Two separate studies published in GigaScience report the nearly complete reference genomes of the central bearded dragon (Pogona vitticeps), a dragon lizard native to central eastern Australia and widely kept as a pet in Europe, Asia, and North America. This species is unusual because both genetics and nest temperature determine its sex.
Because of this, the species has long served as a valuable model for studying the biology of sex determination. Recent advances in genomics have now pinpointed a specific genomic region and a possible master sex-determining gene that appears to play a key role in male development. The fact that two separate research groups confirmed this result using different methods makes the discovery particularly robust.
Bearded Dragons Can Switch Sex Under High Incubation Temperatures
Bearded dragons possess an uncommon sex determination system shaped by both genetic and environmental influences, especially temperature.
Unlike most animals, where chromosomes alone determine sex, high incubation temperatures can reverse bearded dragons from male to female. So, when incubated at sufficiently warm temperatures, a lizard with male chromosomes can still develop into a fully functional female.
Similar to birds and many reptiles, bearded dragons follow a ZZ/ZW sex chromosome system, with females carrying dissimilar ZW chromosomes and males carrying two identical ZZ chromosomes.
The process becomes more complex because elevated incubation temperatures can transform ZZ males into phenotypic females without using the W chromosome or W-linked genes.
Thanks to new ultra-long nanopore sequencing, researchers can now produce telomere-to-telomere (T2T) assemblies of sex chromosomes and pinpoint non-recombining regions, helping to narrow down potential sex-determining genes in species with chromosomal sex determination.
New Sequencing Technologies Enable Clearer Insights into Z and W Chromosomes
This technology’s ability to more clearly separate maternal and paternal genome halves now makes it much easier to compare Z and W sequences, helping researchers assess whether key sex-related genes may have lost or altered functions.
Researchers at BGI, the Chinese Academy of Sciences, and Zhejiang University produced the first genome by combining DNBSEQ short reads with long reads from the new CycloneSEQ nanopore sequencer—marking the first animal genome published with this platform.
The second genome was generated under the leadership of the University of Canberra, with analysis contributions from the Australian National University, Garvan Institute of Medical Research, University of New South Wales, CSIRO, and the Universitat Autònoma de Barcelona (UAB) in Spain.
This assembly combines PacBio HiFi, ONT ultralong reads, and Hi-C sequencing. Publishing reference genomes with two distinct technologies now makes it possible, for the first time, to directly compare ONT and CycloneSEQ performance. The two methods also complement one another by addressing the question of sex determination from different angles.
Male and Female Genomes Reveal Missing Sequences and Key Sex Determination Clues
In the first effort, researchers sequenced a ZZ male central bearded dragon, providing the first full characterization of the Z sex chromosome. The second assembly focused on the genome of a female ZW individual.
The new nanopore sequencer also recovered about 124 million base pairs of previously missing sequences—nearly 7% of the genome—including many genes and regulatory elements, offering new insights into the species’ complex sex determination system.
Both projects produced 1.75 Gbp genome assemblies of outstanding quality, resolving all but one telomere, with only a few remaining gaps, mostly within the microchromosomes.
The data revealed that the Z- and W-specific sex chromosomes were assembled into single scaffolds, and a “pseudo-autosomal region” (PAR), where the sex chromosomes pair and recombine, was identified on chromosome 16.
BGI Team Identifies Amh, Amhr2, and Bmpr1a as Key Sex-Determining Candidates
In the male dragon genome sequenced by the BGI team, researchers searched for genes present on the Z but absent on the W chromosome. They identified Amh and Amhr2 (the Anti-Müllerian hormone gene and its receptor), along with Bmpr1a, as strong sex-determining candidates.
Similarly, the Australian-led team’s sequencing of the female dragon genome pointed to the same candidate Sex Determination Region (SDR) and also highlighted Amh and Amhr2 as the most likely sex-determining genes.
Analysis of gene expression at different developmental stages showed that Amh displayed strong male-biased expression, making it the leading candidate for the master sex-determining gene.
However, the differing expression of another sex-related gene, Nr5a1, located in the PAR, suggests a more complex mechanism. Nr5a1 encodes a transcription factor that binds to the Amh promoter region. Unlike in many fish species that use Amh-like genes for sex determination, the autosomal copies of Amh and its receptor gene Amhr2 remain intact and active in bearded dragons.
This raises the possibility that sex determination may involve a kind of “council” of genes on the sex chromosomes, influenced by their remaining autosomal counterparts.
Amh and Amhr2 Emerge as Strong Candidates for Master Sex-Determining Genes
The key outcome of these assemblies is the identification of genetic elements on the sex chromosomes that are crucial to male sexual differentiation in vertebrates.
The Amh gene and its receptor Amhr2 have been duplicated onto the Z chromosome within the non-recombining region, making them strong candidates for the master sex-determining gene in this species, likely operating through a dosage-based mechanism—a finding that has remained elusive for years.
Until now, no reptile has been shown to possess a definitive master sex-determining gene comparable to Sry in mammals or Dmrt1 in birds. This study identifies Amh as a compelling candidate, present in two copies in ZZ males but only one in ZW females.
Arthur Georges, from the University of Canberra and senior author of the second paper, emphasized the broader impact of this research: “We expect these new assemblies to accelerate research in diverse fields, including cranial and brain development, behavior, gene–gene and gene–environment interactions in vertebrate sex determination, and many other areas seeking a robust squamate model for comparison with established model organisms such as mice, humans, or birds.”
“I am continually impressed by how quickly Chinese science has advanced. In just a short time, BGI and its partner institutions have developed sequencing technologies that not only match the quality of competitors but also surpass them in throughput and cost-effectiveness. These genome assemblies clearly demonstrate that achievement.”
BGI Team Chose Bearded Dragon Genome to Mark the Year of the Dragon
Qiye Li of BGI, senior author of the first paper and lead author of the Chinese project, explained their reasoning for this choice: We chose the bearded dragon genome as the first animal genome for the new sequencer last year because it coincided with the Year of the Dragon in China.
“With the unbiased long reads produced by the CycloneSEQ sequencer, we were able to generate a highly contiguous genome assembly and resolve regions with high repetitiveness and GC content that have traditionally posed challenges. The two reference genomes, representing opposite sexes and built using different technologies, truly complement one another.”
“I’m thrilled that both genomes highlight the central role of AMH signaling in this species’ sex determination. But an important question remains: how did these sex chromosomes originate? We expect that sequencing additional high-quality genomes from related species will shed light on the evolutionary development of the ZW system and help complete the picture.”
The fact that two independent projects identified the same candidate master genes strongly reinforces the reliability of these results. Moreover, openly sharing the data enables other researchers to build on this foundation, particularly since the precise roles of several other transcription factors involved in sex determination remain unclear.
Still, producing these two high-quality genome assemblies marks a major advance in unraveling the full story of sex determination in the bearded dragon.
Read the original article on: Phys.Org
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