Supporting data for "A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes"

Vertebrate sex is typically determined either by genetic factors, such as sex chromosomes, or by environmental cues like temperature. Therefore, the agamid dragon lizard <i>Pogona vitticeps</i> is remarkable in this regard, as it exhibits both ZZ/ZW genetic and temperature-dependent sex determination. However, the complete sequence and full gene content of <i>P. vitticeps</i> sex chromosomes remain unclear, hindering the investigation of the sex-determining cascade in this model lizard.<br>Using CycloneSEQ and DNBSEQ sequencing technologies, we generated a near-complete chromosome-scale genome assembly for a ZZ male <i>P. vitticeps</i>. Compared with the previous reference genome (GCF_900067755.1/Pvi1.1), this ~1.8 Gb new assembly displayed &gt;5,700-fold improvement in contiguity (contig N50: 202.5 Mb vs. 35.5 kb) and achieved complete chromosome anchoring (16 vs. 13,749 scaffolds). We found that over 80% of the <i>P. vitticeps</i> Z chromosome remains as a pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as <i>AMH</i>, <i>AMHR2</i>, and <i>BMPR1A</i>. Finally, by tracking the evolutionary origin and developmental expression of SDR genes, we proposed a model for the origin of <i>P. vitticeps</i> sex chromosomes, which is considered the Z-linked <i>AMH</i> as the master sex-determining gene.<br>In this study, we fully characterized the Z sex chromosome of <i>P. vitticeps</i>, identified <i>AMH</i> as the candidate sex-determining gene, and proposed a new model for the origin of <i>P. vitticeps</i> sex chromosomes. The near-complete <i>P. vitticeps</i> reference genome will also benefit future studies of reptile evolution.