High-quality chromosome-level genome assembly of female Artemia franciscana reveals sex chromosome and Hox gene organization

<i>Artemia</i> is a crustacean genus belonging to the order Anostraca in the class Branchiopoda and lives in inland hypersaline lakes. Among the genus, <i>A. franciscana</i> is a valuable species as a fish food in the aquaculture industry or as an aquatic model organism for toxicity tests. However, genomic data for <i>A. franciscana</i> remains incomplete. In this study, high-quality genome assembly at the chromosome level of female <i>A. franciscana</i> was conducted by combining various sequencing and assembly technologies. The final <i>A. franciscana</i> assembled genome was 1.27 Gb in length, containing 21 chromosomal scaffolds (>10 Mb). The scaffold N50 was 45.3 Mb, with a complete BUSCO value of 91.0 %, thereby confirming that a high-quality genome was assembled. Gene annotation shows that the <i>A. franciscana</i> genome contained 67.26 % of repetitive sequences, and a total of 26,923 protein-coding genes were predicted. Among the 21 chromosome-scale scaffolds, chromosome 1 was identified as a sex chromosome Z. Additionally, five contigs of putative W chromosome fragments and the candidate sex-determining genes were suggested. Ten homeobox (<i>Hox</i>) genes were identified in <i>A. franciscana</i> on the chromosome 14, which were in two subclusters with a large gap. <i>Hox</i> gene organizations within 13 arthropods showed that four anostracans had conserved synteny. This study provides a new female <i>Artemia</i> genome with sex chromosome and the first complete genomic arrangement of the <i>Hox</i> cluster in Anostraca. This study will be a useful genomic and genetic reference for understanding the evolution and development of <i>A. franciscana</i>.