High‐Quality Annotated ZZ Male Genome Assembly of Eulimnadia texana

ABSTRACT

In many animals, sexual differences are predominantly determined by sex chromosomes and therefore understanding the underlying evolutionary mechanisms that affect these chromosomes is crucial. Most studies on sex chromosome evolution have employed model organisms with ancient sex chromosome systems, which have already undergone evolutionary degradation thereby hindering the detection of early evolutionary processes. Androdioecious crustaceans in the genus Eulimnadia have a unique sex‐determining system that allows examination of evolutionary models of early sex chromosome evolution. In typical ZW sex chromosome systems, the Z is usually homogametic (i.e., ZZ) and the W is heterogametic (i.e., ZW), the latter being prone to long‐term degeneration due to a lack of recombination. In Eulimnadia texana , both Z and W chromosomes are found in homogametic form (i.e., ZZ and WW) retarding the buildup of deleterious recessive alleles thereby keeping these chromosomes in the “proto‐sex chromosome” stage of evolutionary development. Therefore, the E. texana system allows exploration of the early stages of W and Z sex chromosome development. Although there is a high‐quality assembly of WW hermaphrodites, there is no complementary high‐quality male (ZZ) genome assembly yet for E. texana . In the current study, we generate PacBio HiFi sequencing data from a ZZ male, construct a contamination‐filtered de novo genome assembly, and then scaffold this assembly against the WW hermaphrodite reference. The de novo ZZ contig assembly spans ~113 Mb with an N50 of 3.5 Mb and 98.1% complete Arthropoda BUSCO genes, and scaffolding against the WW reference yields a chromosome‐scale ZZ genome (12 scaffolds, total length ~113 Mb, scaffold N50 18 Mb, 0.18% gaps). Together with its gene annotation, this scaffold‐level ZZ genome complements the WW assembly and enables future comparative analyses of the Z and W proto‐sex chromosomes.