Novel mitochondrial genome rearrangements including duplications and extensive heteroplasmy could underlie temperature adaptations in Antarctic notothenioid fishes

Scientific Reports, Год журнала: 2023, Номер 13(1)

Опубликована: Апрель 28, 2023

Mitochondrial genomes are known for their compact size and conserved gene order, however, recent studies employing long-read sequencing technologies have revealed the presence of atypical mitogenomes in some species. In this study, we assembled annotated five Antarctic notothenioids, including four icefishes (Champsocephalus gunnari, C. esox, Chaenocephalus aceratus, Pseudochaenichthys georgianus) cold-specialized Trematomus borchgrevinki. notothenioids to harbor rearrangements mt genomes, however extensive duplications observed our study never been reported before. icefishes, protein coding ND6, two transfer RNAs, control region with different copy number variants present within same individuals ND6 appearing follow canonical Duplication-Degeneration-Complementation (DDC) model esox gunnari. addition, using k-mer analysis, were able detect heteroplasmy aceratus esox. We also a large inversion mitogenome T. borchgrevinki, along tandem repeats its region. This is first assemble identify structural notothenioid signifies importance long-reads resolving complex mitochondrial architectures. Identification such wide-ranging these fishes could provide insight into genetic basis icefish physiology more generally may insights about potential role cold adaptation.

Язык: Английский

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Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

Genetics, Год журнала: 2022, Номер 220(3)

Опубликована: Фев. 10, 2022

Abstract Single-cell RNA sequencing is a powerful technique that continues to expand across various biological applications. However, incomplete 3′-UTR annotations can impede single-cell analysis resulting in genes are partially or completely uncounted. Performing with hinder the identification of cell identities and gene expression patterns lead erroneous inferences. We demonstrate performing isoform tandem rapidly improve annotations. Using threespine stickleback fish (Gasterosteus aculeatus), we show models from minimal embryonic dataset retained 26.1% greater reads than Ensembl alone. Furthermore, pooling our isoforms previously published adult bulk Iso-Seq stickleback, merging annotation models, resulted marginal improvement (+0.8%) over only dataset. In addition, identified by included thousands new splicing variants. The improved obtained using led successful types increased many Our work illuminates as cost-effective efficient mechanism annotate genomes for sequencing.

Язык: Английский

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Phylogenomics analyses of all species of Swordtails (GenusXiphophorus) highlights hybridization precedes speciation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 1, 2024

Abstract Hybridization has been recognized as an important driving force for evolution, however studies of the genetic consequence and its cause are still lagging behind in vertebrates due to lack appropriate experimental systems. Fish central American genus Xiphophorus were proposed have evolved with multiple ancient ongoing hybridization events, served a valuable research model evolutionary biology biomedical on human disease more than century. Here, we provide complete genome resource annotation all 26 species. On this dataset resolved so far conflicting phylogeny. Through comparative genomic analyses investigated molecular evolution genes related melanoma, main sexually selected trait control puberty timing, which predicted be involved pre-and postzygotic isolation thus influence probability interspecific . We demonstrate dramatic size-variation some gene families across species, despite reticulate short divergence time. Finally, clarify history genus, settle long dispute origin two Southern swordtails, highlight hybridizations precedes speciation, reveal distribution ancestry remaining fused genome.

Язык: Английский

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Cichlid fishes are promising underutilized models to investigate helminth-host-microbiome interactions

Frontiers in Immunology, Год журнала: 2025, Номер 16

Опубликована: Фев. 13, 2025

The “Old Friends Hypothesis” suggests insufficient exposure to symbionts hinders immune development, contributing increased immune-related diseases in the Global North. microbiome is often focus; helminths, potentially also offering health benefits, lack attention. Infection and effect of helminths are influenced perhaps determined by micro-organisms. Mechanisms behind parasite-microbiome interactions poorly understood, despite implications on host health. These typically studied for single helminth species laboratory animal models, overlooking diversity. Reviewing research relationships between microbial diversity yielded 27 publications; most focused human or other mammalian hosts, relying natural rather than experimental inoculation. Only about half investigated outcomes. Remaining knowledge gaps warrant considering additional candidate model systems. Given high helminthiasis burden we propose seeking models South, where a considerable proportion aspects helminth-microbiome took place. Low availability genomic resources however, necessitates more integrative helminthological efforts. substantial similarities systems, several fishes health/disease. More effort could be done establish this cichlids, whose representatives African Great Lakes provide well-delineated, closed system relevant view fish-borne zoonoses water-borne parasites. A good baseline exists these cichlids’ genomics, parasitology, microbiology. We suggest exploring Lake cichlids as hosts diversity,

Язык: Английский

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Fish as biological models: Implications for gut microbiota research in biomedical and aquaculture sciences

Aquaculture International, Год журнала: 2025, Номер 33(4)

Опубликована: Май 2, 2025

Язык: Английский

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High-throughput and genome-scale targeted mutagenesis using CRISPR in a nonmodel multicellular organism,Bombyx mori

Genome Research, Год журнала: 2024, Номер 34(1), С. 134 - 144

Опубликована: Янв. 1, 2024

Large-scale genetic mutant libraries are powerful approaches to interrogating genotype–phenotype correlations and identifying genes responsible for certain environmental stimuli, both of which the central goal life science study. We produced first large-scale CRISPR-Cas9-induced library in a nonmodel multicellular organism, Bombyx mori . developed piggyBac -delivered binary genome editing strategy, can simultaneously meet requirements mixed microinjection, efficient multipurpose operation, preservation growth-defect lines. constructed single-guide RNA (sgRNA) plasmid containing 92,917 sgRNAs targeting promoters exons 14,645 protein-coding genes, established 1726 transgenic sgRNA lines following microinjection 66,650 embryos, generated 300 with diverse phenotypic changes. Phenomic characterization identified large set visual or economically valuable trait Next, we performed pooled context-specific positive screens tolerance pollutant cadmium exposure, KWMTBOMO12902 as strong candidate gene breeding applications sericulture industry. Collectively, our results provide novel versatile approach functional B. genomics, well resource potential key improving various economic traits. This study also shows effectiveness, practicality, convenience other organisms.

Язык: Английский

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Pathways to polar adaptation in fishes revealed by long‐read sequencing

Molecular Ecology, Год журнала: 2022, Номер 32(6), С. 1381 - 1397

Опубликована: Май 13, 2022

Long-read sequencing is driving a new reality for genome science in which highly contiguous assemblies can be produced efficiently with modest resources. Genome from long-read sequences are particularly exciting understanding the evolution of complex genomic regions that often difficult to assemble. In this study, we utilized data generate high-quality assembly an Antarctic eelpout, Ophthalmolycus amberensis, first globally distributed family Zoarcidae. We used understand how O. amberensis has adapted harsh Southern Ocean and compared it another group fishes: notothenioids. showed selection largely acted on different targets eelpouts relative However, did find some overlap; both groups, genes involved membrane structure, thermal tolerance vision have evidence positive selection. found historical shifts transposable element activity other polar fishes, perhaps reflecting response environmental change. were specifically interested two loci known underlie key adaptations seas: haemoglobin antifreeze proteins (AFPs). observed unique MN cluster related fishes suborder Zoarcoidei Perciformes. For AFPs, identified species no afpIII (Cebidichthys violaceus) region where they all Zoarcoidei, potentially lineage-specific loss cluster. Beyond our results highlight power evolution.

Язык: Английский

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A novel gnotobiotic experimental system for Atlantic salmon (Salmo salar L.) reveals a microbial influence on mucosal barrier function and adipose tissue accumulation during the yolk sac stage

Frontiers in Cellular and Infection Microbiology, Год журнала: 2023, Номер 12

Опубликована: Фев. 1, 2023

Gnotobiotic models have had a crucial role in studying the effect that commensal microbiota has on health of their animal hosts. Despite physiological and ecological diversity, teleost fishes are still underrepresented gnotobiotic research. Moreover, better understanding host-microbe interactions farmed fish potential to contribute sustainable global food supply. We developed novel experimental system includes derivation fertilized eggs wild Atlantic salmon, husbandry fry during yolk sac stage. used microscopy-based approach estimate barrier function skin mucus layer this measurement select procedure minimized adverse effects mucosa. also method demonstrate was reduced germ-free when compared colonized with two different bacterial communities. This alteration preceded by an increase number cells containing neutral mucosubstances anterior segment body, but without changes acidic substances any other segments studied along body axis. In addition, we showed how microbial status temporarily affected size utilization internal stores Finally, presence communities associated fry, as well composition, adipose tissue. Fry water from lake larger visceral tissue depot than both conventionally raised fry. Together, our results show is useful tool for study species aquacultural importance.

Язык: Английский

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High resolution genomes of multipleXiphophorusspecies provide new insights into microevolution, hybrid incompatibility, and epistasis

Genome Research, Год журнала: 2023, Номер 33(4), С. 557 - 571

Опубликована: Апрель 1, 2023

Because of diverged adaptative phenotypes, fish species the genus Xiphophorus have contributed to a wide range research for century. Existing genome assemblies are not at chromosomal level and prone sequence gaps, thus hindering advancement intra- inter-species differences evolutionary, comparative, translational biomedical studies. Herein, we assembled high-quality chromosome-level three distantly related species, namely, X. maculatus, couchianus, hellerii Our overall goal is precisely assess microevolutionary processes in clade ascertain molecular events that led divergence progress understanding genetic incompatibility disease. In particular, measured assessed gene expression dysregulation reciprocal interspecies hybrids among species. We found expanded families positively selected genes associated with live bearing, special mode reproduction. also significantly enriched nonpolymorphic transposable elements, suggesting dispersal these elements has accompanied evolution genes, possibly by incorporating new regulatory support Britten-Davidson hypothesis. characterized inter-specific polymorphisms, structural variants, polymorphic element insertions their association hybridization-induced specific disease states humans.

Язык: Английский

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Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Авг. 4, 2024

Abstract Hybridization has been recognized to play important roles in evolution, however studies of the genetic consequence are still lagging behind vertebrates due lack appropriate experimental systems. Fish genus Xiphophorus proposed have evolved with multiple ancient and ongoing hybridization events. They served as an informative research model evolutionary biology biomedical on human disease for more than a century. Here, we provide complete genomic resource including annotations all described 26 species three undescribed taxa resolve uncertain phylogenetic relationships. We investigate molecular evolution genes related cancers such melanoma control puberty timing, focusing that predicted be involved pre-and postzygotic isolation thus affect hybridization. discovered dramatic size-variation some gene families. These persisted despite reticulate rapid speciation short divergence time. Finally, clarify history entire settling disputed two Southern swordtails. Our comparative analyses revealed ancestries manifested mosaic fused genomes show often preceded speciation.

Язык: Английский

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