A telomere to telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps
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Abstract
Background The central bearded dragon ( Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon. Results Genome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome. This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1 , suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon. Conclusion This high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally. Species Taxonomy Eukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona ; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695). Graphical Abstract
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Abstract
Background The central bearded dragon (Pogona vitticeps) is widely distributed in central eastern Australia and adapts readily to captivity. Among other attributes, it is distinctive because it undergoes sex reversal from ZZ genotypic males to phenotypic females at high incubation temperatures. Here, we report an annotated telomere to telomere phased assembly of the genome of a female ZW central bearded dragon.
Results
Genome assembly length is 1.75 Gbp with a scaffold N50 of 266.2 Mbp, N90 of 28.1 Mbp, 26 gaps and 42.2% GC content. Most (99.6%) of the reference assembly is scaffolded into 6 macrochromosomes and 10 microchromosomes, including the Z and W microchromosomes, corresponding to the karyotype. The genome assembly exceeds standard recommended by the Earth Biogenome Project (6CQ40): 0.003% collapsed sequence, 0.03% false expansions, 99.8% k-mer completeness, 97.9% complete single copy BUSCO genes and an average of 93.5% of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731 bp) and the model rDNA repeat unit (length 9.5 Kbp) were assembled. Male vertebrate sex genes Amh and Amhr2 were discovered as copies in the small non-recombining region of the Z chromosome, absent from the W chromosome.
This, coupled with the prior discovery of differential Z and W transcriptional isoform composition arising from pseudoautosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies and their resultant transcription factors and intermediaries, determines sex in the bearded dragon.
Conclusion
This high-quality assembly will serve as a resource to enable and accelerate research into the unusual reproductive attributes of this species and for comparative studies across the Agamidae and reptiles more generally.
Species Taxonomy Eukaryota; Animalia; Chordata; Reptilia; Squamata; Iguania; Agamidae; Amphibolurinae; Pogona; Pogona vitticeps (Ahl, 1926) (NCBI:txid103695).
Competing Interest Statement
H.R.P., I.W.D., A.L.M-R., A.G. have previously received travel and accommodation expenses from ONT and/or PacBio to speak at conferences. I.W.D. has a paid consultant role with Sequin Pty Ltd. The authors declare no other competing interests.
Abbreviations
- BAC
- Bacterial Artificial Chromosome
- BUSCO
- Benchmarking Universal Single-Copy Orthologs
- EBP
- Earth BioGenome Project
- HiC
- High-throughput Chromosome Conformation Capture
- HiFi
- High Fidelity
- L50
- min number of contigs (or scaffolds) to add in length to 50% of assembly length
- L90
- min number of contigs (or scaffolds) to add in length to 90% of assembly length
- LINE
- Long Interspersed Nuclear Element
- LTR
- Long Terminal Repeat
- N50
- median (50th percentile) contig or scaffold length
- N90
- 90th percentile of contig or scaffold length
- NCBI
- The National Center for Biotechnology information
- ONT
- Oxford Nanopore Technologies
- PacBio
- Pacific Biosciences
- PAR
- pseudoautosomal region
- PCR
- polymerase chain reaction
- Q20
- Phred score of 20 corresponding to a 1% error rate
- Q30
- Phred score of 30 corresponding to a 0.01% error rate
- rDNA
- ribosomal DNA
- RNAseq
- RNA-sequencing
- rRNA
- ribosomal RNA
- SINE
- Short Interspersed Nuclear Element
- snRNA
- small nuclear RNA
- T2T
- telomere-to-telomere
- tRNA
- transfer RNA
- UTR
- Untranslated Region
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- last seen: 2026-05-20T01:45:00.602351+00:00