Chironomid midges (Diptera) provide insights into genome evolution in extreme environments

Detrimental effects of thiamethoxam on the physiological status, gut microbiota, and gut metabolomics profile of Propsilocerus akamusi chironomid larvae (Diptera: Chironomidae)

Thiamethoxam, a widely applied neonicotinoid pesticide, poses a non-negligible risk to aquatic organisms and has garnered considerable attention. The biological impacts of thiamethoxam on chironomid larvae and protective strategies for tolerance remain to be investigated. In this study, we addressed the functional role of gut microbiota and determined the potential effects of thiamethoxam on physiological status, microbial commensals, and gut metabolome profile. A disturbed physiological status was induced by semi-lethal and sub-lethal thiamethoxam, with a higher concentration resulting in a more rapid and stronger response, as reflected by a conspicuous alteration of detoxifying and oxidative markers. Our results also demonstrated that an intact gut microflora was necessary for chironomid larvae to survive better under thiamethoxam-challenged condition. A low dosage of thiamethoxam could remarkably decrease the relative abundance of beneficial bacterial strains (e.g. Cetobacterium and Tyzzerella) while significantly increase the prevalence of opportunistic pathogens, including the genera Serratia, Shewanella, Aeromonas and Pseudomonas. Additionally, an evident variability of bacterial correlations was observed, and the thiamethoxam exposure impaired the genus-genus interaction and destabilized the whole community structure. The metabolome profile revealed that the toxic factor induced a significant downregulation of metabolites involved in glycolysis, amino acid metabolism and fatty acid metabolism pathways. Notably, the integration of metabolomics and gut microbiota data highlighted that representative substrates related to energy metabolism were negatively correlated with the elevated opportunities pathogens when chironomid larvae were challenged with thiamethoxam. These results suggested that a balanced microbial community was pivotal for maintaining energy expenditure and intake system, thus conferring benefits for chironomid larvae to defend against the invading thiamethoxam and preserve their physical well-being. This work provides theoretical guidance for the practical use of thiamethoxam in aquatic ecosystem and offers insights into the potential mechanisms utilized by chironomid larvae to detoxify pesticides.

Genome-wide phylogenetic analysis and expansion of gene families involved in detoxification in Smittia aterrima (Meigen)and Smittia pratorum (Goetghebuer) (Diptera, Chironomidae)

Smittia aterrima (Meigen, 1818) and Smittia pratorum (Goetghebuer, 1927) are important indicator insects for aquatic environments, showing extensive tolerance to the environment. However, the genome-wide phylogenetic relationships and characteristics of the detoxification mechanisms in S. aterrima and S. pratorum remain unclear. Based on the genomes of the two species obtained in our preliminary studies and nine genomes from the NCBI database, we found that chironomids diverged from other mosquitoes approximately 200 million years ago (MYA), and S. aterrima and S. pratorum diverged about 30 MYA according to phylogenetic analysis. Gene family evolution analysis showed significant expansion of 43 and 15 gene families in S. aterrima and S. pratorum, respectively, particularly those related to detoxification pathways. Positive selection analysis reveals that genes under positive selection are crucial for promoting environmental adaptation. Additionally, the detoxification-associated gene families including Cytochrome P450 (CYP), Glutathione S-transferases (GST), ATP-binding cassette (ABC), carboxylesterase (CCE), and UDP-glucuronosyltransferase (UGT) were annotated. Our analysis results show that these five detoxification gene families have significantly expanded in the chironomid genomes. This study highlights the genome evolution of chironomids and their responses to mechanisms of tolerance to environmental challenges.

Functional and evolutionary analysis of key enzymes triacylglycerol lipase, glycogen hydrolases in the glycerol and glucose biosynthesis pathway and cellular chaperones for freeze-tolerance of the Rice stem borer, Chilo suppressalis

Freeze-tolerance is an important physiological trait for terrestrial environmental adaptation and intraspecific geographic-lineage diversification in ectothermic animals, yet there remains a lack of systematic studies on its underlying genetic mechanisms and evolution. To address this problem, we employed the widely distributed rice pest, the Chilo suppressalis, as a model to explore the genetic mechanisms and evolutionary history of freeze-tolerance. First, we systematically characterized its antifreeze mechanisms by performing functional validation of potential key genes in laboratory-reared lines. This revealed the functional roles of glycerol biosynthesis in freeze-tolerance, including the triacylglycerol-originated pathway via triacylglycerol lipase (Tgl) hydrolysis and the glycogen-originated pathway via α-amylase (Aa) and maltase (Ma) hydrolysis, as well as the roles of the cellular chaperones Hsc70 and Hsf1. Then, we investigated the evolution of freeze-tolerance by collecting representative geographical samples and performing population genetic analyses, which suggested differentiated strategies of cold adaptation in different geographic populations. Taken together, our findings demonstrate the functional basis of cold resistance in Chilo suppressalis and reveal the evolutionary history of freeze-tolerance in natural populations, providing insights into organismal freeze-tolerance and clues for pest control.

The sediment of a river having ''good ecological status" turned out to be toxic to midge Chironomus riparius larvae: Implication for environmental monitoring?

Globally, monitoring of the surface waters is largely limited to the physico-chemical analysis of water in rivers and lakes. Sediment state in the aquatic systems including sediment chemical content or the structure and diversity of benthic communities or ecotoxicological studies with natural sediments remains largely overlooked by the monitoring programs. Hence we assessed the potential toxicity of three riverine sediments on the life-cycle traits (emergence and reproduction) of midge Chironomus riparius via an ecotoxicological testing method over two generations (according to OECD test 233 guidelines). In addition, the riverine sediments were spiked with polyamide (nylon) microplastic particles (1 g kg-1) to analyze an additive effect of microplastic on the sediment toxicity. As model river systems, three rivers (Karchaghbyur, Gavaraget, Argichi) in the Lake Sevan basin (Armenia) were selected. Results of ecotoxicity testing were compared with the indices of water quality (derived from the physico-chemical analysis) and the indices of the ecological status of the rivers (derived from the analysis of benthic communities). The results of testing demonstrated an unexpectedly low emergence of midges after the first generation exposed to the sediment of the river having ''good ecological status'' - the Argichi. Sediments of the Karchaghbyur and Gavaraget rivers impeded the emergence and reproduction of midges after the second generation. An addition of polyamide particles to the sediments did not significantly affect the life-cycle traits of C. riparius indicating the primary effect of the sediments' condition. The discrepancy of biotesting result with that of the other two methods (which indicated ''average water quality'' and "good ecological status") underlies the importance of designing more comprehensive monitoring programs for better assessment and protection of aquatic systems and resources.

The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation

Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

Two chromosome-level genomes of Smittia aterrima and Smittia pratorum (Diptera, Chironomidae)

Chironomids are one of the most abundant aquatic insects and are widely distributed in various biological communities. However, the lack of high-quality genomes has hindered our ability to study the evolution and ecology of this group. Here, we used Nanopore long reads and Hi-C data to produce two chromosome-level genomes from mixed genomic data. The genomes of Smittia aterrima (SateA) and Smittia pratorum (SateB) were assembled into three chromosomes, with sizes of 78.45 Mb and 71.56 Mb, scaffold N50 lengths of 25.73 and 23.53 Mb, and BUSCO completeness of 98.5% and 97.8% (n = 1,367), 5.68 Mb (7.24%) and 1.94 Mb (2.72%) of repetitive elements, and predicted 12,330 (97.70% BUSCO completeness) and 11,250 (97.40%) protein-coding genes, respectively. These high-quality genomes will serve as valuable resources for comprehending the evolution and environmental adaptation of chironomids.

Chromosome-level genome assembly of the deep-sea snail Phymorhynchus buccinoides provides insights into the adaptation to the cold seep habitat

BACKGROUND

The deep-sea snail Phymorhynchus buccinoides belongs to the genus Phymorhynchus (Neogastropoda: Raphitomidae), and it is a dominant specie in the cold seep habitat. As the environment of the cold seep is characterized by darkness, hypoxia and high concentrations of toxic substances such as hydrogen sulfide (H2S), exploration of the diverse fauna living around cold seeps will help to uncover the adaptive mechanisms to this unique habitat. In the present study, a chromosome-level genome of P. buccinoides was constructed and a series of genomic and transcriptomic analyses were conducted to explore its molecular adaptation mechanisms to the cold seep environments.

RESULTS

The assembled genome size of the P. buccinoides was approximately 2.1 Gb, which is larger than most of the reported snail genomes, possibly due to the high proportion of repetitive elements. About 92.0% of the assembled base pairs of contigs were anchored to 34 pseudo-chromosomes with a scaffold N50 size of 60.0 Mb. Compared with relative specie in the shallow water, the glutamate regulative and related genes were expanded in P. buccinoides, which contributes to the acclimation to hypoxia and coldness. Besides, the relatively high mRNA expression levels of the olfactory/chemosensory genes in osphradium indicate that P. buccinoides might have evolved a highly developed and sensitive olfactory organ for its orientation and predation. Moreover, the genome and transcriptome analyses demonstrate that P. buccinoides has evolved a sulfite-tolerance mechanism by performing H2S detoxification. Many genes involved in H2S detoxification were highly expressed in ctenidium and hepatopancreas, suggesting that these tissues might be critical for H2S detoxification and sulfite tolerance.

CONCLUSIONS

In summary, our report of this chromosome-level deep-sea snail genome provides a comprehensive genomic basis for the understanding of the adaptation strategy of P. buccinoides to the extreme environment at the deep-sea cold seeps.

Population Genomics of Two Closely Related Anhydrobiotic Midges Reveals Differences in Adaptation to Extreme Desiccation

The sleeping chironomid Polypedilum vanderplanki is capable of anhydrobiosis, a striking example of adaptation to extreme desiccation. Tolerance to complete desiccation in this species is associated with emergence of multiple paralogs of protective genes. One of the gene families highly expressed under anhydrobiosis and involved in this process is protein-L-isoaspartate (D-aspartate) O-methyltransferases (PIMTs). Recently, another closely related midge was discovered, Polypedilum pembai, which is able not only to tolerate desiccation but also to survive multiple desiccation-rehydration cycles. To investigate the evolution of anhydrobiosis in these species, we sequenced and assembled the genome of P. pembai and compared it with P. vanderplanki and also performed a population genomics analysis of several populations of P. vanderplanki and one population of P. pembai. We observe positive selection and radical changes in the genetic architecture of the PIMT locus between the two species, including its amplification in the P. pembai lineage. In particular, PIMT-4, the most highly expressed of these PIMTs, is present in six copies in the P. pembai; these copies differ in expression profiles, suggesting possible sub- or neofunctionalization. The nucleotide diversity of the genomic region carrying these new genes is decreased in P. pembai, but not in the orthologous region carrying the ancestral gene in P. vanderplanki, providing evidence for a selective sweep associated with postduplication adaptation in the former. Overall, our results suggest an extensive relatively recent and likely ongoing adaptation of the mechanisms of anhydrobiosis.