Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

Sammanfattning

High-throughput sequencing platforms are continuing to increase resulting read lengths, which is allowing for a deeper and more accurate depiction of environmental microbial diversity. With the nascent Reagent Kit v3, Illumina MiSeq now has the ability to sequence the eukaryotic hyper-variable V4 region of the SSU-rDNA locus with paired-end reads. Using DNA collected from soils with analyses of strictly- and nearly identical amplicons, here we ask how the new Illumina MiSeq data compares with what we can obtain with Roche/454 GS FLX with regard to quantity and quality, presence and absence, and abundance perspectives. We show that there is an easy qualitative transition from the Roche/454 to the Illumina MiSeq platforms. The ease of this transition is more nuanced quantitatively for low-abundant amplicons, although estimates of abundances are known to also vary within platforms.

Nyckelord

454; abundances; Illumina; MiSeq; next-generation sequencing; pyrosequencing; Roche

Publicerad i

Journal of Eukaryotic Microbiology
2015, volym: 62, nummer: 3, sidor: 338-345
Utgivare: WILEY-BLACKWELL

SLU författare

• Mayor, Jordan

  • Institutionen för skogens ekologi och skötsel, Sveriges lantbruksuniversitet
    

UKÄ forskningsämne

Skogsvetenskap

Publikationens identifierare

• DOI: https://doi.org/10.1111/jeu.12187

Permanent länk till denna sida (URI)

https://res.slu.se/id/publ/68446