scholarly journals Plant genera Cannabis and Humulus share the same pair of well-differentiated sex chromosomes

2021 ◽  
Author(s):  
D Prentout ◽  
N Stajner ◽  
A Cerenak ◽  
T Tricou ◽  
C Brochier-Armanet ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Cannabis Sativa ◽  
Sex Chromosome ◽  
Probabilistic Method ◽  
List Type ◽  
Recombination Suppression ◽  
Sex Chromosome System ◽  
The Common ◽  
Well Differentiated ◽  
First Time

SummaryWe recently described, in Cannabis sativa, the oldest sex chromosome system documented so far in plants. Based on our estimate of its age, we predicted that it should be shared by its sister genus Humulus, which is known to also possess XY sex chromosomes.Here, we used transcriptome sequencing of a F1 family of Humulus lupulus to identify and study the sex chromosomes in this species using the probabilistic method SEX-DETector.We identified 265 sex-linked genes in H. lupulus, located on the chromosome that is also the C. sativa sex chromosome pair. Using phylogenies of sex-linked genes, we show that a region of these chromosomes had already stopped recombining in the common ancestor of the two species. Furthermore, as in C. sativa, Y gene expression was reduced in correlation to the position on the X chromosome, and strongly Y degenerated genes showed dosage compensation.Here we report, for the first time in the Angiosperms, a sex chromosome system that is shared by two different genera. Recombination suppression started at least 21-25 My ago, and then (either gradually or step-wise) spread to a large part of the sex chromosomes, leading to a strongly degenerated Y.

scholarly journals A high-throughput segregation analysis identifies the sex chromosomes of Cannabis sativa

2019 ◽  
Author(s):  
Djivan Prentout ◽  
Olga Razumova ◽  
Bénédicte Rhoné ◽  
Hélène Badouin ◽  
Hélène Henri ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Segregation Analysis ◽  
Cannabis Sativa ◽  
Sex Chromosome ◽  
Probabilistic Method ◽  
Female Offspring ◽  
Single Chromosome ◽  
Sex Chromosome System ◽  
Plant Sex Chromosomes ◽  
Plant Sex

AbstractCannabis sativa-derived tetrahydrocannabinol (THC) production is increasing very fast worldwide. C. sativa is a dioecious plant with XY chromosomes, and only females (XX) are useful for THC production. The C. sativa sex chromosomes sequence would improve early sexing and better management of this crop; however, the C. sativa genome projects failed to identify the sex chromosomes so far. Moreover, dioecy in the Cannabaceae family is ancestral, C. sativa sex chromosomes are potentially old and thus very interesting to study as little is known about the last steps of sex chromosome evolution in plants. Here we RNA-sequenced a C. sativa family (2 parents and 10 male and female offspring) and performed a segregation analysis for all C. sativa genes using the probabilistic method SEX-DETector. We identified >500 sex-linked genes. Mapping of these sex-linked genes to a C. sativa genome assembly identified a single chromosome pair with a large non-recombining region. Further analysis of the >500 sex-linked genes revealed that C. sativa has a strongly degenerated Y chromosome and represents the oldest plant sex chromosome system documented so far. Our study revealed that old plant sex chromosomes can have large non-recombining regions and be very differentiated and still be of similar size (homomorphic).

scholarly journals Homomorphic ZW chromosomes 1 in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region

2015 ◽  
Author(s):  
Jacob A Tennessen ◽  
Rajanikanth Govindarajulu ◽  
Aaron Liston ◽  
Tia-Lynn Ashman
Keyword(s):  
Sex Chromosomes ◽  
Recombination Rate ◽  
Sex Chromosome ◽  
Pseudoautosomal Region ◽  
List Type ◽  
Recombination Suppression ◽  
Female Function ◽  
Wild Strawberry ◽  
Plant Sex Chromosomes ◽  
Recombination Dynamics

SummaryRecombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes.We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome.The SDR of this ZW system is located within a 280kb window, in which the maternal recombination rate is lower than the paternal. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex.Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.

scholarly journals Guppy Y Chromosome Integrity Maintained by Incomplete Recombination Suppression

2020 ◽  
Vol 12 (6) ◽  
pp. 965-977 ◽  
Author(s):  
Iulia Darolti ◽  
Alison E Wright ◽  
Judith E Mank
Keyword(s):  
Y Chromosome ◽  
X Chromosome ◽  
Sex Chromosomes ◽  
Poecilia Reticulata ◽  
Sex Chromosome ◽  
Rna Seq ◽  
Recombination Suppression ◽  
Sex Chromosome System ◽  
Chromosome Integrity ◽  
Heterogametic Sex

Abstract 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.

Great Abundance of Satellite DNA in Proceratophrys (Anura, Odontophrynidae) Revealed by Genome Sequencing

2020 ◽  
Vol 160 (3) ◽  
pp. 141-147 ◽  
Author(s):  
Marcelo J. da Silva ◽  
Raquel Fogarin Destro ◽  
Thiago Gazoni ◽  
Hideki Narimatsu ◽  
Paulo S. Pereira dos Santos ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Satellite Dna ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Centromere Function ◽  
Sex Chromosome System ◽  
First Time ◽  
Eukaryotic Genomes

Most eukaryotic genomes contain substantial portions of repetitive DNA sequences. These are located primarily in highly compacted heterochromatin and, in many cases, are one of the most abundant components of the sex chromosomes. In this sense, the anuran Proceratophrys boiei represents an interesting model for analyses on repetitive sequences by means of cytogenetic techniques, since it has a karyotype with large blocks of heterochromatin and a ZZ/ZW sex chromosome system. The present study describes, for the first time, families of satellite DNA (satDNA) in the frog P. boiei. Its genome size was estimated at 1.6 Gb, of which 41% correspond to repetitive sequences, including satDNAs, rDNAs, transposable elements, and other elements characterized as non-repetitive. The satDNAs were mapped by FISH in the centromeric and pericentromeric regions of all chromosomes, suggesting a possible involvement of these sequences in centromere function. SatDNAs are also present in the W sex chromosome, occupying the entire heterochromatic area, indicating a probable contribution of this class of repetitive DNA to the differentiation of the sex chromosomes in this species. This study is a valuable contribution to the existing knowledge on repetitive sequences in amphibians. We show the presence of repetitive DNAs, especially satDNAs, in the genome of P. boiei that might be of relevance in genome organization and regulation, setting the stage for a deeper functional genome analysis of Proceratophrys.

scholarly journals Detecting sex-linked genes using genotyped individuals sampled in natural populations

Genetics ◽  
2021 ◽  
Author(s):  
Jos Käfer ◽  
Nicolas Lartillot ◽  
Gabriel A B Marais ◽  
Franck Picard
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Natural Populations ◽  
Simulated Data ◽  
Statistical Testing ◽  
Silene Latifolia ◽  
Recombination Suppression ◽  
Genotype Frequencies ◽  
Sex Chromosome System ◽  
Different Sources

Abstract We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans), and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.

scholarly journals Differential Gene Expression between Fungal Mating Types Is Associated with Sequence Degeneration

2020 ◽  
Vol 12 (4) ◽  
pp. 243-258 ◽  
Author(s):  
Wen-Juan Ma ◽  
Fantin Carpentier ◽  
Tatiana Giraud ◽  
Michael E Hood
Keyword(s):  
Differential Expression ◽  
Differentially Expressed Genes ◽  
Mating Type ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Gc Content ◽  
Differentially Expressed ◽  
Mating Types ◽  
Sexual Antagonism ◽  
Recombination Suppression

Abstract Degenerative mutations in non-recombining regions, such as in sex chromosomes, may lead to differential expression between alleles if mutations occur stochastically in one or the other allele. Reduced allelic expression due to degeneration has indeed been suggested to occur in various sex-chromosome systems. However, whether an association occurs between specific signatures of degeneration and differential expression between alleles has not been extensively tested, and sexual antagonism can also cause differential expression on sex chromosomes. The anther-smut fungus Microbotryum lychnidis-dioicae is ideal for testing associations between specific degenerative signatures and differential expression because 1) there are multiple evolutionary strata on the mating-type chromosomes, reflecting successive recombination suppression linked to mating-type loci; 2) separate haploid cultures of opposite mating types help identify differential expression between alleles; and 3) there is no sexual antagonism as a confounding factor accounting for differential expression. We found that differentially expressed genes were enriched in the four oldest evolutionary strata compared with other genomic compartments, and that, within compartments, several signatures of sequence degeneration were greater for differentially expressed than non-differentially expressed genes. Two particular degenerative signatures were significantly associated with lower expression levels within differentially expressed allele pairs: upstream insertion of transposable elements and mutations truncating the protein length. Other degenerative mutations associated with differential expression included nonsynonymous substitutions and altered intron or GC content. The association between differential expression and allele degeneration is relevant for a broad range of taxa where mating compatibility or sex is determined by genes located in large regions where recombination is suppressed.

scholarly journals Evolution of a Multiple Sex-Chromosome System by Three-Sequential Translocations among Potential Sex-Chromosomes in the Taiwanese Frog Odorrana swinhoana

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 661
Author(s):  
Ikuo Miura ◽  
Foyez Shams ◽  
Si-Min Lin ◽  
Marcelo de Bello Cioffi ◽  
Thomas Liehr ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Rare Case ◽  
Sex Chromosome ◽  
Sex Chromosome System ◽  
Brown Frog ◽  
Male Specific

Translocation between sex-chromosomes and autosomes generates multiple sex-chromosome systems. It happens unexpectedly, and therefore, the evolutionary meaning is not clear. The current study shows a multiple sex chromosome system comprising three different chromosome pairs in a Taiwanese brown frog (Odorrana swinhoana). The male-specific three translocations created a system of six sex-chromosomes, ♂X1Y1X2Y2X3Y3 -♀X1X1X2X2X3X3. It is unique in that the translocations occurred among three out of the six members of potential sex-determining chromosomes, which are known to be involved in sex-chromosome turnover in frogs, and the two out of three include orthologs of the sex-determining genes in mammals, birds and fishes. This rare case suggests sex-specific, nonrandom translocations and thus provides a new viewpoint for the evolutionary meaning of the multiple sex chromosome system.

scholarly journals Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lingzhan Xue ◽  
Yu Gao ◽  
Meiying Wu ◽  
Tian Tian ◽  
Haiping Fan ◽  
...  
Keyword(s):  
Y Chromosome ◽  
Sex Chromosomes ◽  
Chromosome Pair ◽  
Sex Chromosome ◽  
Structural Variations ◽  
Recombination Suppression ◽  
Chromosome Differentiation ◽  
Y Chromosomes ◽  
Recent Origin ◽  
Mastacembelus Armatus

Abstract Background The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Results Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Conclusions Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.

scholarly journals A new sympatric region for distinct karyotypic forms of Hoplias malabaricus (Pisces, Erythrinidae)

2006 ◽  
Vol 66 (1b) ◽  
pp. 205-210 ◽  
Author(s):  
G. G. Born ◽  
L. A. C. Bertollo
Keyword(s):  
Sex Difference ◽  
Sex Chromosomes ◽  
Diploid Number ◽  
Sex Chromosome ◽  
Minas Gerais ◽  
Female Specimen ◽  
Male Specimen ◽  
Hoplias Malabaricus ◽  
Sex Chromosome System ◽  
Sympatric Cytotypes

Specimens of Hoplias malabaricus from Lagoa Carioca, an isolated lake of the Rio Doce State Park (state of Minas Gerais, Brazil), were cytogenetically studied. The diploid number was found to be constant, i.e., 2n = 42 chromosomes, although two karyotypic forms were found: karyotype A, characterized by 22M + 20SM chromosomes, observed only in a male specimen, and karyotype B, characterized by 24M + 16SM + 2ST and 24M + 17SM + 1ST chromosomes in female and male specimens, respectively. This sex difference found in karyotype B is related to an XX/XY sex chromosome system. Another female specimen of H. malabaricus, also carrying karyotype A, had previously been found in the same lake. The available data indicate that two sympatric cytotypes of H. malabaricus exist in the Lagoa Carioca, with cytotype A occurring at a lower frequency and differing from cytotype B by undifferentiated sex chromosomes.

scholarly journals Comparative cytogenetics of two species of Dermanura (Chiroptera, Phyllostomidae) in Midwestern Brazil

2021 ◽  
Vol 15 (2) ◽  
pp. 89-99
Author(s):  
Ricardo Firmino de Sousa ◽  
Paulo Cesar Venere ◽  
Karina de Cassia Faria
Keyword(s):  
Diploid Number ◽  
Constitutive Heterochromatin ◽  
Sex Chromosome ◽  
Type System ◽  
Pericentromeric Region ◽  
Morphological Characters ◽  
Comparative Cytogenetics ◽  
Taxonomic Implications ◽  
Sex Chromosome System ◽  
First Time

Dermanura Gervais, 1856 is represented by small frugivorous bats of the Stenodermatinae subfamily. The taxonomy of this group presents controversies and has been subject to changes, especially since the morphological characters evaluated have left gaps that are difficult to fill regarding good species characterization. Previous studies performed in Dermanura cinerea Gervais, 1856 found that the karyotype of this species has a diploid number of chromosomes equal to 30 and 56 autosomal arms. The objective of the present study was to describe, for the first time, the karyotypes of the species Dermanura anderseni (Osgood, 1916) and Dermanura gnoma (Handley, 1987) based on classical cytogenetic markers. For both species, the diploid number found was 2n = 30 and NFa = 56. Two pairs of chromosomes showed markings of the nucleolus organizing regions (AgNORs) in the species D. anderseni and only one pair in D. gnoma, differing from what has already been described for D. cinerea. The two species analyzed here also showed differences in the sex chromosome system, with D. gnoma showing a neo-XY type system while in D. anderseni the classic XY sexual system was observed. In both species, visualization of the constitutive heterochromatin occurred in the pericentromeric region of all chromosomes, as well as in the short arms of the subtelocentric chromosomes. The present work represents an important expansion of karyotypic information for the subfamily Stenodermatinae, bringing chromosomal features that are possible to use in the taxonomic implications of the group.

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