Vertical distribution of epiphytic diatoms in relation to the eelgrass Zostera noltii canopy biomass and height

Празукин, А. В.; Lee, Raisa I.; Firsov, Yuriy K.; Kapranov, Sergey V.

doi:10.1016/j.aquabot.2021.103466

Cited by 6 publications

(3 citation statements)

References 62 publications

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“…protein BLAST of some of the translated sequences finds that these have their best hits to a variety of organisms other than eelgrass, notably diatoms. This was a surprise to us, but in fact it has long been known that eelgrass is extensively colonized by epiphytes 47 , of which diatoms predominate 48 and may provide as much as 71-83% of the primary production by the community 49 . For the most enriched protein domain, we investigated an anchor with high effect size (0.66); its consensus matches to "fucoxanthin chlorophyll a/c protein" (FCP) in several diatoms, for example, Phaeodactylum tricornutum (95% amino acid identity, 81% nucleotide identity; Figure S7C); given that the matches are imperfect, the true species of origin may not be in the NCBI database.…”

Section: W I T H D R a W Nmentioning

confidence: 99%

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Chaung

Baharav

Henderson

et al. 2023

Preprint

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Today's genomics workflows typically require alignment to a reference sequence, which limits discovery. We introduce a new unifying paradigm, SPLASH (Statistically Primary aLignment Agnostic Sequence Homing), an approach that directly analyzes raw sequencing data to detect a signature of regulation: sample-specific sequence variation. The approach, which includes a new statistical test, is computationally efficient and can be run at scale. SPLASH unifies detection of myriad forms of sequence variation. We demonstrate that SPLASH identifies complex mutation patterns in SARS-CoV-2 strains, discovers regulated RNA isoforms at the single cell level, documents the vast sequence diversity of adaptive immune receptors, and uncovers biology in non-model organisms undocumented in their reference genomes: geographic and seasonal variation and diatom association in eelgrass, an oceanic plant impacted by climate change, and tissue-specific transcripts in octopus. SPLASH is a new unifying approach to genomic analysis that enables an expansive scope of discovery without metadata or references.

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Section: W I T H D R a W Nmentioning

confidence: 99%

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Chaung

Baharav

Henderson

et al. 2023

Preprint

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“…Furthermore, they act as natural barriers, limiting the proliferation of bacterial pathogens that pose a threat to human health. Moreover, seagrasses serve as critical habitats for various marine species, playing a fundamental role in the preservation of biodiversity [29].…”

Section: Introductionmentioning

confidence: 99%

Rare Earth Elements in the Seagrass Zostera noltei and Sediments from the Black Sea Coast of Crimea

Ryabushko,

Kapranov,

Gureeva

et al. 2023

JMSE

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In the present work, we assessed the contents of rare earth elements (REEs), including yttrium and scandium, in rhizomes and leaves of the widespread seagrass Zostera noltei Hornemann 1832 and in the nearby sediments from the Black Sea coast. The total REE content in the sediments was found to be much higher than in Z. noltei. The order of decrease in the major REE contents in the sediments and the seagrass rhizomes was identical, except for La and Y. La was the most abundant in the sediments, and Y in the rhizomes. The contents of all REEs in rhizomes of Z. noltei were 1.5–10 times higher than in the leaves. The highest difference in the REE contents was found for the minor elements (Sm–Lu). The translocation factors for Sc and the minor elements (excluding Tb) from the sediments to the rhizomes and from the rhizomes to the leaves turned out to be pairwise equal, which indicates the similarity of the REE translocation mechanisms. Comparing our results with the literature data, it is possible to conclude that the seagrass Z. noltei does not have an advantage in the REE accumulation over marine macroalgae. At the same time, large coastal deposits of this seagrass after storms allow us to consider it as a possible source of REEs in the future.

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“…As global oceans warm, eelgrass has established habitats in low-daylight arctic conditions, a requirement for the species as global temperatures force it to acclimate to high latitudes. Genetic and post-transcriptional adaptation that allow eelgrass to survive at low and high latitudes with greatly varying dynamic ranges of daylight exposure are unknown (Rock and Daru, 2021), but ecological studies have shown that eelgrass is extensively colonized by epiphytic diatoms (Jacobs and Noten, 1980) which have significant impacts on global carbon pumps (Tréguer et al ., 2018), and regulate seagrass biomass and growth (Jacobs and Noten, 1980; Prazukin et al ., 2022).…”

Section: Introductionmentioning

confidence: 99%

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Chaung

Baharav

Zheludev

et al. 2022

Preprint

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We present a unifying statistical formulation for many fundamental problems in genome science and develop a reference-free, highly efficient algorithm that solves it. Sequence diversification - nucleic acid mutation, rearrangement, and reassortment - is necessary for the differentiation and adaptation of all replicating organisms. Identifying sample-dependent sequence diversification, e.g. adaptation or regulated isoform expression, is fundamental to many biological studies, and is achieved today with next-generation sequencing. Paradoxically, current analyses begin with attempts to align to or assemble necessarily incomplete reference genomes, a step that is at odds with detecting the most important examples of sequence diversification. In addition to being computationally expensive, reference-first approaches suffer from diminished discovery power: they are blind to unaligned or mis-aligned sequences. We provide a unifying formulation for detecting sample-dependent sequence diversification that subsumes core problems faced in diverse biological fields. This formulation allows us to construct an algorithm that performs inference on raw reads, avoiding references completely. We illustrate the power of our approach for new data-driven biological discovery with examples of novel single-cell resolved, cell-type-specific isoform expression, including expression in the major histocompatibility complex, and de novo prediction of viral protein adaptation including in SARS-CoV-2.

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Vertical distribution of epiphytic diatoms in relation to the eelgrass Zostera noltii canopy biomass and height

Cited by 6 publications

References 62 publications

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

Rare Earth Elements in the Seagrass Zostera noltei and Sediments from the Black Sea Coast of Crimea

SPLASH: a statistical, reference-free genomic algorithm unifies biological discovery

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