Supporting data for "Genomic evidence for hybridization and introgression between blue peafowl and endangered green peafowl and molecular foundation of peafowl white plumage"

The blue peafowl (<i>Pavo cristatus</i>) and the green peafowl (<i>Pavo muticus</i>) have garnered significant public affection due to their stunning appearance, although the green peafowl is currently endangered. The causative mutation for the white plumage color of blue peafowl (also called white peafowl) remains unknown. <br>In this study, we generated a chromosome-level reference genome of the blue peafowl with a contig N50 of 30.6 Mb, including the autosomes, Z and W sex chromosomes, as well as a complete mitochondrial DNA sequence. Data from 77 peafowl whole genomes, 76 peafowl mitochondrial genomes and 33 peafowl W chromosome genomes provided the first substantial genetic evidence for recent hybridization between green peafowls and blue peafowls. We found three hybrid green peafowls in zoo samples rather than in wild samples, with blue peafowl genomic content of 16-34%. Maternal genetic analysis showed that two of the hybrid female green peafowls contained complete blue peafowl mitochondrial genomes and W chromosomes. Some animal protection agencies release captive green peafowls to maintain the wild population of green peafowls. Therefore, to better protect the endangered green peafowl, we suggest that purebred identification must be carried out before releasing green peafowls from zoos into the wild in order to prevent the hybrid green peafowl from contaminating the wild green peafowl. In addition, we also found that there were historical introgression events of green peafowl to blue peafowl in four zoo blue peafowl individuals. The introgressed genomic regions contain<em> </em><i>IGFBP1</i><em> </em>and <i>IGFBP3</i> genes that could affect blue peafowl body size. Finally, we identified that the nonsense mutation (g.4:12583552G&gt;A) in the <i>EDNRB2</i><em> </em>gene is the genetic causative mutation for white plumages color of blue peafowl, preventing melanocytes from being transported into plumages, thereby inhibiting melanin deposition. <br>Our research provides both theoretical and empirical support for the conservation of the endangered green peafowl. The high-quality genome and genomic data also provide valuable resource for blue peafowl genomics-assisted breeding.