Reconstruction of ancient homeobox gene linkages inferred from a new high-quality assembly of the Hong Kong oyster (Magallana hongkongensis) genome

<b>Abstract</b><b><br></b> <b>Background</b> Homeobox-containing genes encode crucial transcription factors in animal and plant development, and changes to these genes have been linked to the evolution of body plans and morphologies. In animals some homeobox genes are clustered in the genome, due to either coordinated gene regulation or as remnants from ancestral genomic arrangements. Analyses of homeobox gene organization across a range of species thus helps to better understand the evolution of genome organization and developmental gene control, and the possible interactions between the two. However, homeobox gene organization in several key animal ancestors, including those of molluscs, lophotrochozoans and bilaterians, remains to be fully elucidated.<br> <b>Results</b> Here, we present a high-quality chromosome-level genome assembly of <i>Magallana hongkongensis</i> (2n = 20), for which 93.2% of the genomic sequences are contained on 10 pseudomolecules (~758Mb, scaffold N50 = 72.3Mb). A total of 46,963 predicted gene models (45,308 protein coding genes) were incorporated for this genome, and genome completeness estimated by BUSCO was 94.6%. Homeobox gene linkages were analysed in detail relative to available data in other mollusc species. Our chromosome-level assembly allows the inference of ancient gene linkages (synteny) for the homeobox-containing genes, even though a number of the homeobox gene clusters, like the Hox/ParaHox clusters, are undergoing dispersal in molluscs such as this oyster. <br> <b>Conclusions</b> The analyses performed in this study and the accompanying genome sequence provide important genetic resources for this economically and culturally valuable oyster species, and offer a platform to improve understanding of animal biology and evolution more generally.<b></b><br>