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907c370e1ae74c642e75d6be9120d0684e220eddec4838feacc8df742f656216  85_Patel_et_al_Giga_Science_25_.pdf

Title:           A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps
Subject:         DOI: 10.1093/gigascience/giaf085 GigaScience, 14, 1, 00-00-2025. Abstract: 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 near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.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 ribosomal DNA 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 pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.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.
Keywords:        
Author:          Patel Hardip R., Alreja Kirat, Reis Andre L.M., Chang J. King, Chew Zahra A., Jung Hyungtaek, Hammond Jillian M., Deveson Ira W., Ruiz-Herrera Aurora, Marin-Gual Laia, Holleley Clare E., Zhang Xiuwen, Lister Nicholas C., Whiteley Sarah, Xiong Lei, Dissanayake Duminda S.B., Waters Paul D., Georges Arthur
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     Item: 
      Title: Species Taxonomy
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     Item: 
      Title: Introduction
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     Item: 
      Title: Materials and Methods
      Destination: section.3.3.0
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      Title: Results and Discussion
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      Title: Chromosome Assembly
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      Title: Gene Annotation
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      Title: Conclusion
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      Title: Funding
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     Item: 
      Title: Data Availability
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     Item: 
      Title: Competing Interests
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     Item: 
      Title: References
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    Title: A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps
    Author: Patel Hardip R., Alreja Kirat, Reis Andre L.M., Chang J. King, Chew Zahra A., Jung Hyungtaek, Hammond Jillian M., Deveson Ira W., Ruiz-Herrera Aurora, Marin-Gual Laia, Holleley Clare E., Zhang Xiuwen, Lister Nicholas C., Whiteley Sarah, Xiong Lei, Dissanayake Duminda S.B., Waters Paul D., Georges Arthur
    Subject: DOI: 10.1093/gigascience/giaf085 GigaScience, 14, 1, 00-00-2025. Abstract: 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 near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.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 ribosomal DNA 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 pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.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.
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         <prism:copyright>© The Author(s) 2025. Published by Oxford University Press on behalf of GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</prism:copyright>
         <dc:rightsHolder>All Rights Reserved</dc:rightsHolder>
         <dc:format>application/pdf</dc:format>
         <dc:identifier>doi:10.1093/gigascience/giaf085</dc:identifier>
         <dc:rights>
            <rdf:Alt>
               <rdf:li xml:lang="x-default">© The Author(s) 2025. Published by Oxford University Press on behalf of GigaScience. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</rdf:li>
            </rdf:Alt>
         </dc:rights>
         <dc:title>
            <rdf:Alt>
               <rdf:li xml:lang="x-default">A near telomere-to-telomere phased genome assembly and annotation for the Australian central bearded dragon Pogona vitticeps</rdf:li>
            </rdf:Alt>
         </dc:title>
         <dc:description>
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               <rdf:li xml:lang="x-default">DOI: 10.1093/gigascience/giaf085 GigaScience, 14, 1, 00-00-2025. Abstract: 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 near telomere-to-telomere phased assembly of the genome of a female ZW central bearded dragon.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&amp;#x0025; GC content. Most (99.6&amp;#x0025;) 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&amp;#x0025; collapsed sequence, 0.03&amp;#x0025; false expansions, 99.8&amp;#x0025; k-mer completeness, 97.9&amp;#x0025; complete single-copy BUSCO genes, and an average of 93.5&amp;#x0025; of transcriptome data mappable back to the genome assembly. The mitochondrial genome (16,731&amp;#x00A0;bp) and the model ribosomal DNA repeat unit (length 9.5&amp;#x00A0;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 pseudo-autosomal sex gene Nr5a1, suggests that complex interactions between these genes, their autosomal copies, and their resultant transcription factors and intermediaries determine sex in the bearded dragon.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.</rdf:li>
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         <dc:contributor>
            <rdf:Seq>
               <rdf:li>Patel Hardip R.</rdf:li>
               <rdf:li>Alreja Kirat</rdf:li>
               <rdf:li>Reis Andre L.M.</rdf:li>
               <rdf:li>Chang J. King</rdf:li>
               <rdf:li>Chew Zahra A.</rdf:li>
               <rdf:li>Jung Hyungtaek</rdf:li>
               <rdf:li>Hammond Jillian M.</rdf:li>
               <rdf:li>Deveson Ira W.</rdf:li>
               <rdf:li>Ruiz-Herrera Aurora</rdf:li>
               <rdf:li>Marin-Gual Laia</rdf:li>
               <rdf:li>Holleley Clare E.</rdf:li>
               <rdf:li>Zhang Xiuwen</rdf:li>
               <rdf:li>Lister Nicholas C.</rdf:li>
               <rdf:li>Whiteley Sarah</rdf:li>
               <rdf:li>Xiong Lei</rdf:li>
               <rdf:li>Dissanayake Duminda S.B.</rdf:li>
               <rdf:li>Waters Paul D.</rdf:li>
               <rdf:li>Georges Arthur</rdf:li>
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         </dc:contributor>
         <dc:publisher>
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               <rdf:li>Oxford University Press</rdf:li>
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         <dc:subject>
            <rdf:Bag>
               <rdf:li>Squamata</rdf:li>
               <rdf:li>Agamidae</rdf:li>
               <rdf:li>lizard</rdf:li>
               <rdf:li>AusARG</rdf:li>
               <rdf:li>sex determination</rdf:li>
            </rdf:Bag>
         </dc:subject>
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            <rdf:Seq>
               <rdf:li>Patel Hardip R., Alreja Kirat, Reis Andre L.M., Chang J. King, Chew Zahra A., Jung Hyungtaek, Hammond Jillian M., Deveson Ira W., Ruiz-Herrera Aurora, Marin-Gual Laia, Holleley Clare E., Zhang Xiuwen, Lister Nicholas C., Whiteley Sarah, Xiong Lei, Dissanayake Duminda S.B., Waters Paul D., Georges Arthur</rdf:li>
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   Type: CRC32
  Checksum: 125f36c36ba25fbabd489a596a86b2e2
   Type: MD5
  Checksum: 560f4af9be3580fcb3a1ed591d9f4163b93ee75e
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  Checksum: 907c370e1ae74c642e75d6be9120d0684e220eddec4838feacc8df742f656216
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