Cristin-resultat-ID: 981333
Sist endret: 4. januar 2013 23:06
Resultat
Vitenskapelig foredrag
2012

A strategy for 454-pyrosequencing of ribosomal SSU DNA and RNA to more accurately assess protist diversity and relative abundance

Bidragsytere:
  • Bente Edvardsen
  • Elianne Sirnæs Egge
  • Lucie Bittner
  • Stéphane Audic og
  • Colomban de Vargas

Presentasjon

Navn på arrangementet: ISOP and ISEP International conference, Protist2012
Sted: Oslo
Dato fra: 29. juli 2012
Dato til: 3. august 2012

Arrangør:

Arrangørnavn: ISOP og ISEP

Om resultatet

Vitenskapelig foredrag
Publiseringsår: 2012

Beskrivelse Beskrivelse

Tittel

A strategy for 454-pyrosequencing of ribosomal SSU DNA and RNA to more accurately assess protist diversity and relative abundance

Sammendrag

Next generation sequencing of ribosomal DNA is increasingly used to assess the biodiversity and structure in microbial communities. Our aim was to develop a method to depict the diversity and community structure of marine planktonic haptophytes to species level. We used a mock community consisting of equal number of cells of 11 species representing all known haptophyte orders to investigate the ability to detect and assess the number of species present, and assess the relative abundance in terms of cell numbers and biomass by 454-pyrosequencing. We compared DNA to RNA/cDNA, 454-pyrosequencing to Sanger sequencing of clone libraries, and two different V4-SSU rDNA haptophyte biased primer pairs. Further, we tested 5 different strategies to clean the sequence data from errors. Up to 6000 unique tags per sample (with avg. 16500 reads) were obtained before sequence cleaning and clustering, and higher diversity was obtained from cDNA than DNA. The distribution of reads assigned to a species was significantly different from the initial proportions of cells or biomass in the culture mix, but cell numbers were better reflected by proportion of cDNA than DNA reads. Here we propose a strategy to more accurately depict the haptophyte diversity and assess relative abundance using 454-pyrosequencing.

Bidragsytere

Aktiv cristin-person

Bente Edvardsen

  • Tilknyttet:
    Forfatter
    ved Marinbiologi ved Universitetet i Oslo

Elianne Dunthorn Egge

Bidragsyterens navn vises på dette resultatet som Elianne Sirnæs Egge
  • Tilknyttet:
    Forfatter
    ved Institutt for biovitenskap (tidl. BIO) ved Universitetet i Oslo

Lucie Bittner

  • Tilknyttet:
    Forfatter

Stéphane Audic

  • Tilknyttet:
    Forfatter

Colomban de Vargas

  • Tilknyttet:
    Forfatter
1 - 5 av 5