Transposable element expansion and low-level piRNA silencing in grasshoppers may cause genome gigantism

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: Oct. 28, 2022

Abstract Background Transposable elements (TEs) have been likened to parasites in the genome that reproduce and move ceaselessly host, continuously enlarging host genome. However, Piwi-interacting RNA (piRNA) pathway defends animal genomes against harmful consequences of TE invasion by imposing small-RNA-mediated silencing. Here we compare activity two grasshopper species with different sizes Acrididae ( Locusta migratoria manilensis ♀1C = 6.60 pg, Angaracris rhodopa 16.36 pg) ascertain influence piRNAs. Results We discovered repetitive sequences accounted for 74.56% A. rhodopa, more than 56.83% L. , large-genome contained a higher TEs proportions. The comparative analysis revealed 41 (copy number > 500) were shared both species. exhibited distinct “landscapes” divergence. outbreaks small-genome occurred at ancient times, while maintains active transposition events recent past. Evolutionary history studies on suggest may be subject dynamics resistances these found transcript abundance was TE-derived piRNAs lower grasshopper. In addition, piRNA methylase HENMT, which is underexpressed grasshopper, impedes silencing level. Conclusions Our study gigantic small key gene HENMT biogenesis (Ping-Pong cycle) underexpressed. hypothesize low-level unbalances original positive correlation between piRNAs, triggers proliferate out control, one reasons gigantism genomes.

Language: Английский

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Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: Feb. 3, 2025

Parasitism as a life strategy has independently evolved multiple times within the eukaryotic tree of life. Each lineage developed mechanisms to invade hosts, exploit resources, and ensure replication, but our knowledge survival in many parasitic taxa remain extremely limited. One such group is Myxozoa, which are obligate, dixenous cnidarians. Evidence suggests that myxozoans from free-living ancestors endoparasites around 600 million years ago likely one first metazoan parasites on Earth. Some pose significant threats farmed wild fish populations, negatively impacting aquaculture stocks; example Sphaerospora molnari, forms spores gills common carp (Cyprinus carpio), disrupting gill epithelia causing somatic respiratory failure. molnari undergoes sequential development different organs its host, with large numbers morphologically distinct stages occurring blood, liver, carp. We hypothesize these parasite life-stages differ regards their host exploitation, pathogenicity, immune evasion strategies mechanisms. performed stage-specific transcriptomic profiling identify differentially expressed key functional gene groups relate functions provide fundamental understanding S. uses optimize lifestyle. aimed genes related pathogenicity cell exploitation mechanisms, we unique might be indicative evolutionary innovations specific adaptations environments. used isolation protocols comparative transcriptomics study early proliferative spore-forming unveiling variation expression between each stage. discovered several apparent transcriptome, including proteins function uptake previously unknown nutrients, factors may contribute long-term improve adhesion cells have arisen horizontal transfer. Notably, identified similar known virulence other organisms, particularly blood intestinal like Plasmodium, Trypanosoma, Giardia. Many absent published cnidarian myxozoan datasets appear molnari; they therefore represent potential enabling host's system. In order address threat posed by both cultured species stocks, it imperative deepen genetics. offers an appealing model for identifying development. thus far reveal novelty role niches. addition, describe pathogenicity-associated genetic toolbox discuss implications discoveries disease control shedding light targets intervention strategies. revealed developmental profiles infected tissues. stage parasites, cytoskeletal rearrangements mostly up-regulated, while those up-regulated bloodstream metabolism propose list "pathogenicity-related" families. uncovered up-regulation no homologues or were not found lineages.

Language: Английский

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Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 13, 2025

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) a phylogenetic context. We sequenced assembled de novo the genome of Actinostella flosculifera analyzed total 38 nuclear genomes to create first ActiniariaREP library (Actiniaria-REPlib). compared Actiniaria-REPlib with Repbase RepeatModeler2 libraries, used dnaPipeTE annotate from genomic short-read datasets 36 species for divergence landscapes. Our annotated mitochondrial genomes, including 27 newly ones. re-annotated ~92% unknown initial library, finding that 6.4-30.6% were transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, 1.2-7% unclassifiable sequences. recovered 9.4x more REP actiniarian than Dfam 10.4x Repbase. It yielded 79,903 TE consensus (74,643 known, 5,260 unknown), 7,697 (3,742 3,944 unknown) Repbae (763 known). significantly enhances characterization DNA, assembling re-annotating identifying diverse elements. vastly outperforms existing databases, recovering providing comprehensive resource future evolutionary studies Actiniaria.

Language: Английский

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A myxozoan genome reveals mosaic evolution in a parasitic cnidarian

BMC Biology, Journal Year: 2022, Volume and Issue: 20(1)

Published: Feb. 18, 2022

Abstract Background Parasite evolution has been conceptualized as a process of genetic loss and simplification. Contrary to this model, there is evidence expansion conservation gene families related essential functions parasitism in some parasite genomes, reminiscent widespread mosaic —where subregions genome have different rates evolutionary change. We found the cnidarian Myxobolus honghuensis , myxozoan fish, with extremely simple morphology. Results compared M. other myxozoans free-living cnidarians, determined that it relatively larger (206 Mb), which less reduced compact due retention, large introns, transposon insertion, but not polyploidy. Relative metazoans, depleted neural genes only simplest animal immune components. Conversely, more involved stress resistance, tissue invasion, energy metabolism, cellular processes cnidarians. postulate these result adaptations endoparasitism. retains Cnidaria, including nervous system, myogenic components, ANTP class Homeobox genes, components Wnt Hedgehog pathways. Conclusions Our analyses suggest evolved conservative, divergent, depleted, enhanced These findings illustrate are genetically previously regarded, driven by both genomic streamlining expansion.

Language: Английский

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Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(3)

Published: Jan. 21, 2023

Abstract Ion channels are highly diverse in the cnidarian model organism Nematostella vectensis (Anthozoa), but little is known about evolutionary origins of this channel diversity and its conservation across Cnidaria. Here, we examined evolution voltage-gated K+ Cnidaria by comparing genomes transcriptomes species from Anthozoa Medusozoa. We found an average over 40 genes per species, a phylogenetic reconstruction Kv, KCNQ, Ether-a-go-go (EAG) gene families identified 28 present last common ancestor Medusozoa (23 1 4 EAG). Thus, much diversification these took place stem lineage prior to emergence modern classes. In contrast, bilaterian lineage, which humans evolved, contained no more than nine channels. These results hint at complexity electrical signaling all cnidarians that contrasts with perceived anatomical simplicity their neuromuscular systems. data provide foundation function can be investigated, will undoubtedly important insights into physiology.

Language: Английский

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Evolution of myxozoan mitochondrial genomes: insights from myxobolids

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: April 22, 2024

Abstract Background Myxozoa is a class of cnidarian parasites that encompasses over 2,400 species. Phylogenetic relationships among myxozoans remain highly debated, owing to both lack informative morphological characters and shortage molecular markers. Mitochondrial (mt) genomes are common marker in phylogeny biogeography. However, only five complete myxozoan mt have been sequenced: four belonging two closely related genera, Enteromyxum Kudoa , one from the genus Myxobolus . Interestingly, while cytochrome oxidase genes could be identified no such were found squamalis another member Myxobolidae ( Henneguya salminicola ) was lost its entire genome. To evaluate utility reconstruct understand if loss characteristic myxobolids, we sequenced genome wulii, M. honghuensis shantungensis, Thelohanellus kitauei and, Sphaeromyxa zaharoni using Illumina Oxford Nanopore platforms. Results Unlike which possesses partitioned genome, encoded on single circular chromosomes. An plasmid wulii as described previously iwatai In all new genomes, protein-coding cob, cox1, cox2, nad1 nad5 rRNAs rnl rns recognized, but tRNA. We species shared unidentified reading frames, supporting view these open frames functional. Our phylogenetic reconstructions based conserved agree with published trees 18S rRNA gene. Conclusions results suggest not ancestral likely chromosome, plasmids exist few lineages. findings indicate sequences poor markers for reconstructing because their fast-evolutionary rates abundance repeated elements, complicates assembly.

Language: Английский

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Apoptotic gene loss in Cnidaria is associated with transition to parasitism

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 17, 2023

Abstract The phylum Cnidaria consists of several morphologically diverse classes including Anthozoa, Cubozoa, Hydrozoa, Polypodiozoa, Scyphozoa, Staurozoa, and Myxozoa. Myxozoa comprises two subclasses obligate parasites—Myxosporea Malacosporea, which demonstrate various degrees simplification. Myxosporea were previously reported to lack the majority core protein domains apoptotic proteins caspases, Bcl-2, APAF-1 homologs. Other sequenced Cnidaria, parasite Polypodium hydriforme from Polypodiozoa do not share this genetic feature. Whether loss is unique or also present in its sister subclass Malacosporea was investigated. We show that presence gradually diminishes free-living Myxosporea. This observation does favor hypothesis catastrophic simplification at level, but rather supports a stepwise adaptation parasitism likely started early parasitic ancestors gave rise

Language: Английский

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Highly Dynamic Gene Family Evolution Suggests Changing Roles forPONGenes Within Metazoa

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(2)

Published: Jan. 31, 2023

Abstract Change in gene family size has been shown to facilitate adaptation different selective pressures. This includes duplication increase dosage or diversification of enzymatic substrates and deletion due relaxed selection. We recently found that the PON1 gene, an enzyme with arylesterase lactonase activity, was lost repeatedly aquatic mammalian lineages, suggesting PON is responsive environmental change. further investigated if these fluctuations were restricted mammals approximately when this expanded within mammals. Using 112 metazoan protein models, we explored evolutionary history characterize dynamic evolution family. there have multiple, independent expansion events tardigrades, cephalochordates, echinoderms. In addition, partial loss monotremes sea cucumbers what appears be complete arthropods, urochordates, platyhelminths, ctenophores, placozoans. show three paralogs occurred ancestor all after divergence sauropsida but before from therians. also provide evidence a novel brushtail possum. face repeated expansions deletions context changing environments, suggest range pressures, including pathogen infection mitigation oxidative damage, are likely influencing across metazoa.

Language: Английский

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Transcriptomic Insights into the Diversity and Evolution of Myxozoa (Cnidaria, Endocnidozoa) Toxin-like Proteins

Marine Drugs, Journal Year: 2022, Volume and Issue: 20(5), P. 291 - 291

Published: April 26, 2022

Myxozoa is a speciose group of endoparasitic cnidarians that can cause severe ecological and economic effects. Their cnidarian affinity affirmed by genetic relatedness the presence nematocysts, historically called “polar capsules”. Previous studies have revealed toxin-like proteins in myxozoans; however, diversity evolution venom are not fully understood. Here, we performed comparative analysis using newly sequenced transcriptomes five Myxobolidae species as well some public datasets. Toxin mining myxozoans lost most their toxin families, while retained Kunitz, M12B, CRISP, which may play role endoparasitism. The composition Endocnidozoa (Myxozoa + Polypodium) differs from free-living be influenced environmental factors. Phylogenetic analyses showed families were clustered into different clades. Selection purifying selection was dominant evolutionary pressure toxins, they still episodic adaptive selection. This suggests potency or specificity particular might increase. Overall, our findings provide more comprehensive framework for understanding venoms.

Language: Английский

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The highly repetitive genome of Myxobolus sp., a myxozoan parasite of fathead minnows

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Feb. 12, 2024

Background: The Myxozoa is a group of at least 2,400 endoparasites within the phylum Cnidaria. All myxozoans have greatly reduced in size and morphology compared to free-living members phylum. They are best known for causing disease economically important fish across world; example, Myxobolus cerebralis causes Whirling Disease, which can kill 90% infected juvenile salmonid fish. In 2017, potentially new myxozoan species was identified Alberta. sp. distinct lesions fathead minnows, ultimately fatal. Here, we sequenced, assembled analyzed genome understand how parasite interacts with its host identify potential strategies counter this emerging threat. Results: At 185 Mb, largest sequenced so far. This large is, part, due high repetitive content; 68% interspersed repeats, MULE-MuDR transposon covering 18% genome. Similar genomes, has lost many genes well conserved other eukaryotes. However, also multiple expansions gene families (serine proteases, hexokinases, FLYWCH-domain containing proteins) suggests their functional importance parasite. mitochondrial encodes only five thirteen protein-coding typically found animals. We that atp6 transferred nucleus acquired mitochondria-targeting signal Conclusions: Our study provides valuable insights into biology promising avenues future research. propose M. rasmusseni model explore host-parasite interactions these parasites.

Language: Английский

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