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

Shaikhutdinov, Nurislam; Gusev, Oleg

doi:10.1016/j.cois.2021.12.009

Cited by 10 publications

(5 citation statements)

References 46 publications

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“…To reveal the genomic patterns that underly estimates of population history, we uncover the genome-wide landscape of recombination rates also looking at the potential role of a particular TE in these patterns. Over and above these novel genomic insights into the genomic landscape of C. riparius , these genomic resources will be more generally valuable for comparative studies on insect genomics (Blackmon et al 2017), experimental population genomics (Foucault et al 2019) and chromosome evolution (Shaikhutdinov & Gusev 2022).…”

Section: Discussionmentioning

confidence: 99%

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

Pettrich,

King,

Field

et al. 2024

Preprint

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Genome resolution is often constrained for non-model species. This can be challenging for population genomic studies as estimations are highly dependent on the quality of the reference genome. This is the case for population history inferences where accuracy relies on the correct detection of single-nucleotide polymorphisms (SNPs) and accurate recombination rates. Here, we utilize a novel long-read genome assembly ofChironomus ripariuswith high resolution at a chromosome-scale and reanalyse Illumina resequencing data of five European populations. With the model MSMC2, new population demographies were inferred and compared to an older study based on a fragmented genome. Assembly contiguity and completeness led to an increase in accuracy of past demography, suggesting the onset of divergence of an ancestral population between late Pleistocene and early Holocene. These estimates are additionally supported by paleotemperature data, which reveal significant climate shifts in Central Europe during these times. Recombination severely influences population history estimates. With the new reference genome, it was possible to resolve the recombination landscape on the genome-wide scale across different populations using the tool iSMC. Recombination and the dispersal of transposable elements (TEs) in the genome are suspected to influence each other. One TE, known asCla-element, is suspected to be involved in the divergence of the differentC. ripariuspopulations. As it seems to be highly dynamic in the genome, its potential impact on the recombination landscape was explored. No global pattern could be detected which demonstrated a higher resistance of the recombination landscape to the impact of repetitive elements on genome integrity.

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Section: Discussionmentioning

confidence: 99%

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

Pettrich,

King,

Field

et al. 2024

Preprint

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“…striatipennis has many special repeats sequence. The content of long terminal repeated (LTR) predicted by de novo makes up 21.14% of the repeat sequences of C. striatipennis (Supplementary Table 10-11) (Cornette et al, 2017;Kaiser et al, 2016;Kelley et al, 2014;Kutsenko et al, 2014;Shaikhutdinov & Gusev, 2022;Sun et al, 2021;Vicoso & Bachtrog, 2015).…”

Section: Gene Prediction and Annotationmentioning

confidence: 99%

“…Chironomid midge with same life history asC. striatipennis may also expand similar gene families to adapt to the external environment (Cornette et al, 2017;Kaiser et al, 2016;Kelley et al, 2014;Kutsenko et al, 2014;Shaikhutdinov & Gusev, 2022;Sun et al, 2021;Vicoso & Bachtrog, 2015).…”

Section: Genome Evolutionmentioning

confidence: 99%

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

Guo

2022

Preprint

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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.

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“…Dicrotendipes sinicus Qi & Lin, 2018 invades marine habitats by undergoing various morphological modifications (Qi et al 2019). These remarkable adaptations are believed to be driven by natural selection pressure arising from various living conditions (Shaikhutdinov & Gussev 2022). Nevertheless, despite the growing interest in chironomid midges' genomic features, the specific impact of the environmental stress on their mitochondrial genomes remains unexplored.…”

Section: Introductionmentioning

confidence: 99%

Codon bias analysis of the mitochondrial genome reveals natural selection in the nonbiting midge Microtendipes umbrosus Freeman, 1955 (Diptera: Chironomidae)

Cao,

Lei,

et al. 2023

The Pan-Pacific Entomologist

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

Cited by 10 publications

References 46 publications

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

The interplay of recombination landscape, a transposable element and population history in European populations ofChironomus riparius

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

Codon bias analysis of the mitochondrial genome reveals natural selection in the nonbiting midge Microtendipes umbrosus Freeman, 1955 (Diptera: Chironomidae)

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