Quantitative assessment of reef foraminifera community from metabarcoding data DOI Creative Commons
Elsa B. Girard, Emilie A. Didaskalou,

Andi Muh. Agung Pratama

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 23, 2024

Abstract Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it challenging produce fast and accurate depiction of due methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative genes that may not correctly represent communities from environmental DNA assessed morphological methods. However, has the potential deliver descriptions provided interpreted validated species‐specific calibrations reference databases. Here, we developed quantitative approach retrieve data assemblages large benthic foraminifera (LBF), photosymbiotic calcifying protists, Indonesian coral reefs are under increasing anthropogenic pressure. To depict diversity, calculated taxon‐specific correction factors reduce biological biases by comparing surface area, biovolume calcite volume, number mitochondrial gene copies seven common LBF species. validate approach, compared calibrated datasets mock samples bulk reef sediment; both sample types were metabarcoded. The calibration significantly improved estimations genus abundance, difference ±5% on average, allowing for comparison past future molecular ones. Our results also highlight application our support monitoring operations capturing fine‐scale processes, such as seasonal pollution‐driven dynamics, require high‐throughput sampling treatment.

Language: Английский

Mitochondrial genomes revisited: why do different lineages retain different genes? DOI Creative Commons
Anzhelika Butenko, Julius Lukeš, Dave Speijer

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Jan. 25, 2024

Abstract The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by ancestor, only between 1 and about 70 are on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number sequenced annotated mitogenomes coherent picture why some were lost, or relocated the nucleus, is emerging. In this review, we describe characteristics mitochondria-to-nucleus gene transfer resulting varied content across eukaryotes. We introduce ‘burst-upon-drift’ model best explain nuclear-mitochondrial population genetics with flares due genetic drift.

Language: Английский

Citations

22
The global genetic diversity of planktonic foraminifera reveals the structure of cryptic speciation in plankton DOI Creative Commons
Raphaël Morard, Kate Darling, Agnes K. M. Weiner

et al.

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: 99(4), P. 1218 - 1241

Published: Feb. 13, 2024

ABSTRACT The nature and extent of diversity in the plankton has fascinated scientists for over a century. Initially, discovery many new species remarkably uniform unstructured pelagic environment appeared to challenge concept ecological niches. Later, it became obvious that only fraction had been formally described, because assemblages are dominated by understudied eukaryotic lineages with small size lack clearly distinguishable morphological features. high confirmed comprehensive metabarcoding surveys, but interpretation underlying molecular taxonomies is hindered insufficient integration genetic taxonomy observations. Here we use planktonic foraminifera as study model reveal full their investigate geographical patterns distribution. To this end, assembled global data set ~7600 ribosomal DNA sequences obtained from morphologically characterised individual foraminifera, established robust taxonomic framework observed diversity, used query covering ~1700 samples ~2.48 billion reads. This allowed us extract assign 1 million reads, enabling characterisation structure group across ~1100 oceanic stations worldwide. Our sampling revealed existence of, at most, 94 distinct operational units (MOTUs) level divergence indicative biological species. doubles number described identified Furthermore, allocation morphospecies uneven. Only 16 disguise evolutionarily significant proportion show increases poleward. Finally, observe MOTUs have narrower geographic distribution than some cases belonging same (cryptic species) different environmental preferences. Overall, our analysis reveals even light sampling, modest finite. However, cryptic diversification decoupled diversification, hinting mechanisms acting levels divergence.

Language: Английский

Citations

8
The persistent homology of mitochondrial ATP synthases DOI Creative Commons
Savar Sinha, Jeremy G. Wideman

iScience, Journal Year: 2023, Volume and Issue: 26(5), P. 106700 - 106700

Published: April 19, 2023

Relatively little is known about ATP synthase structure in protists, and the investigated ones exhibit divergent structures distinct from yeast or animals. To clarify subunit composition of synthases across all eukaryotic lineages, we used homology detection techniques molecular modeling tools to identify an ancestral set 17 subunits. Most eukaryotes possess comparable those animals fungi, while some have undergone drastic divergence (e.g., ciliates, myzozoans, euglenozoans). Additionally, a ∼1 billion-year-old gene fusion between stator subunits was identified as synapomorphy SAR (Stramenopila, Alveolata, Rhizaria) supergroup (stramenopile, alveolate, rhizaria). Our comparative approach highlights persistence even amidst major structural changes. We conclude by urging that more jakobids, heteroloboseans, stramenopiles, rhizarians) are needed provide complete picture evolution diversity this ancient essential complex.

Language: Английский

Citations

11
Converting Blastocrithidia Nonstop, a Trypanosomatid With Non‐Canonical Genetic Code, Into a Genetically‐Tractable Model DOI Creative Commons

Arnau Galan,

Natalya Kraeva, Kristína Záhonová

et al.

Molecular Microbiology, Journal Year: 2025, Volume and Issue: unknown

Published: April 9, 2025

ABSTRACT Blastocrithidia nonstop is a protist with highly unusual nuclear genetic code, in which all three standard stop codons are reassigned to encode amino acids, UAA also serving as sole termination codon. In this study, we demonstrate that parasitic flagellate amenable manipulation, enabling gene ablation and protein tagging. Using preassembled Cas9 ribonucleoprotein complexes, successfully disrupted tagged the non‐essential encoding catalase. These advances establish single‐celled eukaryote model organism for investigating malleability evolution of code eukaryotes.

Language: Английский

Citations

0
Quantitative assessment of reef foraminifera community from metabarcoding data DOI Creative Commons
Elsa B. Girard, Emilie A. Didaskalou,

Andi Muh. Agung Pratama

et al.

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 23, 2024

Abstract Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it challenging produce fast and accurate depiction of due methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative genes that may not correctly represent communities from environmental DNA assessed morphological methods. However, has the potential deliver descriptions provided interpreted validated species‐specific calibrations reference databases. Here, we developed quantitative approach retrieve data assemblages large benthic foraminifera (LBF), photosymbiotic calcifying protists, Indonesian coral reefs are under increasing anthropogenic pressure. To depict diversity, calculated taxon‐specific correction factors reduce biological biases by comparing surface area, biovolume calcite volume, number mitochondrial gene copies seven common LBF species. validate approach, compared calibrated datasets mock samples bulk reef sediment; both sample types were metabarcoded. The calibration significantly improved estimations genus abundance, difference ±5% on average, allowing for comparison past future molecular ones. Our results also highlight application our support monitoring operations capturing fine‐scale processes, such as seasonal pollution‐driven dynamics, require high‐throughput sampling treatment.

Language: Английский

Citations

1