Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution DOI Creative Commons
Claudia Weber, Michael Paulini, Mark Blaxter

et al.

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

Published: Nov. 3, 2024

Myxozoans are obligate endoparasites that belong to the phylum Cnidaria . Compared their closest free-living relatives, they have evolved highly simplified body plans and reduced genomes. Kudoa iwatai , for example, has lost upwards of two thirds genes thought been present in its ancestors. However, little is known about myxozoan genome architecture because a lack sufficiently contiguous assemblies. This work presents new, near-chromosomal genomes, built entirely from low-coverage long reads infected fish samples. The results illustrate potential using unsupervised learning methods disentangle sequences different sources, facilitate producing genomes undersampled taxa. Extracting distinct components chromatin interaction networks allows scaffolds mixed samples be assigned source Meanwhile, low-dimensional embeddings read composition permit targeted assembly parasite reads. Despite drastic changes lineage leading considerable sequence divergence between gene order conserved. Although parasitic cnidarians show rapid protein evolution compared there limited evidence less efficient selection. While deleterious substitutions may become fixed at higher rate, large evolutionary distances species make robustly analysing patterns molecular challenging. These observations highlight importance filling taxonomic gaps, allow comprehensive assessment impacts parasitism on evolution.

Language: Английский

Convergent pathways of reductive mitochondrial evolution characterised with hypercubic inference DOI Creative Commons
Robert C. Glastad, Iain G. Johnston

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: May 4, 2025

Abstract For a striking example of mitochondrial behaviour beyond ATP generation, consider mitochondrion-related organelles (MROs). Hydrogenosomes, mitosomes, and other reduced forms have evolved through the loss physical functional features, from individual ETC complexes to oxidative phosphorylaytion very ability produce (and further). Reduction mitochondria is dramatic convergent evolution, occuring in every eukaryotic kingdom many parallel times. Here, we use hypercubic inference, class methods evolutionary accumulation modelling (EvAM), explore pathways reduction across eukaryotes. We find that most MRO diversity can be explained by small variations on two distinct pathways, starting with either Complex I or Complexes III/IV, which tend proceed over different characteristic timescales. show clades, including ciliates apicomplexans, reflect particular instances these pathways. Using metabolic modelling, connect structure impact changes involved, suggesting plausible explanation for dramatically nature reductive evolution. discuss this approach connection related theory genetic organisms.

Language: Английский

Citations

0
The highly repetitive genome of Myxobolus rasmusseni, an emerging myxozoan parasite of fathead minnows DOI Creative Commons
Viraj Muthye, Aralia Leon‐Coria, Hongrui Liu

et al.

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(11)

Published: Oct. 15, 2024

Abstract Myxozoans are a monophyletic taxon of approximately 2,400 described species parasites from the phylum Cnidaria. The recent focus on their negative impacts fisheries, evolution free-living ancestors, and emergence into new fish host populations has stressed critical need for genomic resources this parasitic group. Here, we describe genome assembly annotation Myxobolus rasmusseni, an emerging parasite fathead minnows in Alberta, Canada. is 174.6 Mb size, 68% which made up repetitive elements, making it one most animal genomes sequenced to date. Through comparisons other myxozoans, show that widespread gene loss, known phenomenon group parasites, consistent with closely related species. Additionally, assembled M. rasmusseni mitochondrial genome, nearly twice size typical yet contains only five canonical protein-coding genes open reading frames not found myxozoans. These results add our understanding gene- genome-level diversity observed

Language: Английский

Citations

0
Kudoa genomes from contaminated hosts reveal extensive gene order conservation and rapid sequence evolution DOI Creative Commons
Claudia Weber, Michael Paulini, Mark Blaxter

et al.

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

Published: Nov. 3, 2024

Myxozoans are obligate endoparasites that belong to the phylum Cnidaria . Compared their closest free-living relatives, they have evolved highly simplified body plans and reduced genomes. Kudoa iwatai , for example, has lost upwards of two thirds genes thought been present in its ancestors. However, little is known about myxozoan genome architecture because a lack sufficiently contiguous assemblies. This work presents new, near-chromosomal genomes, built entirely from low-coverage long reads infected fish samples. The results illustrate potential using unsupervised learning methods disentangle sequences different sources, facilitate producing genomes undersampled taxa. Extracting distinct components chromatin interaction networks allows scaffolds mixed samples be assigned source Meanwhile, low-dimensional embeddings read composition permit targeted assembly parasite reads. Despite drastic changes lineage leading considerable sequence divergence between gene order conserved. Although parasitic cnidarians show rapid protein evolution compared there limited evidence less efficient selection. While deleterious substitutions may become fixed at higher rate, large evolutionary distances species make robustly analysing patterns molecular challenging. These observations highlight importance filling taxonomic gaps, allow comprehensive assessment impacts parasitism on evolution.

Language: Английский

Citations

0