Morphological Identification and Single-Cell Genomics of Marine Diplonemids

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F16%3A00468235" target="_blank" >RIV/60077344:_____/16:00468235 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60076658:12310/16:43890670

Výsledek na webu

<a href="http://dx.doi.org/10.1016/j.cub.2016.09.013" target="_blank" >http://dx.doi.org/10.1016/j.cub.2016.09.013</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cub.2016.09.013" target="_blank" >10.1016/j.cub.2016.09.013</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

Popis výsledku v původním jazyce

Recent global surveys of marine biodiversity have revealed that a group of organisms known as "marine diplonemids" constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2, 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean. Phylogenetic analysis confirms that the isolates reflect the entire range of marine diplonemid diversity, and comparisons to environmental SSU surveys show that sequences from the isolates range from rare to superabundant, including the single most common marine diplonemid known. SCG generated a total of similar to 915 Mbp of assembled sequence across all ten cells and similar to 4,000 protein-coding genes with homologs in the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expected for heterotrophic protists. Models of highly conserved genes indicate a high density of non-canonical introns, lacking conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG assemblies reveals virtually no overlap, suggesting that nuclear genomic diversity is too great for representative SCG data to provide meaningful phylogenetic context to metagenomic datasets. This work provides an entry point to the future identification, isolation, and cultivation of these elusive yet ecologically important cells. The high density of nonconventional introns, however, also portends difficulty in generating accurate gene models and highlights the need for the establishment of stable cultures and transcriptomic analyses.

Název v anglickém jazyce

Morphological Identification and Single-Cell Genomics of Marine Diplonemids

Popis výsledku anglicky

Recent global surveys of marine biodiversity have revealed that a group of organisms known as "marine diplonemids" constitutes one of the most abundant and diverse planktonic lineages [1]. Though discovered over a decade ago [2, 3], their potential importance was unrecognized, and our knowledge remains restricted to a single gene amplified from environmental DNA, the 18S rRNA gene (small subunit [SSU]). Here, we use single-cell genomics (SCG) and microscopy to characterize ten marine diplonemids, isolated from a range of depths in the eastern North Pacific Ocean. Phylogenetic analysis confirms that the isolates reflect the entire range of marine diplonemid diversity, and comparisons to environmental SSU surveys show that sequences from the isolates range from rare to superabundant, including the single most common marine diplonemid known. SCG generated a total of similar to 915 Mbp of assembled sequence across all ten cells and similar to 4,000 protein-coding genes with homologs in the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology database, distributed across categories expected for heterotrophic protists. Models of highly conserved genes indicate a high density of non-canonical introns, lacking conventional GT-AG splice sites. Mapping metagenomic datasets [4] to SCG assemblies reveals virtually no overlap, suggesting that nuclear genomic diversity is too great for representative SCG data to provide meaningful phylogenetic context to metagenomic datasets. This work provides an entry point to the future identification, isolation, and cultivation of these elusive yet ecologically important cells. The high density of nonconventional introns, however, also portends difficulty in generating accurate gene models and highlights the need for the establishment of stable cultures and transcriptomic analyses.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

EB - Genetika a molekulární biologie

OECD FORD obor

—

Projekt

—

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2016

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Current Biology

ISSN

0960-9822

e-ISSN

—

Svazek periodika

26

Číslo periodika v rámci svazku

22

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

7

Strana od-do

3053-3059

Kód UT WoS článku

000388545900024

EID výsledku v databázi Scopus

2-s2.0-84997078012