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The ability to sex individuals is an important component of many behavioural and ecological investigations and provides information for demographic models used in conservation and species management. However, many birds are difficult to sex using morphological characters or traditional molecular sexing methods. In this study, we developed probabilistic models for sexing birds using quantitative PCR (qPCR) data. First, we quantified distributions of gene copy numbers at a set of six sex‐linked genes, including the sex‐determining gene DMRT1, for individuals across 17 species and seven orders of birds (n = 150). Using these data, we built predictive logistic models for sex identification and tested their performance with independent samples from 51 species and 13 orders (n = 209). Models using the two loci most highly correlated with sex had greater accuracy than models using the full set of sex‐linked loci, across all taxonomic levels of analysis. Sex identification was highly accurate when individuals to be assigned were of species used in model building. Our analytical approach was widely applicable across diverse neognath bird lineages spanning millions of years of evolutionary divergence. Unlike previous methods, our probabilistic framework incorporates uncertainty around qPCR measurements as well as biological variation within species into decision‐making rules. We anticipate that this method will be useful for sexing birds, including those of high conservation concern and/or subsistence value, that have proven difficult to sex using traditional approaches. Additionally, the general analytical framework presented in this paper may also be applicable to other organisms with sex chromosomes. [ABSTRACT FROM AUTHOR]

In plant development, flowering is the most widely studied process. Floral forms show large diversity in different species due to simple variations in basic architecture. To determine the floral gene expression during the past decade, MADS-box genes have identified as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by various molecular technologies such as ChIP and next-generation DNA sequencing, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Likewise, the big data analysis revealed combined activity of transcriptional regulators and floral organ identity factors regulate the flower developmental programs. Thus, with the help of cutting-edge technologies like RNA-Sequencing, sex determination is now better understood in few non-model plants Therefore, the recent advances in next-generation sequencing (NGS) should enable researchers to identify the full range of floral gene functions, which will significantly help to understand plant development and evolution. This review summarizes the floral homeotic genes in model and non-model species to understand the flower development genes and dioecy evolution. [ABSTRACT FROM AUTHOR]

Abstract Background Incilaria (= Meghimatium) fruhstorferi is an air-breathing land slug found in restricted habitats of Japan, Taiwan and selected provinces of South Korea (Jeju, Chuncheon, Busan, and Deokjeokdo). The species is on a decline due to depletion of forest cover, predation by natural enemies, and collection. To facilitate the conservation of the species, it is important to decide on a number of traits related to growth, immunity and reproduction addressing fitness advantage of the species. Results The visceral mass transcriptome of I. fruhstorferi was enabled using the Illumina HiSeq 4000 sequencing platform. According to BUSCO (Benchmarking Universal Single-Copy Orthologs) method, the transcriptome was considered complete with 91.8% of ortholog genes present (Single: 70.7%; Duplicated: 21.1%). A total of 96.79% of the raw read sequences were processed as clean reads. TransDecoder identified 197,271 contigs that contained candidate-coding regions. Of a total of 50,230 unigenes, 34,470 (68.62% of the total unigenes) annotated to homologous proteins in the Protostome database (PANM-DB). The GO term and KEGG pathway analysis indicated genes involved in metabolism, phosphatidylinositol signalling system, aminobenzoate degradation, and T-cell receptor signalling pathway. Many genes associated with molluscan innate immunity were categorized under pathogen recognition receptor, TLR signalling pathway, MyD88 dependent pathway, endogenous ligands, immune effectors, antimicrobial peptides, apoptosis, and adaptation-related. The reproduction-associated unigenes showed homology to protein fem-1, spermatogenesis-associated protein, sperm associated antigen, and testis expressed sequences, among others. In addition, we identified key growth-related genes categorized under somatotrophic axis, muscle growth, chitinases and collagens. A total of 4822 Simple Sequence Repeats (SSRs) were also identified from the unigene sequences of I. fruhstorferi. Conclusions This is the first available genomic information for non-model land slug, I. fruhstorferi focusing on genes related to growth, immunity, and reproduction, with additional focus on microsatellites and repeating elements. The transcriptome provides access to greater number of traits of unknown relevance in the species that could be exploited for in-depth analyses of evolutionary plasticity and making informed choices during conservation planning. This would be appropriate for understanding the dynamics of the species on a priority basis considering the ecological, health, and social benefits.

Abstract Background S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences. Results Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway. Conclusions We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization.

The loss of recombination triggers divergence between the sex chromosomes and promotes degeneration of the sex-limited chromosome. Several livebearers within the genus Poecilia share a male-heterogametic sex chromosome system that is roughly 20 Myr old, with extreme variation in the degree of Y chromosome divergence. In Poecilia picta , the Y is highly degenerate and associated with complete X chromosome dosage compensation. In contrast, although recombination is restricted across almost the entire length of the sex chromosomes in Poecilia reticulata and Poecilia wingei , divergence between the X chromosome and the Y chromosome is very low. This clade therefore offers a unique opportunity to study the forces that accelerate or hinder sex chromosome divergence. We used RNA-seq data from multiple families of both P. reticulata and P. wingei , the species with low levels of sex chromosome divergence, to differentiate X and Y coding sequences based on sex-limited SNP inheritance. Phylogenetic tree analyses reveal that occasional recombination has persisted between the sex chromosomes for much of their length, as X- and Y-linked sequences cluster by species instead of by gametolog. This incomplete recombination suppression maintains the extensive homomorphy observed in these systems. In addition, we see differences between the previously identified strata in the phylogenetic clustering of X–Y orthologs, with those that cluster by chromosome located in the older stratum, the region previously associated with the sex-determining locus. However, recombination arrest appears to have expanded throughout the sex chromosomes more gradually instead of through a stepwise process associated with inversions. [ABSTRACT FROM AUTHOR]

In order to learn the sex determination and differentiation process in shrimp, we performed sex-specific transcriptome sequencing of the Zoea I larvae in Litopenaeus vannamei (L. vannamei) using a DNA/RNA co-extraction method. The sex-specific genes and the sex-linked SNPs were identified. De novo assembly of all the clean reads generated 41,270 unigenes with an average length of 1026 bp and an N50 of 1922 bp. A total of 60 differentially expressed genes (DEGs) between females and males at Zoea I stage were obtained, in which 41 unigenes had annotations. DEGs that might be related to sex development in L. vannamei were analyzed. Besides, paralogous genes of some known sex-related genes in model organisms such as sex-lethal (Sxl) showed no sex-biased difference, which indicated they may not play roles in sex development at Zoea I stage. Candidate sex-linked SNPs were validated in six populations of L. vannamei, and SNPs in Unigene0020898 and Unigene0020336 were fully linked to genders, suggesting the two genes located in the sex-determining region of L. vannamei. Our report provided the sex-specific gene expression in early developmental stage of L. vannamei, and found some sex-biased genes that may participate in the sex development process. We also detected two sex-linked genes which may be located in the sex determination region of L. vannamei through bulked segregant analysis, and the SNPs on these genes also provided a method for genetic sex identification at transcriptional level. Our findings will facilitate further researches on molecular mechanism of sex determination and differentiation in shrimps. [ABSTRACT FROM AUTHOR]

Background: S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over time resulting in the formation of evolutionary strata. Non-recombination and later accumulation of repetitive sequences is a putative cause of the size increase in the Y chromosome. Gene decay and accumulation of repetitive DNA are identified as key evolutionary events. Transposons in the X and Y chromosomes are distributed differently and there is a regulation of transposon insertion by DNA methylation of the target sequences, this points to an important role of DNA methylation during sex chromosome evolution in Silene latifolia. The aim of this study was to elucidate whether the reduced expression of the Y allele in S. latifolia is caused by genetic degeneration or if the cause is methylation triggered by transposons and repetitive sequences. Results: Gene expression analysis in S. latifolia males has shown expression bias in both X and Y alleles. To determine whether these differences are caused by genetic degeneration or methylation spread by transposons and repetitive sequences, we selected several sex-linked genes with varying degrees of degeneration and from different evolutionary strata. Immunoprecipitation of methylated DNA (MeDIP) from promoter, exon and intron regions was used and validated through bisulfite sequencing. We found DNA methylation in males, and only in the promoter of genes of stratum I (older). The Y alleles in genes of stratum I were methylation enriched compared to X alleles. There was also abundant and high percentage methylation in the CHH context in most sequences, indicating de novo methylation through the RdDM pathway. Conclusions: We speculate that TE accumulation and not gene decay is the cause of DNA methylation in the S. latifolia Y sex chromosome with influence on the process of heterochromatinization. [ABSTRACT FROM AUTHOR]

We propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either because they require a reference genome, or because they are designed for evolutionarily old systems. Sequencing a cross (parents and progeny) by RNA-seq to study the segregation of alleles and infer sexlinked genes is a cost-efficient strategy, which also provides expression level estimates. However, the lack of a proper statistical framework has limited a broader application of this approach. Testsonempirical Silene data show that our method identifies 20-35% more sex-linked genes than existing pipelines, while making reliable inferences for downstream analyses. Approximately 12 individuals are needed for optimal results based on simulations. For species with an unknown sex-determination system, the method can assess the presence and type (XY vs. ZW) of sex chromosomes through a model comparison strategy. The method is particularly well optimized for sex chromosomes of young or intermediate age, which are expected in thousands of yet unstudied lineages. Any organisms, including non-model ones for which nothing is known a priori, that can be bred in the lab, are suitable for our method. SEX-DETector and its implementation in a Galaxy workflow are made freely available. [ABSTRACT FROM AUTHOR]

Background: Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes. Results: Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30% of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome. Conclusions: Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30%, higher than previous estimates of 10-20%. [ABSTRACT FROM AUTHOR]

Background The pathogenesis of cardiovascular (CV) mortality, whose rate is increased in type 2 diabetes, is poorly understood. While high serum adiponectin is associated with increased CV mortality in the general population, no data are available in type 2 diabetes. We here investigated whether this counterintuitive association was observable also in diabetic patients and whether it was sex-specific. Methods Three prospective cohorts were analyzed: 1) Gargano Heart Study (GHS; 359 patients, 58 events/1,934 person-years; py); 2) Health Professional Follow-up Study (HPFS; 833 men, 146 events/10,024 py); 3) Nurses' Health Study (NHS; 902 women, 144 events/15,074 py). Results In GHS serum adiponectin predicted CV mortality in men (hazard ratio, HR, and 95% CI per standard deviation, SD, increment = 1.54, 1.19-2.01), but not women (HR = 0.98, 0.48-2.01). Circulating adiponectin predicted CV mortality in men from HPFS (HR = 1.44, 1.21-1.72), but not in women from NHS (HR = 1.08, 0.86-1.35), used as replication samples. In a pooled analysis, HRs were 1.47 (1.27-1.70) in 1,075 men and 1.07 (0.86-1.33) in 1,019 women (p for HRs heterogeneity across sexes = 0.018). Conclusions This is the first report showing that high circulating adiponectin predicts increased CV mortality in men, but not in women with type 2 diabetes. Further studies are necessary to unravel the mechanisms through which adiponectin influences CV mortality in a sex-specific manner. [ABSTRACT FROM AUTHOR]

OBJECTIVE: To evaluate whether differences between pediatric male and female mortality are due to differences in specific age ranges, specific disease categories, or differences in the risk of developing specific conditions versus the risk of dying once having developed the condition. METHODS: Using 1999-2008 mortality data for all deaths of individuals <20 years of age from the Centers for Disease Control and Prevention's WONDER database, we calculated male-to-female relative risks (RRs), standardized to the 2000 US Census, by age and International Classification of Diseases, 10th revision (ICD-10), chapters. By using the Centers for Disease Control and Prevention's record of linked birth and infant death records between 1999 and 2007, we also calculated male-to-female RRs stratified by gestational age; and by using Surveillance, Epidemiology, and End Results cancer registries for 1999-2008, we calculated incidence and mortality RRs for the 7 leading types of cancer. RESULTS: Males experience higher mortality rates in all age groups from birth to age 20 years (RR: 1.44; 95% confidence interval [CI]: 1.44-1.45) and among infant deaths in nearly all weekly gestational age strata (RR: 1.12; 95% CI: 1.11-1.12). Stratified by ICD-10 major disease categories, males experience higher mortality rates in 17 of 19 categories. For the 7 types of pediatric cancers, the overall pattern was similarly greater male incidence (RR: 1.13; 95% CI: 1.12-1.14), fatality rate (RR: 1.10; 95% CI: 1.07-1.13), and overall mortality (RR: 1.21; 1.18-1.25). CONCLUSIONS: Under 20 years of age, males die more than females from a wide array of underlying conditions. The potential genetic and hormonal mechanisms for the mortality difference between males and females warrant investigation. [ABSTRACT FROM AUTHOR]

For haplotype analysis of the X chromosome, haplotype-sharing (HS) statistics with sliding windows are defined for males and females separately, which are then combined to a single HS test for the X chromosome. When independent replication samples are not available, the training-testing sets approach is used to validate this procedure and a permutation method is used to obtain its P-value. We applied this method to the X chromosome (with 1804 SNPs) for age-related macular degeneration (AMD). We found a window of five SNPs over a 272 kb region associated with AMD after Bonferroni correction. An examination of the odds ratio and the population attributable risks revealed a disease-preventive haplotype, ATGAC, on these five SNPs. For elderly females without this haplotype, the likelihood of AMD is increased by a factor of 4.75 with a 95% confidence interval (1.43, 15.82). The frequency of ATGAC in HapMap CEU is 0.276. These five SNPs are covered by the gene DIAPH2, which is known to cause premature ovarian failure (POF) in females. Our results indicated that DIAPH2 may be a polygenic pleiotropy for POF and AMD. [ABSTRACT FROM AUTHOR]

Thirty-three male canaries were reared as isolates in acoustic chambers. Each male's sexchromosomes and autosomal background were known to strain. The research included two experiments. One tested the hypothesis that the low-pitched songs of waterslager canaries is due to a partial hearing deficit in the high frequency range of their hearing, limiting learning high-pitched syllables. That hypothesis was falsified and the apparent cause for the low-pitched songs was uncovered in the second experiment. That experiment tutored the males with a tutor tape that offered six different canary songs to learn from. The experimental subjects included roller, waterslager, and border canaries, their hybrids and backcrosses. The selective learning of each genetically different group was closely associated with their specific genetic background, and the results revealed that roller and waterslager canaries have very different genetic mechanisms affecting their song learning, and that a waterslager, recessive, autosomal factor, when homozygous, was associated with that strain's low-pitched songs. On the other hand, the low-pitched songs of roller canaries were primarily affected by a recessive sex-linked factor. Border canary selective learning was biased toward learning the higher-pitched syllables and tours characteristic of the songs of border and other type canary strains. [ABSTRACT FROM AUTHOR]

The objective of this work was to identify papaya hermaphrodite plants of the hybrid "Pococí" at the seedling stage using the Polymerase Chain Reaction (PCR). Sex identification was achieved according to the methodology described by Deputy et al. (2002) with some modifications. This methodology employs a multiplex- PCR assay that allows simultaneous amplification of two fragments (800 bp and 1300 respectively) for hermaphrodite plants and one fragment (1300 bp) for female plants. Genomic DNA was extracted from leaves and two extraction protocols were evaluated, CTAB and rapid alkalinelysis (NaOH). The amplification reaction yielded the expected size of the fragments with both methods of DNA extraction. PCR sex determination of 1500 seedlings yielded 46 % of hermaphrodite and 54 % of female plants. The female: hermaphrodite plant ratio observed did not vary from the expected (1:1) ratio according to the chi-square test (p = 0.4237). Hermaphrodite plants were planted in the field in San Carlos region, Costa Rica, and sex was determined at flowering. The correspondence between the PCR sexed plants and sexual expression in the field was 98 %. [ABSTRACT FROM AUTHOR]

It is commonly believed that the rate of mutation is much higher in males than in females because the number of germ-cell divisions per generation is much larger in males than in females. However, the precise magnitude of the male-to-female mutation rate ratio (α) remains unknown. Recently there have been efforts to estimate α by using DNA sequence data from different species. We have studied the potential problems in such an approach. We found that the rate of synonymous substitution varies about fivefold among X-linked genes, as large as the variation among autosomal genes. This large variation makes the assumption of selective neutrality of synonymous changes dubious, so one should be cautious in using the synonymous rates in X-linked and autosomal genes to estimate α. A similar difficulty was also observed in using nonhomologous intron sequences to estimate α. Contrary to the expectation that X-linked sequences should evolve more slowly than autosomal sequences, the Alu repeat in the last intron of the X-linked zinc finger gene has evolved faster than the four autosomal Alu repeats used in this study. It appears that the best way to estimate α is to use homologous sequences. However, such sequences may be involved in gene conversion events. In fact, we found evidence that the Y-linked and X-linked zinc finger genes have been involved in multiple conversion events during primate evolution. Thus, the possibility of gene conversion should be considered when using homologous sequences to estimate α. [ABSTRACT FROM AUTHOR]

Genetic analysis of mME variants (mitochondrial malic enzyme, E.C. 1.1.1.40) in Xenopus laevis revealed sex linkage of the mMe locus and indicated a WZ/ZZ type of sex determination. Codominant mMe alleles occur on both W and Z chromosomes, with a recombination frequency of 6.1%±1.5% between mMe and the sex-determining locus (or region). [ABSTRACT FROM AUTHOR]

Sex chromosomes and sex-linked genes usually show unusual features comparing to the rest of the genome and thus are of particular interests to evolutionary and developmental biologists. Here we describe recently developed bioinformatic methods for identifying sex-linked sequences, in a genome without priori linkage information. Some are developed during our course of studying avian genomes. These methods require sequence data, either assembled draft genome or raw sequences derived from the heterogametic sex (e.g., a female bird or a male mammal). Their application is not restricted to birds but can be used for any species with a sex chromosome pair that has diverged from each other for a substantial degree.

A general model describing the evolution of genotypic frequencies at a heterosomal locus with n alleles is introduced. The treatment includes as a special case the standard derivation for X-linked loci as well as different concepts encountered in the literature which seem to contradict this derivation. The disagreement, however, is easily solved by distinguishing between gene and gametic frequencies. [ABSTRACT FROM AUTHOR]