Foraminifera as a model of the extensive variability in genome dynamics among eukaryotes

Goetz, Eleanor J.; Greco, Mattia; Rappaport, Hannah B.; Weiner, Agnes; Walker, Laura M.; Bowser, Samuel S.; Goldstein, Susan T.; Katz, Laura A.

doi:10.1002/bies.202100267

Cited by 9 publications

(13 citation statements)

References 85 publications

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“…This trend in foraminiferans might be attributed to their frequent endoreplication processes, which could lead to high rates of gene duplication as a side effect. These processes might also necessitate the separation of germline from somatic genomes 17 , potentially making LGT xation more challenging, especially if foreign genes are inserted into somatic rather than germline DNA.…”

Section: Extensive Gene Acquisition In Rhizaria Through Lgt From Prok...mentioning

confidence: 99%

Lateral gene transfer leaves lasting traces in Rhizaria

Eme,

Hooff

2024

Preprint

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Lateral gene transfer (LGT) is a fundamental process that has contributed to the genetic makeup of various eukaryotic lineages. Yet our comprehension of its prevalence and significance across the eukaryotic domain remains incomplete, particularly when it comes to eukaryote-to-eukaryote transfers. The Rhizaria forms an expansive, ancient, and morphologically diverse clade of mostly free-living, single-celled phagotrophs, whose genetic diversity reflects their adaptability and evolutionary success across a range of habitats. Here, we undertake a comprehensive investigation of LGT within Rhizaria, tracing its role from the clade's emergence to the present day, employing advanced phylogenetic analyses and machine learning techniques. Contrary to previous assertions that LGT in eukaryotes is rare, our findings suggest that at least 8% of genes in contemporary rhizarian genomes were acquired through LGT at various points during their billion-year history. Our analysis reveals that although gene duplications exceed the number of LGT events, the duplicated genes that were originally acquired through LGT have a visible effect on the evolutionary trajectory of the recipient organisms. Our results also indicate that LGTs originating from other eukaryotes are more common than those from prokaryotes and exhibit unique patterns. By offering both quantitative and qualitative insights into the role of LGT in shaping the evolution of a major eukaryotic lineage, this work further demystifies lateral gene transfer in eukaryotes.

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Section: Extensive Gene Acquisition In Rhizaria Through Lgt From Prok...mentioning

confidence: 99%

Lateral gene transfer leaves lasting traces in Rhizaria

Eme,

Hooff

2024

Preprint

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“…In general, the number of copies of the SSU rDNA varies immensely between different groups of protists, and even within the same species it may scale exponentially with cell volume (Fu & Gong, 2017). Foraminifera are likely to represent an extreme case of this variation due to their complex life cycle involving endoreplication (Goetz et al, 2022). Endoreplication occurs both at haploid and diploid stages and may involve duplications of the whole genome or its parts.…”

Section: Evaluation Of Dpcr To Detect Invasive Foraminiferal Speciesmentioning

confidence: 99%

“…Endoreplication occurs both at haploid and diploid stages and may involve duplications of the whole genome or its parts. As a result, DNA content in foraminiferal cells greatly depends on the life stage and cell size (Goetz et al, 2022).…”

Section: Evaluation Of Dpcr To Detect Invasive Foraminiferal Speciesmentioning

confidence: 99%

Hidden aliens: Application of digital PCR to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis

Morin,

Panova,

Schweizer

et al. 2023

Environmental Microbiology

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The problem of invasive species is a well‐studied one, but knowledge of free‐living unicellular eukaryotic invasive species is lacking. A potentially invasive foraminifer (Rhizaria), Nonionella sp. T1, was recently discovered in the Skagerrak and its fjords. Digital polymerase chain reaction (dPCR) was applied to track the spread of this non‐indigenous species using a new dPCR assay (T1‐1). The use of dPCR appears highly complementary to traditional hand picking of foraminiferal shells from the sediment, and is far less time‐consuming. This study indicates that Nonionella sp. T1 has bypassed the outer Skagerrak strait, instead becoming established in Swedish west coast fjords, constituting up to half of the living foraminiferal community in fjord mouth areas. The ecology of Nonionella sp. T1 and its potential invasive impacts are still largely unknown, but it appears to be an opportunist using several energy sources such as nitrate respiration and kleptoplasty along with a possibly more efficient reproductive strategy to gain an advantage over the native foraminiferal species. Future ecological studies of Nonionella sp. T1 could be aided by dPCR and the novel Nonionella sp. T1‐specific T1‐1 assay.

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“…The schematic life cycle has been refined and amended by various authors over the years (e.g. Goetz et al., 2022) and the current concept comprises an alternation of haploid and diploid generations, with a possibility to maintain multiple generations of schizogony. The cells releasing gametes are named “gamonts” and are considered haploid.…”

Section: Introductionmentioning

confidence: 99%

Continuous reproduction of planktonic foraminifera in laboratory culture

Meilland,

Siccha,

Morard

et al. 2024

J Eukaryotic Microbiology

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Planktonic foraminifera were long considered obligate sexual outbreeders but recent observations have shown that nonspinose species can reproduce by multiple fission. The frequency of multiple fission appears low but the survival rate of the offspring is high and specimens approaching fission can be distinguished. We made use of this observation and established a culturing protocol aimed at enhancing the detection and frequency of fission. Using this protocol, we selectively cultured specimens of Neogloboquadrina pachyderma and raised the frequency of reproduction by fission in culture from 3% in randomly selected specimens to almost 60%. By feeding the resulting offspring different strains of live diatoms, we obtained a thriving offspring population and during the subsequent 6 months of culturing, we observed two more successive generations produced by fission. This provides evidence that in nonspinose species of planktonic foraminifera, reproduction by multiple fission is likely clonal and corresponds to the schizont phase known from benthic foraminifera. We subsequently tested if a similar culturing strategy could be applied to Globigerinita glutinata, representing a different clade of planktonic foraminifera, and we were indeed able to obtain offspring via multiple fission in this species. This work opens new avenues for laboratory‐based experimental work with planktonic foraminifera.

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Foraminifera as a model of the extensive variability in genome dynamics among eukaryotes

Cited by 9 publications

References 85 publications

Lateral gene transfer leaves lasting traces in Rhizaria

Lateral gene transfer leaves lasting traces in Rhizaria

Hidden aliens: Application of digital PCR to track an exotic foraminifer across the Skagerrak (North Sea) correlates well with traditional morphospecies analysis

Continuous reproduction of planktonic foraminifera in laboratory culture

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