Chromosome-level genome assembly of Chironomus striatipennis Kieffer provides insights into benthic adaptation and metamorphosis mechanism

Chironomid is the most important macroinvertebrate species in aquatic ecosystem. Chironomus represents the most important genus of the Chironomidae. However, the species of this genus lack a high-quality assembled genome. Here, a high-quality chromosome-level assembled genome of Chironomus striatipennis which is an important model organism in aquatic ecological detection and toxicological application has been reported. The assembled genome size of C. striatipennis was 181.84 Mb, with a scaffold N50 value of 54.13 Mb. Furthermore, the molecular mechanism of adaptive evolution of Chironomid to benthic environment was elucidated by combining transcriptome data of different stages. The complete metabolic pathway of Hemoglobin was clarified in C. striatipennis for the first time to suggests the regulatory mechanism underlying its adaptation to benthic living. The expansions of CYP450s gene family related to detoxification explain its tolerance to the harsh environment. The key gene family, JHAMT, involved in biosynthesis of juvenile hormone are substantially expanded. The expansion of JHAMT genes and the regular regulation of juvenile hormone and ecdysone explain the developmental plasticity of C. striatipennis. In this study, it was also found that C. striatipennis is more dependent on JNK signal pathway induced metamorphosis than Drosophila melanogaster. This study provides some views into genetic basis of tolerance and adaptation of C. striatipennis to harsh benthic environments and lays a part of the foundation for the adaptive evolution of benthic animals.