of these sex chromosome-linked genes in chickens and to give perspectives and point out questions concerning the mechanisms of avian sex determination.     

Multiple satellite deoxyribonucleic acids in the calf and their relation to the sex chromosomes

Four distinct nuclear satellite DNAs from calf (Bos taurus) were isolated and the physical properties of native, single-stranded and renatured duplex molecules of each of the four satellite DNAs were studied by buoyant density-gradient centrifugation. These DNAs were localized in the calf nucleus and on calf metaphase chromosomes by in situ hybridization. In all cases, the calf satellite DNAs are preferentially situated at the centromeres of the autosomes, whereas the X and Y sex chromosomes contain little or none of the satellite DNAs. C-banding techniques showed constitutive heterochromatin at the centromeres of all the autosomes, but not on the X and Y chromosomes.Calf satellite 1 DNA (p = 1.716 g/ml) is at the centromeres of all of the autosomes. Although calf satellite II DNA (p = 1.722 g/ml) is the most widely dispersed over the karyotype, two-thirds of the grains were over the autosomal centromeres. Calf satellites III (p = 1.706 g/ml) and IV (p = 1.709 g/ml) are localized at the centromeres of most, but not all, of the autosomes. The four satellite DNAs each showed a strongly clumped distribution in interphase nuclei of both confluent and growing calf kidney cells in vitro.     

Genetic affinities of oceanic populations based on RFLP and haplotype analysis of genetic loci on three chromosomes.

Restriction fragment length polymorphisms at the renin and factor 13B loci located at chromosome 1q32-1q42 were studied in 14 ethnic groups in the west Pacific region. The allele frequencies were combined with previously described beta-globin and albumin-vitamin D binding protein haplotype frequencies and used to assess genetic affinities among eight major ethnic-geographic groups in this region. These population groups divide into two clusters with Australian Aborigines, Island Melanesians, and Highland Melanesians forming one cluster and east Asians, Southeast Asians, Micronesians, and Polynesians forming the other. The results indicate that Micronesians and Polynesians are derived from populations in Southeast Asia and that they originated independently of the Melanesian populations.