scholarly journals Recurrent chromosome reshuffling and the evolution of neo-sex chromosomes in parrots

2021 ◽  
Author(s):  
Zhen Huang ◽  
Ivanete Furo ◽  
Valentina Peona ◽  
Jing Liu ◽  
Anderson J. B. Gomes ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Genome Stability ◽  
Sex Chromosome ◽  
Phylogenetic Analyses ◽  
Chromosomal Rearrangements ◽  
Transcriptome Profiling ◽  
Chromosome 11 ◽  
Satellite Repeat ◽  
Monk Parakeet ◽  
Female Specific

AbstractThe karyotype of most birds has remained considerably stable during more than 100 million years’ evolution, except for some groups, such as parrots. The evolutionary processes and underlying genetic mechanism of chromosomal rearrangements in parrots, however, are poorly understood. Here, using chromosome-level assemblies of three parrot genomes (monk parakeet, blue-fronted amazon, budgerigar), we uncovered frequent chromosome fusions and fissions among parrots, with most of them being lineage-specific. In particular, at least 12 chromosomes recurrently experienced inter-chromosomal fusions in different parrot lineages. Two conserved vertebrate genes, ALC1 and PARP3, with known functions in the repair of double-strand breaks and maintenance of genome stability, were specifically lost in parrots. The loss of ALC1 was associated with multiple deletions and an accumulation of CR1-psi, a novel subfamily of transposable elements (TEs) that recently amplified in parrots, while the loss of PARP3 was associated with an inversion. Additionally, the fusion of the ZW sex chromosomes and chromosome 11 has created a pair of neo-sex chromosomes in the ancestor of parrots, and the chromosome 25 has been further added to the sex chromosomes in monk parakeet. The newly formed neo-sex chromosomes were validated by our chromosomal painting, genomic and phylogenetic analyses. Transcriptome profiling for multiple tissues of males and females did not reveal signals of female-specific selection driving the formation of neo-sex chromosomes. Finally, we identified one W-specific satellite repeat that contributed to the unusual enlargement of the W chromosome in monk parakeet. Together, the combination of our genomic and cytogenetic analyses highlight the role of TEs and genetic drift in promoting chromosome rearrangements, gene loss and the evolution of neo-sex chromosome in parrots.

scholarly journals A 180 Myr-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

2021 ◽  
Vol 376 (1832) ◽  
pp. 20200089
Author(s):  
Heiner Kuhl ◽  
Yann Guiguen ◽  
Christin Höhne ◽  
Eva Kreuz ◽  
Kang Du ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Specific Sequence ◽  
Genome Region ◽  
Acipenser Ruthenus ◽  
Determination System ◽  
Sex Determination System ◽  
Female Specific ◽  
Polyploidization Event

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet ( Acipenser ruthenus ). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages ( A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso ), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species ( A. gueldenstaedtii, A. baerii ). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.

scholarly journals Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

Cells ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 2386
Author(s):  
Worapong Singchat ◽  
Syed Farhan Ahmad ◽  
Nararat Laopichienpong ◽  
Aorarat Suntronpong ◽  
Thitipong Panthum ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Chromosome Analysis ◽  
Chromosome Conformation ◽  
Principal Mechanism ◽  
Squamate Reptiles ◽  
Genomic Landscape ◽  
Heteromorphic Sex Chromosomes

Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

ZZ/ZW Sex Chromosomes in the Endemic Puerto Rican Leaf-Toed Gecko (Phyllodactylus wirshingi)

2019 ◽  
Vol 157 (1-2) ◽  
pp. 89-97 ◽  
Author(s):  
Stuart V. Nielsen ◽  
Juan D. Daza ◽  
Brendan J. Pinto ◽  
Tony Gamble
Keyword(s):  
Dna Sequencing ◽  
Puerto Rican ◽  
Sex Chromosomes ◽  
Restriction Site ◽  
Sex Chromosome ◽  
Effective Alternative ◽  
Sex Chromosome System ◽  
Female Specific ◽  
Cytogenetic Methods

Investigating the evolutionary processes influencing the origin, evolution, and turnover of vertebrate sex chromosomes requires the classification of sex chromosome systems in a great diversity of species. Among amniotes, squamates (lizards and snakes) - and gecko lizards in particular - are worthy of additional study. Geckos possess all major vertebrate sex-determining systems, as well as multiple transitions among them, yet we still lack data on the sex-determining systems for the vast majority of species. We here utilize restriction-site associated DNA sequencing (RADseq) to identify the sex chromosome system of the Puerto Rican endemic leaf-toed gecko (Phyllodactylidae: Phyllodactylus wirshingi), in order to confirm a ZZ/ZW sex chromosome system within the genus, as well as to better categorize the diversity within this poorly characterized family. RADseq has proven an effective alternative to cytogenetic methods for determining whether a species has an XX/XY or ZZ/ZW sex chromosome system - particularly in taxa with non-differentiated sex chromosomes - but can also be used to identify which chromosomes in the genome are the sex chromosomes. We here identify a ZZ/ZW sex chromosome system in P. wirshingi. Furthermore, we show that 4 of the female-specific markers contain fragments of genes found on the avian Z and discuss homology with P. wirshingi sex chromosomes.

scholarly journals A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

2020 ◽  
Author(s):  
Heiner Kuhl ◽  
Yann Guiguen ◽  
Christin Höhne ◽  
Eva Kreuz ◽  
Kang Du ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Specific Sequence ◽  
Genome Region ◽  
Acipenser Ruthenus ◽  
Determination System ◽  
Sex Determination System ◽  
Female Specific ◽  
Polyploidization Event

SummarySeveral hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified a ~16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus vs. A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 My of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives.

scholarly journals Extensive Sex Chromosome Polymorphism of Microtus thomasi/Microtus atticus Species Complex Associated with Cryptic Chromosomal Rearrangements and Independent Accumulation of Heterochromatin

2017 ◽  
Vol 151 (4) ◽  
pp. 198-207 ◽  
Author(s):  
Michail T. Rovatsos ◽  
Juan A. Marchal ◽  
Ismael Romero-Fernández ◽  
Maria Arroyo ◽  
Eva B. Athanasopoulou ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Dna Sequences ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Chromosomal Evolution ◽  
Chromosome Polymorphism ◽  
Random Drift ◽  
X Chromosomes ◽  
Karyotypic Diversity ◽  
Comparative Painting

The sibling species Microtus thomasi and M. atticus represent probably the highest karyotypic diversity within the genus Microtus and are an interesting model for chromosomal evolution studies. In addition to variation in autosomes, they show a high intraspecific variation in the size and morphology of both sex chromosomes. We analyzed individuals with different sex chromosome constitutions using 3 painting probes, 2 from Y chromosome variants and 1 from the small arm of the submetacentric X chromosome. Our comparative painting approach uncovered 12 variants of Y and 14 variants of X chromosomes, which demonstrates that the polymorphism of sex chromosomes is substantially larger than previously reported. We suggest that 2 main processes are responsible for this sex chromosome polymorphism: change of morphology from acrocentric to submetacentric or metacentric chromosomes and increase in size due to accumulation of repetitive DNA sequences, generating heterochromatic blocks. Strong genetic drift in small and fragmented populations of these 2 species could be related to the origin and maintenance of the large polymorphism of sex chromosomes. We proposed that a similar polymorphism variation combined with random drift fixing the biggest sex chromosomes could have occurred in the origin of some of the actual Microtus species with giant sex chromosomes.

scholarly journals Phylogeny, transposable element and sex chromosome evolution of the basal lineage of birds

2019 ◽  
Author(s):  
Zongji Wang ◽  
Jilin Zhang ◽  
Xiaoman Xu ◽  
Christopher Witt ◽  
Yuan Deng ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Sequence Divergence ◽  
South American ◽  
Sex Chromosome Evolution ◽  
Rapid Speciation ◽  
Genome Wide ◽  
Divergence Pattern ◽  
Female Specific

AbstractSex chromosomes of mammals and most birds are heteromorphic, while those of many paleognaths (ratites and tinamous) are inexplicably homomorphic. To dissect the mechanisms underlying the different tempo of sex chromosome evolution, we produced high-quality genomes of 12 paleognathous species, and reconstructed their phylogeny based on alignments of the non-coding sequences extending to nearly 40% of the genome. Our phylogenomic tree grouped the South American rheas and tinamous together, and supported the independent evolution of gigantism and loss of flight among ratites. The small-bodied tinamous have much higher rates of genome-wide substitutions and transposon turnovers. Yet majorities of both have retained exceptionally long recombining regions occupying over half of the entire sex chromosome, with the rest sex-linked regions diverging from each other at a much lower rate relative to neognathous birds. Each species exhibits a punctuated sequence divergence pattern between sex chromosomes termed ‘evolutionary strata’, because of stepwise suppression of recombination. We concluded that all paleognaths share one evolutionary stratum with all other birds, and convergently formed between one to three strata after their rapid speciation. Contrary to the classic notion, we provided clear evidence that the youngest stratum of some tinamous formed without chromosomal inversion. Intriguingly, some of the encompassing W-linked genes have upregulated their expression levels in ovary, probably due to the female-specific selection. We proposed here that the unique male-only parental care system of paleognaths has reduced the intensity of sexual selection, and contributed to these species’ low rates of sex chromosome evolution. We also provided novel insights into the evolution of W-linked genes at their early stages.

scholarly journals Repeated translocation of a gene cassette drives sex chromosome turnover in strawberries

2017 ◽  
Author(s):  
Jacob A Tennessen ◽  
Na Wei ◽  
Shannon Straub ◽  
Rajanikanth Govindarajulu ◽  
Aaron Liston ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Gene Cassette ◽  
Specific Sequence ◽  
New Genes ◽  
Genomic Location ◽  
History Of ◽  
Causal Sequence ◽  
Female Specific ◽  
First Time

AbstractTurnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes, but conservation of the master sex-determining genes, characterize distantly-related animal lineages. Yet in plants, where separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive turnovers within closely related groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to at least three different chromosomes. To characterize these turnovers, we sequenced the complete genomes of 60 plants of known sex from five Fragaria taxa. We identified 31-mers unique to females and assembled their reads into contigs. Remarkably, a short (13 kb) sequence is observed in nearly all females and never in male-fertile individuals, implicating it as the sex-determining region (SDR). This female-specific “SDR cassette” contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Comparing SDR cassettes across taxa reveals a history of repeated translocation, which can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of these “souvenirs” suggests an adaptive basis for the expanding (up to at least 23 kb) hemizygous region. This is the first plant SDR known to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes.Significance StatementSex chromosomes frequently restructure themselves during organismal evolution, often becoming highly differentiated. This dynamic process is poorly understood for most taxa, especially during the early stages typical of many dioecious plants. In wild strawberries, a sex-determining region of DNA has repeatedly changed its genomic location, each time increasing the size of the hemizygous female-specific sequence. This observation shows for the first time that plant sex regions can “jump”, and suggests that this phenomenon may be adaptive by gathering and locking new genes into linkage with sex. This conserved and presumed causal sequence with a variable genomic location presents a unique opportunity to understand how sex chromosomes first begin to differentiate.

scholarly journals Whole-chromosome fusions in the karyotype evolution of Sceloporus (Iguania, Reptilia) are more intense in sex chromosomes than autosomes

2020 ◽  
Author(s):  
Artem P. Lisachov ◽  
Katerina V. Tishakova ◽  
Svetlana A. Romanenko ◽  
Anna S. Molodtseva ◽  
Dmitry Yu. Prokopov ◽  
...  
Keyword(s):  
Sex Chromosomes ◽  
Complex Analysis ◽  
Sex Chromosome ◽  
Chromosome 11 ◽  
Evolutionary Forces ◽  
Chromosome Synapsis ◽  
Synaptonemal Complex Analysis ◽  
Chromosome Fusions ◽  
Chromosome Formation ◽  
Pseudoautosomal Regions

AbstractThere is a growing body of evidence that the common ancestor of vertebrates had a bimodal karyotype, i.e. consisting of large macrochromosomes and small microchromosomes. This type of karyotype organization is preserved in most reptiles. However, certain species independently experience microchromosome fusions. The evolutionary forces behind this are unclear. We investigated the karyotype of the green spiny lizard, Sceloporus malachiticus, an iguana species which has 2n=22, whereas the ancestral karyotype of iguanas had 2n=36. We obtained and sequenced flow-sorted chromosome-specific DNA samples and found that most of the microchromosome fusions in this species involved sex chromosomes. We found that certain ancestral squamate chromosomes, such as the homologue of the Anolis carolinensis chromosome 11, are repeatedly involved in sex chromosome formation in different species. To test the hypothesis that the karyotypic shift could be associated with changes in recombination patterns, and to study sex chromosome synapsis and recombination in meiosis, we performed synaptonemal complex analysis in this species and in S. variabilis, a related species with 2n=34. We found that in the species studied the recombination patterns correlate more with phylogeny than with the structure of the karyotype. The sex chromosomes had two distal pseudoautosomal regions and a medial differentiated region.

Cytogenetic Insights into the Evolution of Chromosomes and Sex Determination Reveal Striking Homology of Turtle Sex Chromosomes to Amphibian Autosomes

2016 ◽  
Vol 148 (4) ◽  
pp. 292-304 ◽  
Author(s):  
Eugenia E. Montiel ◽  
Daleen Badenhorst ◽  
Ling S. Lee ◽  
Robert Literman ◽  
Vladimir Trifonov ◽  
...  
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Diploid Number ◽  
Sex Chromosome ◽  
Chromosomal Rearrangements ◽  
Interspecific Variation ◽  
C Banding ◽  
Interstitial Telomeric Sites ◽  
Secondary Constrictions ◽  
Genomic Reorganization

Turtle karyotypes are highly conserved compared to other vertebrates; yet, variation in diploid number (2n = 26-68) reflects profound genomic reorganization, which correlates with evolutionary turnovers in sex determination. We evaluate the published literature and newly collected comparative cytogenetic data (G- and C-banding, 18S-NOR, and telomere-FISH mapping) from 13 species spanning 2n = 28-68 to revisit turtle genome evolution and sex determination. Interstitial telomeric sites were detected in multiple lineages that underwent diploid number and sex determination turnovers, suggesting chromosomal rearrangements. C-banding revealed potential interspecific variation in centromere composition and interstitial heterochromatin at secondary constrictions. 18S-NORs were detected in secondary constrictions in a single chromosomal pair per species, refuting previous reports of multiple NORs in turtles. 18S-NORs are linked to ZW chromosomes in Apalone and Pelodiscus and to X (not Y) in Staurotypus. Notably, comparative genomics across amniotes revealed that the sex chromosomes of several turtles, as well as mammals and some lizards, are homologous to components of Xenopus tropicalis XTR1 (carrying Dmrt1). Other turtle sex chromosomes are homologous to XTR4 (carrying Wt1). Interestingly, all known turtle sex chromosomes, except in Trionychidae, evolved via inversions around Dmrt1 or Wt1. Thus, XTR1 appears to represent an amniote proto-sex chromosome (perhaps linked ancestrally to XTR4) that gave rise to turtle and other amniote sex chromosomes.

Sign in / Sign up

Export Citation Format

Share Document