Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

Genome Research, Journal Year: 2023, Volume and Issue: 33(10), P. 1708 - 1717

Published: Sept. 22, 2023

Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species report wide variation RE dynamics Analysis associations between protein-coding genes revealed dynamic evolution at interface coding regions insects, including notably elevated RE-gene lineages with abundant long interspersed nuclear (LINEs). leveraged this large, empirical data set quantify impacts long-read technology on detection investigate fundamental challenges annotation diverse In assemblies, we detected ∼36% more than short-read terminal repeats (LTRs) showing 162% increased detection, whereas DNA transposons LINEs showed less respective technology-related bias. lineages, 25%-85% repetitive sequences were "unclassified" following automated annotation, compared only ∼13% Drosophila species. Although diversity available genomes has rapidly expanded, show rate community contributions databases not kept pace, preventing efficient high-resolution study highlight tremendous opportunity need for biodiversity genomics field embrace suggest collective steps making progress toward goal.

Language: Английский

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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Oct. 27, 2022

Parasitoid wasps are rapidly developing as a model for evolutionary biology. Here we present chromosomal genomes of two Anastatus wasps, A. japonicus and fulloi, leverage these to study fundamental questions-genome size evolution venom evolution. shows much larger genome than is known among other with unexpectedly recent bursts LTR retrotransposons. Importantly, several genomic innovations, including Piwi gene family expansion, ubiquitous expression profiles, well transposable element-piRNA coevolution, have likely emerged element silencing maintain stability. Additionally, show that the co-option arose by shifts in gland plays dominant role turnover. We also highlight potential importance non-venom genes coexpressed during Our findings greatly advance current understanding evolution, resources will facilitate comparative genomics studies insects future.

Language: Английский

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A universal DNA barcode for the Tree of Life

Published: Jan. 18, 2024

Species identification using DNA barcodes has revolutionized biodiversity sciences and society at large. However, conventional barcoding methods do not reflect genomic complexity, may lack sufficient variation, rely on limited loci that are universal across the Tree of Life. Here, we develop a novel method uses exceptionally low-coverage genome skim data to create “varKode”, two-dimensional image representing landscape species. Using these varKodes, then train neural networks for precise taxonomic identification. Applying an expertly annotated dataset including hundreds newly sequenced samples from plant clade Malpighiales, demonstrate >91% precision when identifying species or genera. Remarkably, high accuracy remains despite minimal amounts lead failure applying alternative methods. We further illustrate broad utility varKodes several focal clades eukaryotes prokaryotes. As final test, classify entire NCBI eukaryote sequence-read archive identify its 861 constituent families with >95% utilizing less than 10 Mbp per sample. Enhanced computational efficiency scalability, inputs robust degraded DNA, modularity development make varKoding ideal approach science.

Language: Английский

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Comparative genomics reveals insights into anuran genome size evolution

BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)

Published: July 6, 2023

Abstract Background Amphibians, particularly anurans, display an enormous variation in genome size. Due to the unavailability of whole datasets past, genomic elements and evolutionary causes anuran size are poorly understood. To address this, we analyzed whole-genome sequences 14 species ranging from 1.1 6.8 Gb. By annotating multiple elements, investigated correlates further examined whether relates habitat types. Results Our results showed that intron expansions or contraction Transposable Elements (TEs) diversity do not contribute significantly variation. However, recent accumulation transposable lack deletion ancient TEs primarily accounted for evolution sizes. study abundance density simple repeat positively correlate with Ancestral state reconstruction revealed exhibits a taxon-specific pattern evolution, families Bufonidae Pipidae experiencing extreme expansion events, respectively. result no relationship between types, although large genome-sized predominantly found humid habitats. Conclusions Overall, our identified element their dynamics accounting variation, thus paving path greater understanding amphibians.

Language: Английский

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Effective population size does not explain long-term variation in genome size and transposable element content in animals

Published: Sept. 11, 2024

Animal genomes exhibit a remarkable variation in size, but the evolutionary forces responsible for such are still debated. As effective population size (N e ) reflects intensity of genetic drift, it is expected to be key determinant fixation rate nearly-neutral mutations. Accordingly, Mutational Hazard Hypothesis postulates lineages with low N have bigger genome sizes due accumulation slightly deleterious transposable elements (TEs), and those high maintain streamlined as consequence more selection against TEs. However, existence both empirical confirmation refutation using different methods scales precludes its general validation. Using high-quality public data, we estimated TE content non-synonymous synonymous substitutions (dN/dS) proxy 807 species including vertebrates, molluscs insects. After collecting available life-history traits, tested associations among proxies, while accounting phylogenetic non-independence. Our results confirm TEs major drivers variation, endorse traits dN/dS reliable proxies . do not find any evidence increased drift result an across animals. Within closely related clades, only few isolated weak emerge fishes birds. outline scenario where dynamics vary according lineage-specific patterns, lending no support predominant force driving long-term evolution

Language: Английский

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Evolutionary genomics of camouflage innovation in the orchid mantis

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: Aug. 10, 2023

Abstract The orchid mantises achieve camouflage with morphological modifications in body color and pattern, providing an interesting model for understanding phenotypic innovation. However, a reference genome is lacking the order Mantodea. To unveil mechanisms of plant-mimicking coloration patterns, we performed de novo assembly two chromosome-level genomes mantis its close relative, dead leaf mantis. Comparative genomic analysis revealed that Scarlet gene plays important role synthesis xanthommatin, pigment coloration. Combining developmental transcriptomic genetic engineering experiments, found cuticle was essential component ‘petal-like’ enlargement, specific expression ventral femur controlled by Wnt signaling. prolonged Ultrabithorax (Ubx) accompanied femoral expansion suggested Ubx determines leg remodeling early stage. We also evidence evolution Trypsin family insectivory adaptation ecdysone-dependent sexual dimorphism size. Overall, our study presents new catalogs reveals evolutionary underlying unique praying mantis, insights into innovation adaptation.

Language: Английский

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Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects

Molecular and Cellular Endocrinology, Journal Year: 2024, Volume and Issue: 585, P. 112178 - 112178

Published: Feb. 9, 2024

Language: Английский

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Evolutionary dynamics of genome size and transposable elements in crickets (Ensifera: Gryllidea)

Systematic Entomology, Journal Year: 2024, Volume and Issue: 49(4), P. 549 - 564

Published: March 8, 2024

Abstract Orthoptera species are characterised by their expansive genomes. However, crickets, the third largest group of this order, have notably smaller genomes than grasshoppers or katydids. The evolutionary drivers behind these differences in genome size (GS) remain largely uncharted. In our study involving 56 cricket species, we assessed GS using flow cytometry and assembled 43 novel mitochondrial for phylogenetic analysis. Model fitting indicated that generally conformed to an Ornstein‐Uhlenbeck adaptive model, displaying a 5.1‐fold range variation GS, from 0.82 pg Myrmecophilus quadrispina Perkins 4.68 Ornebius formosanus Shiraki. Remarkably, despite such variations, no significant trends contraction expansion were detected, suggesting stabilisation. We found strong evidence expansions repeat elements, particularly transposable elements (TEs), key large crickets. Across analysed, TE content exhibited substantial variability, spanning mere 3.63% pronounced 31.22%. Clades exhibiting as mole crickets (Gryllotalpidae), ant‐loving (Myrmecophilidae) scaly (Mogoplistidae), often observed at basal nodes exhibit distinct ecological niches morphological divergences. This implies undergo early mutations stabilise throughout evolution. Our findings shed light on common patterns uncover lineage‐specific evolution TEs anticipate will provide foundation future comparative research insect repertoire.

Language: Английский

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The state of parasitoid wasp genomics

Trends in Parasitology, Journal Year: 2024, Volume and Issue: 40(10), P. 914 - 929

Published: Sept. 2, 2024

Language: Английский

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The Genomics Revolution Drives a New Era in Entomology

Annual Review of Entomology, Journal Year: 2025, Volume and Issue: 70(1), P. 379 - 400

Published: Jan. 28, 2025

Thanks to the fast development of sequencing techniques and bioinformatics tools, genome an insect species for specific research purposes has become increasingly popular practice. Insect genomes not only provide sets gene sequences but also represent a change in focus from reductionism systemic biology field entomology. Using genomes, researchers are able identify study functions all members family, pathway, or network associated with trait interest. Comparative genomics studies new insights into evolution, addressing long-lasting controversies taxonomy. It is now feasible uncover genetic basis important traits by identifying variants using resequencing data individual insects, followed genome-wide association analysis. Here, we review current progress projects application uncovering phylogenetic relationships between insects unraveling mechanisms life-history traits. We summarize challenges sharing possible solutions. Finally, guidance fully deeply mining data.

Language: Английский

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