Non-invasive genetic sexing technique for analysis of short-beaked echidna (Tachyglossus aculeatus) populations

2019 ◽  
Vol 31 (7) ◽  
pp. 1289
Author(s):  
Tahlia Perry ◽  
Deborah Toledo-Flores ◽  
Wan X. Kang ◽  
Arthur Ferguson ◽  
Belinda Laming ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
External Genitalia ◽  
Hair Follicles ◽  
Wild Populations ◽  
Genetic Sexing ◽  
Captive Management ◽  
Non Invasive ◽  
Polymerase Chain ◽  
Male Specific

Identifying male and female echidnas is challenging due to the lack of external genitalia or any other differing morphological features. This limits studies of wild populations and is a major problem for echidna captive management and breeding. Non-invasive genetic approaches to determine sex minimise the need for handling animals and are used extensively in other mammals. However, currently available approaches cannot be applied to monotremes because their sex chromosomes share no homology with sex chromosomes in other mammals. In this study we used recently identified X and Y chromosome-specific sequences to establish a non-invasive polymerase chain reaction-based technique to determine the sex of echidnas. Genomic DNA was extracted from echidna hair follicles followed by amplification of two Y chromosome (male-specific) genes (mediator complex subunit 26 Y-gametolog (CRSPY) and anti-Müllerian hormone Y-gametolog (AMHY)) and the X chromosome gene (anti-Müllerian hormone X-gametolog (AMHX)). Using this technique, we identified the sex of 10 juvenile echidnas born at Perth Zoo, revealing that eight of the 10 echidnas were female. Future use of the genetic sexing technique in echidnas will inform captive management, continue breeding success and can be used to investigate sex ratios and population dynamics in wild populations.

scholarly journals The Size and Content of the Sex-Determining Region of the Y Chromosome in Dioecious Mercurialis annua, a Plant with Homomorphic Sex Chromosomes

2018 ◽  
Author(s):  
Paris Veltsos ◽  
Guillaume Cossard ◽  
Emmanuel Beaudoing ◽  
Genséric Beydon ◽  
Camille Roux ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sequence Length ◽  
Bacterial Artificial Chromosomes ◽  
Dioecious Plants ◽  
Artificial Chromosomes ◽  
Males And Females ◽  
Male Specific ◽  
Y Chromosome Degeneration ◽  
Mercurialis Annua

Many dioecious plants have sex chromosomes that are cytologically heteromorphic, but about half of species lack cytological differences between males and females and are thus homomorphic. Very little is known about the size and content of the non-recombining sex-determining region (SDR) in these species. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, which has homomorphic sex chromosomes and shows signatures of mild Y-chromosome degeneration. We used RNAseq to identify new Y-linked markers for M. annua. Twelve of 24 transcripts with male-specific and male-biased expression could only be PCR-amplified from males and are thus Y-linked. We found a further six Y-linked sequences that were present in males but not females using genome capture data from multiple populations. We used the Y-linked sequences to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequence, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests it is enriched for repeats, has a low gene density and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which is estimated to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, especially given the small genome size of M. annua. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.

scholarly journals Isolation of X and Y Chromosome-Specific DNA Markers From a Liverwort, Marchantia polymorpha, by Representational Difference Analysis

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 981-985
Author(s):  
Masaki Fujisawa ◽  
Kiwako Hayashi ◽  
Tomohisa Nishio ◽  
Tomoyuki Bando ◽  
Sachiko Okada ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Dna Markers ◽  
Representational Difference Analysis ◽  
Marchantia Polymorpha ◽  
Dna Fragments ◽  
Difference Analysis ◽  
Y Chromosomes ◽  
Female Specific ◽  
Male Specific

Abstract The liverwort Marchantia polymorpha has X and Y chromosomes in the respective female and male haploids. Here we report the successful exploitation of representational difference analyses to isolate DNA markers for the sex chromosomes. Two female-specific and six male-specific DNA fragments were genetically confirmed to originate from the X and Y chromosomes, respectively.

scholarly journals Sex-determination and sex chromosomes are shared across the radiation of dioecious Nepenthes pitcher plants

2017 ◽  
Author(s):  
Mathias Scharmann ◽  
T. Ulmar Grafe ◽  
Faizah Metali ◽  
Alex Widmer
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
High Throughput Sequencing ◽  
Silene Latifolia ◽  
Wild Populations ◽  
Sequencing Data ◽  
Pitcher Plants ◽  
Determination System ◽  
Sex Determination System ◽  
Male Specific

AbstractPlants with separate sexes (dioecy) represent a minority but dioecy has evolved multiple times independently in plants. Our understanding of sex determination systems in plants and of the ecological factors and molecular changes associated with the evolution of dioecy remain limited. Here, we study the sex-determination system in dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: Nepenthes pitcher plants. We genotyped wild populations of flowering males and females of three Nepenthes taxa using ddRAD-seq, and sequenced a male inflorescence transcriptome. We developed a novel statistical tool (privacy rarefaction) to distinguish true sex-specificity from stochastic noise in high-throughput sequencing data. Our results support XY-systems in all three Nepenthes taxa and in Silene latifolia which was used as a positive control for its known XY-system. The male-specific region of the Y chromosome showed little conservation among the three Nepenthes taxa, except for the essential pollen development gene DYT1 which was also male-specific in additional taxa. Hence, this homomorphic XY sex-determination system likely has a unique origin older than the crown of the genus Nepenthes at c. 17.7 My. In addition to the characterisation of the previously unknown sex chromosomes of Nepenthes, our work contributes an innovative, highly sensitive statistical method to efficiently detect sex-specific genomic regions in wild populations in general.

scholarly journals Divergence and Remarkable Diversity of the Y Chromosome in Guppies

2020 ◽  
Author(s):  
Pedro Almeida ◽  
Benjamin A Sandkam ◽  
Jake Morris ◽  
Iulia Darolti ◽  
Felix Breden ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Color Variation ◽  
Recombination Suppression ◽  
Specific Sequence ◽  
Y Chromosome Evolution ◽  
Male Specific

Abstract The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.

scholarly journals Divergence and Remarkable Diversity of the Y Chromosome in Guppies

2020 ◽  
Author(s):  
Pedro Almeida ◽  
Benjamin A. Sandkam ◽  
Jake Morris ◽  
Iulia Darolti ◽  
Felix Breden ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Haplotype Diversity ◽  
Low Frequency ◽  
Recombination Suppression ◽  
Specific Sequence ◽  
Y Chromosome Evolution ◽  
Male Specific ◽  
Genome Assemblies

AbstractThe guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared to their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female-preference for rare Y-linked colour variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.

scholarly journals Reconstruction of the birth of a male sex chromosome present in Atlantic herring

2020 ◽  
Vol 117 (39) ◽  
pp. 24359-24368
Author(s):  
Nima Rafati ◽  
Junfeng Chen ◽  
Amaury Herpin ◽  
Mats E. Pettersson ◽  
Fan Han ◽  
...  
Keyword(s):  
Sex Determination ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Small Region ◽  
Atlantic Herring ◽  
Genes Encoding ◽  
Molecular Machinery ◽  
Suppressed Recombination ◽  
Male Specific

The mechanisms underlying sex determination are astonishingly plastic. Particularly the triggers for the molecular machinery, which recalls either the male or female developmental program, are highly variable and have evolved independently and repeatedly. Fish show a huge variety of sex determination systems, including both genetic and environmental triggers. The advent of sex chromosomes is assumed to stabilize genetic sex determination. However, because sex chromosomes are notoriously cluttered with repetitive DNA and pseudogenes, the study of their evolution is hampered. Here we reconstruct the birth of a Y chromosome present in the Atlantic herring. The region is tiny (230 kb) and contains only three intact genes. The candidate male-determining gene BMPR1BBY encodes a truncated form of a BMP1B receptor, which originated by gene duplication and translocation and underwent rapid protein evolution. BMPR1BBY phosphorylates SMADs in the absence of ligand and thus has the potential to induce testis formation. The Y region also contains two genes encoding subunits of the sperm-specific Ca2+ channel CatSper required for male fertility. The herring Y chromosome conforms with a characteristic feature of many sex chromosomes, namely, suppressed recombination between a sex-determining factor and genes that are beneficial for the given sex. However, the herring Y differs from other sex chromosomes in that suppression of recombination is restricted to an ∼500-kb region harboring the male-specific and sex-associated regions. As a consequence, any degeneration on the herring Y chromosome is restricted to those genes located in the small region affected by suppressed recombination.

scholarly journals Epigenetics drive the evolution of sex chromosomes in animals and plants

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Aline Muyle ◽  
Doris Bachtrog ◽  
Gabriel A. B. Marais ◽  
James M. A. Turner
Keyword(s):  
Transposable Elements ◽  
Y Chromosome ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Binding Motif ◽  
X Chromosomes ◽  
Meiotic Sex Chromosome Inactivation ◽  
Compensation Mechanisms ◽  
Male Specific Lethal ◽  
Male Specific

We review how epigenetics affect sex chromosome evolution in animals and plants. In a few species, sex is determined epigenetically through the action of Y-encoded small RNAs. Epigenetics is also responsible for changing the sex of individuals through time, even in species that carry sex chromosomes, and could favour species adaptation through breeding system plasticity. The Y chromosome accumulates repeats that become epigenetically silenced which leads to an epigenetic conflict with the expression of Y genes and could accelerate Y degeneration. Y heterochromatin can be lost through ageing, which activates transposable elements and lowers male longevity. Y chromosome degeneration has led to the evolution of meiotic sex chromosome inactivation in eutherians (placentals) and marsupials, and dosage compensation mechanisms in animals and plants. X-inactivation convergently evolved in eutherians and marsupials via two independently evolved non-coding RNAs. In Drosophila , male X upregulation by the male specific lethal (MSL) complex can spread to neo-X chromosomes through the transposition of transposable elements that carry an MSL-binding motif. We discuss similarities and possible differences between plants and animals and suggest future directions for this dynamic field of research. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

Three plasma-based microRNAs as potent diagnostic biomarkers for endometrial cancer

2021 ◽  
pp. 1-12
Author(s):  
Xingchen Fan ◽  
Minmin Cao ◽  
Cheng Liu ◽  
Cheng Zhang ◽  
Chunyu Li ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Operating Characteristic ◽  
Characteristic Curve ◽  
External Validation ◽  
Diagnostic Value ◽  
Diagnostic Biomarkers ◽  
Non Invasive ◽  
Polymerase Chain ◽  
Public Datasets ◽  
Plasma Mirnas

BACKGROUND: MicroRNAs (miRNAs), with noticeable stability and unique expression pattern in plasma of patients with various diseases, are powerful non-invasive biomarkers for cancer detection including endometrial cancer (EC). OBJECTIVE: The objective of this study was to identify promising miRNA biomarkers in plasma to assist the clinical screening of EC. METHODS: A total of 93 EC and 79 normal control (NC) plasma samples were analyzed using Quantitative Real-time Polymerase Chain Reaction (qRT-PCR) in this four-stage experiment. The receiver operating characteristic curve (ROC) analysis was conducted to evaluate the diagnostic value. Additionally, the expression features of the identified miRNAs were further explored in tissues and plasma exosomes samples. RESULTS: The expression of miR-142-3p, miR-146a-5p, and miR-151a-5p was significantly overexpressed in the plasma of EC patients compared with NCs. Areas under the ROC curve of the 3-miRNA signature were 0.729, 0.751, and 0.789 for the training, testing, and external validation phases, respectively. The diagnostic performance of the identified signature proved to be stable in the three public datasets and superior to the other miRNA biomarkers in EC diagnosis. Moreover, the expression of miR-151a-5p was significantly elevated in EC plasma exosomes. CONCLUSIONS: A signature consisting of 3 plasma miRNAs was identified and showed potential for the non-invasive diagnosis of EC.

scholarly journals PCR vs karyotype for CVS and amniocentesis—the experience at one tertiary fetal medicine unit

2021 ◽  
Author(s):  
Catherine Finnegan ◽  
Suzanne Smyth ◽  
Orla Smith ◽  
Karen Flood ◽  
Jane Dalrymple ◽  
...  
Keyword(s):  
Sex Chromosome ◽  
Pregnancy Termination ◽  
Normal Pregnancy ◽  
Screening Tests ◽  
Fetal Medicine ◽  
Non Invasive ◽  
Fetal Aneuploidy ◽  
Polymerase Chain ◽  
Normal Ultrasound ◽  
Fetal Karyotype

Abstract Purpose Despite the rise of non-invasive screening tests for fetal aneuploidy, invasive testing during pregnancy remains the definitive diagnostic tool for fetal genetic anomalies. Results are rapidly available with polymerase chain reaction (PCR) tests, but cases have been reported whereby initial results were not confirmed after pregnancy termination and the fetal karyotype was ultimately normal. We sought to examine the potential discordance between PCR and karyotype for fetal aneuploidy. Methods The results from all amniocentesis and CVS tests performed over a 6-year period in a large tertiary level fetal medicine unit were reviewed. The results of PCR and karyotype were recorded and discrepancies examined. Pregnancy outcomes were also recorded. Results A total of 1222 invasive tests were performed (716 amniocentesis and 506 CVS). Within the cohort having amniocentesis, 11 had discrepant results (normal QF-PCR result but with a subsequent abnormal karyotype). There was 1 case among this group which QF-PCR should have identified. Within the CVS group, 7 patients had discrepant results. All had a diploid QF-PCR and would not have been identified as abnormal by it. Conclusion PCR can be reliably used to determine aneuploidy of chromosomes 13, 18, and 21. However, in cases of sex chromosome aneuploidy, its performance is less reliable and warrants waiting for a complete karyotype. Given such discordance, we advise waiting for karyotype for all invasive tests performed in the presence of a normal ultrasound before advising a patient of a diploid QF-PCR result or potentially terminating a normal pregnancy.

scholarly journals Genetic analysis of medfly populations in an area of sterile insect technique applications

2021 ◽  
Author(s):  
Rubén Sancho ◽  
Ana Guillem-Amat ◽  
Elena López-Errasquín ◽  
Lucas Sánchez ◽  
Félix Ortego ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Sterile Insect Technique ◽  
Ceratitis Capitata ◽  
Natural Populations ◽  
Low Frequency ◽  
Fruit Fly ◽  
Wild Populations ◽  
Genetic Sexing ◽  
Environmental Implications ◽  
Genetic Sexing Strains

AbstractThe sterile insect technique (SIT) is widely used in integrated pest management programs for the control of the Mediterranean fruit fly (medfly), Ceratitis capitata. The genetic interactions between the released individuals from the genetic sexing strains (GSS), used for SIT applications worldwide, and wild individuals have not been studied. Under the hypothesis that a number of Vienna GSS individuals released to the field might not be completely sterile and may produce viable offspring, we have analyzed medfly Spanish field populations to evaluate the presence of Vienna strain genetic markers. To this goal, we have used contrasted nuclear and mitochondrial genetic markers, and two novel sets of nuclear polymorphisms with the potential to be markers to discriminate between Vienna and wild individuals. Nuclear Vienna markers located on the 5th chromosome of Vienna males have been found in 2.2% (19 from 875) of the Spanish wild medfly females captured at the area where SIT is applied. In addition, a female-inherited mitochondrial Vienna marker has been found in two from the 19 females showing nuclear Vienna markers. The detection of several of these markers in single individuals represents evidence of the introgression of Vienna strain into natural populations. However, alternative explanations as their presence at low frequency in wild populations in the studied areas cannot be fully discarded. The undesired release of non-fully sterile irradiated GSS individuals into the field and their interactions with wild flies, and the potential environmental implications should be taken into account in the application of the SIT.

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