An integrative analysis of Plectocapillus antarcticus gen. et sp. nov. from Antarctica: Morphology, chemical composition, and phylogeny

Marine Micropaleontology, Journal Year: 2025, Volume and Issue: unknown, P. 102451 - 102451

Published: Feb. 1, 2025

Language: Английский

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A needle in a haystack: A new metabarcoding approach to survey diversity at the species level of Arcellinida (Amoebozoa: Tubulinea)

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(5), P. 1034 - 1049

Published: Feb. 17, 2023

Environmental DNA-based diversity studies have increased in popularity with the development of high throughput sequencing technologies. This permits potential simultaneous retrieval vast amounts molecular data from many different organisms and species, thus contributing to a wide range biological disciplines. DNA protocols designed for protists often focused on highly conserved small subunit ribosome gene, that does not permit species-level assignments. On other hand, eDNA aiming at assignments allow fine level ecological resolution reproducible results. These are currently applied living marine shallow lotic freshwater ecosystems, bioindication purpose. Therefore, this study, we present protocol explore Arcellinida (Amoebozoa: Tubulinea) testate amoebae taxa is based mitochondrial cytochrome oxidase I (COI). widespread lentic water bodies soil ecosystems. We 42 samples peatlands, estuaries environments, recovering all infraorders Glutinoconcha (with COI data), except Hyalospheniformes. Our results revealed an unsuspected morphologically homogeneous groups such as Cylindrothecina, Excentrostoma or Sphaerothecina. With expect revolutionize design modern distributional surveys. approach involves rapid cost-effective analysis amoeba contrasted order has be established model group theoretical studies.

Language: Английский

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Mitochondrial cytochrome c oxidase subunit I (COI) metabarcoding of Foraminifera communities using taxon-specific primers

PeerJ, Journal Year: 2022, Volume and Issue: 10, P. e13952 - e13952

Published: Sept. 5, 2022

Foraminifera are a species-rich phylum of rhizarian protists that highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed high, yet undescribed diversity Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for studies on Primers allow amplification foraminiferal mitochondrial cytochrome oxidase I (COI) and identification species were recently published. Here we test performance these primers whole communities, compare their to degenerate LerayXT primers, which amplify same COI region wide range eukaryotes. We applied 48 samples taken along three transects spanning North Sea beach Netherlands from dunes low tide level, analysed both sediment meiofauna samples, contained taxa between 42 µm 1 mm body size obtained by decantation sand samples. used single-cell (Girard et al., 2022) generate reference library containing 32 Foraminifera, this taxonomically annotate our community data. Our analyses show do not while Foraminifera- specific, with about 90% reads assigned amplifying all major groups, i.e., monothalamids, Globothalamea, Tubothalamea. identified 176 ASVs found change composition high dominance single-chambered monothalamid results highlight can be powerful tool assessing Foraminiferal communities.

Language: Английский

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The Morphological Differentiation and Evolutionary Origins of Artemia in China

Diversity, Journal Year: 2024, Volume and Issue: 16(3), P. 144 - 144

Published: Feb. 24, 2024

Artemia is a genus of halophilic zooplanktons comprising bisexual and parthenogenetic forms, which an important model for investigating adaption to hypersaline ecosystems. The in China comprises four species: A. sinica, tibetiana, franciscana parthenogenetica. To investigate the evolutionary relationship China, we analyzed morphometrics phylogenetics among twenty-two geographical populations China. We found significant morphological differentiation across different species strains exhibited high level intra-population variation. also overlaps characteristics between populations, may raise challenges classification using traditional methods. franciscana, originated from various regions America, was generally distributed along Chinese coastlines through multiple human introductions. Additionally, native Asian clades split into Western Eastern Lineages during late Miocene due Himalayan orogeny. Within Lineage, tibetiana can be grouped three taxon units: tibeitiana, sorgeloosi urmiana. that distribution genetic structure sinica were influenced by climate oscillations Pleistocene, might play pivotal role driving formation Lineage. Overall, our study provides new insight invertebrate evolution under climatic impacts environments.

Language: Английский

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Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

mBio, Journal Year: 2023, Volume and Issue: 14(2)

Published: March 20, 2023

Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and transfer to the nuclear genome. The diversity of mitochondrial genomes published date has revealed processes are ongoing in many lineages. Most well-studied eukaryotic lineages represented genome databases, except for superphylum Retaria-the lineage comprising Foraminifera Radiolaria. Using single-cell approaches, we determined two complete nearly radiolarians. We report coding content additional 14 foram species. show foraminiferan radiolarian contain a fully overlapping but reduced complement compared other sequenced rhizarians. In contrast animals fungi, protists encode diverse set proteins on their genomes, including several ribosomal genes; however, some aerobic (euglenids, myzozoans, chlamydomonas-like algae) have lack all genes. Similar these outliers, retarian protein tRNA genes, truncated divergent small large rRNA only or 15 protein-coding

Language: Английский

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Establishment, Genetic Diversity, and Habitat Suitability of Aedes albopictus Populations from Ecuador

Insects, Journal Year: 2022, Volume and Issue: 13(3), P. 305 - 305

Published: March 19, 2022

Aedes albopictus, also known as the tiger mosquito, is widespread worldwide across tropical, subtropical, and temperate regions. This insect associated with transmission of several vector-borne diseases, and, such, monitoring its distribution highly important for public health. In Ecuador, Ae. albopictus was first reported in 2017 Guayaquil. Since then, vector has been identified Northeastern lowlands Amazon basin. study aims to determine genetic diversity Ecuadorian populations through analysis mitochondrial gene COI describe potential areas this species within country. The determined by combining phylogenetic population genetics analyses five localities Ecuador. Results showed two haplotypes albopictus. Haplotype 1 (H1) found coastal individuals, while haplotype 2 (H2) only three northeastern sites. a context, H1 most 21 countries tropical habitats. contrast, H2 limited regions, suggesting fewer adaptation traits. Our prediction model suitable habitat all regions (coastal, basin, Andean lowland Galápagos Islands) Hence, understanding different aspects can help us implement better control strategies surveillance vectorial

Language: Английский

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Quantitative assessment of reef foraminifera community from metabarcoding data

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

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Population genetic structure of Culex tritaeniorhynchus in different types of climatic zones in China

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

Published: July 5, 2024

Abstract Background Culex tritaeniorhynchus is widely distributed in China, from Hainan Island the south to Heilongjiang north, covering tropical, subtropical, and temperate climate zones. carries 19 types of arboviruses. It main vector Japanese encephalitis virus (JEV), posing a serious threat human health. Understanding effects environmental factors on can provide important insights into its population structure or isolation patterns, which currently unclear. Results In total, 138 COI haplotypes were detected 552 amplified sequences, haplotype diversity ( Hd ) value increased (0.534) tropical (0.979) regions. The phylogeny analysis revealed that divided two high-support evolutionary branches. Temperate populations predominantly branch II, showing some genetic tropical/subtropical less gene flow between groups. neutral test results HNQH (Qionghai) HNHK(Haikou) negative P < 0.05), indicating many low-frequency mutations might be process expansion. Moreover, Wolbachia infection was only SDJN (Jining) (2.24%), all genotypes belonged supergroup B. To understand influence mosquito-borne viruses, we examined prevalence three ecological environments Shandong Province. We discovered incidence JEV notably greater lotus ponds compared those irrigation canal this study, overall rate 15.27 per 1000, suggesting current risk outbreaks Conclusions Tropical subtropical showed higher climatic conditions great advantages for establishment expansion tritaeniorhynchus. There are differences rates wild under different conditions. Our suggest complex interplay differentiation, structure, shaping dynamics . low may reflect recent presence invasion

Language: Английский

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COI metabarcoding of large benthic Foraminifera: Method validation for application in ecological studies

Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(11)

Published: Nov. 1, 2022

Abstract Monitoring community composition of Foraminifera (single‐celled marine protists) provides valuable insights into environmental conditions in ecosystems. Despite the efficiency DNA (eDNA) and bulk‐sample (bulk‐DNA) metabarcoding to assess presence multiple taxa, this has not been straightforward for partially due high genetic variability widely used ribosomal markers. Here, we test correctness retrieving foraminiferal communities by mock communities, bulk‐DNA from coral reef sediment samples, eDNA their associated ethanol preservative using recently sequenced cytochrome c oxidase subunit 1 (COI) marker. To detection success, compared our results with large benthic previously reported same sampling sites. Results demonstrate that all species were detected two but one remaining four. Technical replicates highly similar number reads each assigned ASV both samples. Bulk‐DNA showed a significantly higher richness than also additional what was already at specific Our study confirms COI marker adequately retrieves diversity With its decreased commonly nuclear 18 S rRNA, renders powerful tool under condition reference database is adequate target taxa.

Language: Английский

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Macroevolutionary patterns in intragenomic rDNA variability among planktonic foraminifera

PeerJ, Journal Year: 2023, Volume and Issue: 11, P. e15255 - e15255

Published: April 25, 2023

Ribosomal intragenomic variability in prokaryotes and eukaryotes is a genomic feature commonly studied for its inflationary impact on molecular diversity assessments. However, the evolutionary mechanisms distribution of this phenomenon within microbial group are rarely explored. Here, we investigate 33 species planktonic foraminifera, calcifying marine protists, by inspecting 2,403 partial SSU sequences obtained from single-cell clone libraries. Our analyses show that polymorphisms common among foraminifera species, but number polymorphic sites significantly differs clades. With our simulations, could assess most these mutations located paired regions do not affect secondary structure fragment. Finally, mapping phylogeny clades, were able to discuss evolution potential sources linking trait distinctive nuclear dynamics group.

Language: Английский

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