A near-complete genome assembly of the bearded dragonPogona vitticepsprovides insights into the origin ofPogonasex chromosomes

Abstract

AbstractBackgroundThe agamid dragon lizardPogona vitticepsis one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms.ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome forP. vitticeps. The new reference genome is ∼1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded theP. vitticepslncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as 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 asAMH,AMHR2andBMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin ofP. vitticepssex chromosomes which considered the Z-linkedAMHas the master sex-determining gene.ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-completeP. vitticepsreference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.