Chromosome-level genome assembly of Chironomus striatipennis Kieffer provides insights into benthic adaptation and metamorphosis mechanism
Bingxin Guo1, Jinxian Chen1, Liang Lu2, Li Wang2, Liqing Wang1, Chenhong Li2, Wenbing Liu3, Ruilei Zhang1#
1Enginnering Research Center of Environmental DNA and Ecological Water Health Assessment, College of Fisheries and life Science, Shanghai Ocean University, Shanghai 201306, China
2The Lab of Molecular Systematics and Ecology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
3Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
#Bingxin Guo and Jinxian Chen contributed equally to this work.
#To whom correspondence should be addressed. Email:rlzhang@shou.edu.cn
Abstract : 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.
Keywords
Chironomus striatipennis , genome, benthic adaptation, metamorphosis mechanism
1 Introduction
In aquatic ecosystem, benthos can directly or indirectly affect the production of fish or waterfowl (Smith, 2014). In many aquatic ecosystems the number of chironomid species present may account for at least 50% of the total macroinvertebrate species recorded (Armitage et al., 1995) and serve as backbone components of aquatic benthic ecosystem.
Chironomids are the most ubiquitous and frequently the most abundant insects in all types of freshwater. Under certain conditions, such as at low levels of dissolved oxygen, larval chironomid may be the only insect present in benthic sediments (Armitage et al., 1995). Species richness, wide distribution and tolerance to adverse conditions make them be frequently selected as good indicator organisms to detect water environment and pollution in ecological studies (Goto et al., 2011; Hinton H E, 1951; Pinder, 1986; Sogame & Kikawada, 2017). Recent research released the flexibility of Hemoglobin in response to xenobiotics may play a critical role in adaptive evolution in chironomids (Ha & Choi, 2008). Therefore, the regulation of heme metabolic pathway related to hemoglobin activity is particularly important. Another important factor facilitating to adaptation for environment is that many detoxification enzyme genes are highly expressed in chironomid (Kozeretska et al., 2022). Futhermore, chironomids are holometabolous insects undergoing four distinct stages, egg, larva, pupa and adult, and the larval stage accounts for the vast majority of the lifecycle. Specifically, after laying eggs, they hatch into larva in 1-2 day for most Chironomids; after that, chironomid experiences a period of pelagic life before settling on substrates, living benthic; when the external environment and its physiological conditions are suitable, it metamorphoses and emerges into adults (Armitage et al., 1995). Therefore, chironomid must be able to adapt to different living environments and have a set of mechanisms that can regulate metamorphosis and development. However, neither its biological mechanism to cope with the complex external environment nor its regulatory mechanism in the process of metamorphosis and eclosion have been explored. So combing with life cycle characteristics of chironomid, we can focus on exploring adaptation of chironomid larva to benthic life and regulation mechanism of metamorphosis and eclosion.
Using high-quality genome as a “scalpel” will help to probe the genetic basis of environmental adaptation and metamorphosis in these species. In the last decade, with the popularization and application of high-throughput sequencing technology, the genomes of more species have been released. However, in family chironomidae (Diptera, Insecta), the genomes of only 8 species have been sequenced and assembled (Cornette et al., 2016; Kelley et al., 2014; Kutsenko et al., 2014; Sun et al., 2021; Vicoso & Bachtrog, 2015). In previous researches, the genusChironomus has only scaffold level assembled genome (ncbi), the precision and accuracy of its genome may not rest content with the increasingly high standard of experimental research. Meanwihle, it has been proved that there are great differences between the genomes ofChironomus and other genus in Chironomidae (Cornette et al., 2015). Therefore, it is essential to obtain a high-quality genome ofChironomus species.
Chironomus striatipennis Kieffer (Diptera: Chironomidae) is widely distributed in Holarctic, Oriental and Neotropical regions; its larvae frequently present in oligotrophic to eutrophic freshwater, such as lakes, swamps, rivers, sewage ditches, fish ponds and rice fields; it is regarded as an alien species to America derived from Asia by unintentional human transport (Al-Shami et al., 2012; Amora et al., 2015; Martin, 2017) (Figure 1). C. striatipennis is widespread in China (Wang et al., 2020); we had ever found its larvae infected municipal water systems in several cities in South China. Given ease to reproduce, short life cycle and the larval stage accounts for most of life cycle, the species is amenable to being maintained as a laboratory colony for study of various aspects of its biology and toxicology test (Lacerda et al., 2014; Platzer-Schltz & Welsch, 1969; Platzer-Schultz, 1970; Wu et al., 2021; Zhang et al., 2019). It is necessary to understand the genetic mechanism of C. striatipennis for unraveling chironomid adaptability and tolerance (Neff et al., 2021; Zhang et al., 2020; Zhang et al., 2021).
In present research, Oxford Nanepore technology and Hi-C technology were applied to generate a chromosome-level genome assembly of C. striatipennis Kieffer. Further, combined with transcriptome, the genetic basis of adaptation to benthic low oxygen substrate were revealed in chironomid larvae, which will set a foundation for exploring the evolution direction of macrozoobenthos in the benthic environment.