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

Abstract

Background

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.

Results

Here, we present a high-quality chromosome-level genome assembly of Magallana
hongkongensis (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.

Conclusions

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.