From Genes to Genomes: Opportunities, Challenges, and a Roadmap for Synteny-based Phylogenomics

Published: Feb. 9, 2024

Reconstructing the Tree of Life remains a central goal in biology. Early methods, relying on small numbers morphological or genetic characters, often yielded conflicting evolutionary histories, undermining confidence results. Investigations based phylogenomics, which use hundreds to thousands loci for phylogenetic inquiry, have provided clearer picture life's history, but certain branches remain problematic. To resolve difficult nodes Life, two recent studies tested utility synteny, conserved collinearity orthologous more organisms, phylogenetics. Synteny exhibits compelling phylogenomic potential while also raising new challenges. We identify and discuss specific opportunities challenges that bear value synteny data other rare genomic changes studies. Synteny-based analyses highly contiguous genome assemblies mark chapter era quest reconstruct Life.

Language: Английский

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Fusion, fission, and scrambling of the bilaterian genome in Bryozoa

Genome Research, Journal Year: 2025, Volume and Issue: 35(1), P. 78 - 92

Published: Jan. 1, 2025

Groups of orthologous genes are commonly found together on the same chromosome over vast evolutionary distances. This extensive physical gene linkage, known as macrosynteny, is seen between bilaterian phyla divergent Chordata, Echinodermata, Mollusca, and Nemertea. Here, we report a unique pattern genome evolution in Bryozoa, an understudied phylum colonial invertebrates. Using comparative genomics, reconstruct chromosomal history five bryozoans. Multiple ancient fusions followed by mixing led to near-complete loss linkage groups ancestor extant A second wave rearrangements, including fission, then occurred independently two bryozoan classes, further scrambling genomes. We also discover at least derived fusion events shared bryozoans brachiopods, supporting traditional but highly debated Lophophorata hypothesis suggesting macrosynteny be potentially powerful source phylogenetic information. Finally, show that rearrangements dispersion from Hox clusters onto multiple chromosomes. Our findings demonstrate canonical structure has been lost across all studied representatives entire phylum, reveal group fission can occur very frequently specific lineages.

Language: Английский

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

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 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,

Language: Английский

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A “light in the darkness”: First transcriptomic data from deep-sea spiny eels (Notacanthus, Notacanthiformes)

Marine Genomics, Journal Year: 2025, Volume and Issue: 80, P. 101182 - 101182

Published: Feb. 18, 2025

Language: Английский

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Explosion of goby fish diversity at the Eocene-Oligocene transition

Molecular Phylogenetics and Evolution, Journal Year: 2025, Volume and Issue: unknown, P. 108342 - 108342

Published: March 1, 2025

Language: Английский

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From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics

Journal of Experimental Zoology Part B Molecular and Developmental Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

ABSTRACT Interpreting the vast amounts of data generated by high‐throughput sequencing technologies can often present a significant challenge, particularly for non‐model organisms. While automated approaches like GO (Gene Ontology) and KEGG (Kyoto Encyclopedia Genes Genomes) enrichment analyses are widely used, they lack specificity To bridge this gap, we manually curated gene list tailored teleost fish transcriptomics. This resource focuses on key biological processes crucial understanding physiology, development, adaptation, including hormone signaling, various metabolic pathways, appetite regulation, digestion, gastrointestinal function, vision, ossification, osmoregulation, pigmentation. Developed through collaborative efforts specialists in diverse fields, prioritizes genes with established roles experimental evidence, conservation across species. aims to provide researchers reliable starting point transcriptomic analyses, offering carefully evaluated set relevant current research priorities. By streamlining process selection interpretation, supports broader community designing analyzing studies that investigate molecular responses developmental environmental changes. We encourage scientific collaboratively expand refine list, ensuring its continued relevance utility research.

Language: Английский

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The Caudal Neurosecretory System: A Still Enigmatic Second Neuroendocrine Complex in Fish

Neuroendocrinology, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 41

Published: Jan. 16, 2024

The caudal neurosecretory system (CNSS) is a neuroendocrine complex, whose existence specific to fishes. In teleosts, it consists of cells (Dahlgren cells) fibers are associated with neurohemal terminal tissue (urophysis). other actinopterygians as well in chondrichthyes, the devoid urophysis, so that Dahlgren end diffuse region. Structurally, has many similarities hypothalamic-neurohypophysial system. However, differs regarding its position at spinal cord and nature hormones secretes, most notable ones being urotensins. CNSS was first described more than 60 years ago, but embryological origin still hypothetical, role poorly understood. Observations experimental data gave some evidences possible involvement osmoregulation, stress reproduction. But one may question benefit for fish possess this second system, while central hypothalamic-pituitary complex already controls such functions. As an introduction our review, brief report on discovery given. A description organization follows, review then focuses neuroendocrinology different factors produces secretes. current knowledge ontogenesis developmental also reported, evolution. special focus finally given what known potential physiological roles.

Language: Английский

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Elevational patterns of fish functional and phylogenetic community structure in a monsoon climate river basin

Diversity and Distributions, Journal Year: 2024, Volume and Issue: 30(4)

Published: Feb. 13, 2024

Abstract Aim Understanding the patterns and drivers of biodiversity across space time is commonly based on species diversity, which may ignore species' functional role evolutionary history result in an incomplete understanding community assembly. It suggested that integrating species, functional, phylogenetic diversity could provide a more holistic assessment assembly natural ecosystems. This study aimed to explore elevational environmental multiple facets fish structure subtropical river during wet dry seasons. Location The Chishui River basin, China. Methods We investigated responses richness, elevation different Moreover, we compared dispersion mean pairwise distance with those obtained from null models infer mechanisms shaping structure. Additionally, examined (e.g. water chemistry, temperature, size) Results Fish showed negative relationship basin. communities tended be average functionally random but phylogenetically clustered. Furthermore, exhibited decreasing pattern along gradient. Despite no significant seasonal changes for (except diversity), became overdispersed clustered at low high elevations season. variables were not synchronous. Conclusions At basin scale, filtering was prevalent structure, whereas stochasticity likely important ecological individual switched limiting similarity as increased, underlying forces two ends gradient prominent

Language: Английский

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Shark mandible evolution reveals patterns of trophic and habitat-mediated diversification

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: May 8, 2023

Abstract Environmental controls of species diversity represent a central research focus in evolutionary biology. In the marine realm, sharks are widely distributed, occupying mainly higher trophic levels and varied dietary preferences, mirrored by several morphological traits behaviours. Recent comparative phylogenetic studies revealed that present fairly uneven diversification across habitats, from reefs to deep-water. We show preliminary evidence (disparity) feeding system (mandibles) follows these patterns, we tested hypotheses linking patterns specialisation. conducted 3D geometric morphometric analysis methods on 145 specimens representing 90 extant shark using computed tomography models. explored how rates evolution jaw correlate with habitat, size, diet, level, taxonomic order. Our findings relationship between disparity environment, reef deep-water habitats. Deep-water display highly divergent morphologies compared other sharks. Strikingly, associated deep water, but not reefs. The environmental heterogeneity offshore water column exposes importance this parameter as driver at least early part clade history.

Language: Английский

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The myoarchitecture of the vertebrate cardiac ventricles: evolution and classification

Journal of Experimental Biology, Journal Year: 2024, Volume and Issue: 227(20)

Published: Oct. 11, 2024

ABSTRACT The ventricle of the vertebrate heart is main segment cardiac outflow region. Compared with other components, it shows remarkable histomorphological variation among different animal groups. This especially apparent in myocardium, which generally classified into three types: trabeculated, compact and mixed. trabeculated or ‘spongy’ myocardium characterized by existence trabeculae deep recesses intertrabecular spaces, lined endocardium. type composed condensed myocardial fibers, almost no layer. mixed consists an outer layer inner Among vertebrates, fishes show a great diversity types. On this basis, ventricular myoarchitecture has been categorized four groups varying complexity. classification made according to (i) proportion two types versus compact, (ii) vascularization wall. Here, we review morphogenetic mechanisms that give rise gnathostomes (i.e. jawed vertebrates) special emphasis on throughout phylogeny ancient actinopterygians teleosts. Finally, propose should be reconsidered, given degrees compactness current system based do not constitute discrete states, but anatomical continuum.

Language: Английский

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