Two genomes are better than one for studying reptile sex

(Press-News.org) Today marks the publication by two different studies presenting the near-complete reference genomes of the central bearded dragon (Pogona vitticeps), a widely distributed species of dragon lizard common in central eastern Australia and popular as pets in Europe, Asia, and North America. This species has an unusual trait for an animal species: whether this lizard grows up to be a male or a female depends not only on genetics but also on the temperature of its nest. This has long made it a useful model to study the biological basis of sex determination, and the advent of huge technological improvements in genomics has finally found a region of the genome and a potential master sex determination gene likely central to male sexual differentiation. The independent verification of this by two different groups using two different approaches making this a much stronger finding. 

Bearded dragons have an unusual sex determination system which is influenced by both genetics and environmental factors, specifically temperature. Unlike most animals where sex is solely determined by chromosomes, bearded dragons can have their sex reversed from male to female by high incubation temperatures. Meaning a lizard with male chromosomes can develop into a reproductively functional female if the egg is incubated at a warm enough temperature.

Like birds and many reptiles, this species has a ZZ/ZW sex chromosome system where females have a pair of dissimilar ZW chromosomes, and males have two similar ZZ chromosomes. Sex determination in this species is complicated further, as ZZ genotypic males can change to phenotypic females at high incubation temperatures without the help of W chromosome or W-linked genes. New ultra-long nanopore sequencing technology now allows us to generate telomere-to-telomere (T2T) assemblies of the sex chromosomes and identify the non-recombining regions to help narrow the field of candidate sex determining genes in species with chromosomal sex determination. The ability of this technology to better separate out the maternal and paternal halves of the genome now allows much easier comparisons of the Z and W sequences to gauge potential loss or difference in function of key sex gene candidates. 

The first paper from researchers from BGI, Chinese Academy of Sciences and Zhejiang University,  uses DNBSEQ short-reads combined with long-reads from the new CycloneSEQ nanopore sequencer, this being the first animal genome published using this technology. Generation of the second genome was led by researchers from the University of Canberra with funding from Bioplatforms Australia, the Australian Research Council and PacBio Singapore, and with contributions to analyses from researchers of the Australian National University, Garvan Institute for Medical Research, University of New South Wales and CSIRO alongside Universitat Autònoma de Barcelona (UAB) in Spain. This assembly uses PacBio HiFi, ONT ultralong reads and Hi-C sequencing. Having reference genomes published using these two different technologies allows a like-for-like comparison between the ONT and CycloneSEQ technologies for the first time. Both technologies also complement each other by investigating the sex determination question using different approaches. The first genome sequenced a ZZ male central bearded dragon to characterize the whole Z sex chromosome for the first time while the second assembled the genome of a female ZW individual. The new nanopore sequencer also enabled the recovery of around 124 million base pairs of previously undescribed and missing sequences (nearly 7% of the genome), which included numerous genes and regulatory elements to better elucidate the complicated sex determination system.

Both projects assembled 1.75 Gbp genome assemblies of exceptionally high quality to assemble all but one of the telomeres, and only a few gaps remained mostly located in the microchromosomes. Using this data showed 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 also detected on chromosome 16. The sequencing of the male dragon by the BGI team looked for genes specific to Z but not the W chromosomes, and Amh and Amhr2 (the Anti-Müllerian hormone gene and its receptor) plus Bmpr1a were determined as strong candidates for the sex determining genes in this species. The sequencing of the female dragon by the Australian-led team pinpointed to the same candidate Sex Determination Region (SDR) of their dragon genome, and also highlighted Amh and Amhr2 as the likely candidate genes. Studying the expression in different developmental stages found Amh had significant male-biased expression patterns making it the most likely candidate as the master sex-determining gene. The differential expression of another sex-related gene Nr5a1 in the PAR suggests that the story may be more complicated, as Nr5a1 encodes a transcription factor with binding sites on the Amh promoter region. Unlike many fish that enlist Amh-like genes in sex determination, the autosomal copies of Amh and its receptor gene Amhr2 remain intact and functional. It could be that sex is determined by some form of caucus among genes on the sex chromosomes of the bearded dragon moderated by their residual autosomal copies.

The main highlight of these assemblies is therefore the discovery of genetic elements central to male sexual differentiation in vertebrates, on the sex chromosomes. The genes Amh and that coding its receptor AMHR2 have been copied to the Z chromosome in the non-recombining region, and so are obvious candidates for the master sex determining gene working via a dosage-based mechanism in this species, a discovery that has eluded discovery for so many years. No master sex determining gene akin to Sry in mammals or Dmrt1 in birds has to date been discovered in any reptile species. This new work provides a clear candidate in Amh, which is present in double dose in the ZZ male and single dose in the ZW female.

Arthur Georges from University of Canberra and senior author on the second paper says on the utility of this work: “We anticipate accelerated research in other areas arising from these newly available assemblies, such as cranial development, brain development, behavioural studies, gene-gene and gene-environment interactions in comparative studies of vertebrate sex determination and in many other areas looking for a well-supported squamate model against which to compare with their model species be it mouse, human or bird.”

"I never cease to be amazed by the rapidity of progress of Chinese science. In relatively few years, BGI and its companion enterprises have developed sequencing technologies that deliver outcomes as good, and throughput and cost effectiveness that is better, than competing technologies on the market. These genome assemblies are testimony to that level of achievement".

 Qiye Li from BGI and senior author on the first paper Lead author of the Chinese project explains their rationale for using this approach: “We decided to start working on the bearded dragon genome last year as the first animal genome for this new sequencer because it was the Year of the Dragon in China. Benefiting from the unbiased long-reads provided by the CycloneSEQ sequencer, we readily obtained a highly contiguous genome assembly and resolved highly repetitive and high-GC regions that were traditionally challenging for assembly. The two reference genomes, derived from opposite sex and generated by different technologies, are indeed complementary to each other. I am excited that both genomes pinpoint the key role of AMH signaling in sex determination in this species. But how did the sex chromosomes arise? We anticipate that additional high‑quality genomes from related species will further elucidate the evolutionary origin of the ZW system and complete the story”.

Having two separate projects finding the same key candidate master genes independently of each other greatly increases the confidence in these findings. And openly sharing all of the data allows others to build upon this work, especially as the exact role of some of the other contributing transcription factors linked to sex determination are not yet fully resolved. The generation of these two new high quality genome assemblies however, is a massive step forward towards understanding the complete story of sex determination in this species.

A webinar with the two lead authors is organized for 26th August at 10.00am UTC and provides an opportunity to ask them questions on this work. Sign up here to watch and post questions https://cassyni.com/events/SWHReTL1j8YPEvxnLsyKYq
 

References

Guo Q, Pan Y, Dai W et al., A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes. GigaScience 2025. https://doi.org/10.1093/gigascience/giaf079

Patel HR, Alreja K, Reis AML, et al.,  A near telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps. GigaScience 2025. https://doi.org/10.1093/gigascience/giaf085


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