Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
Artikel i vetenskaplig tidskrift, 2012

Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

barcoding

ITS

databases

sequence quality control

sequence reliability

fungi

Författare

R. Henrik Nilsson

Göteborgs universitet

Leho Tedersoo

Kessy Abarenkov

Martin Ryberg

Erik Kristiansson

Göteborgs universitet

Chalmers, Matematiska vetenskaper, matematisk statistik

Martin Hartmann

Conrad L. Schoch

Johan A. A. Nylander

Johannes Bergsten

Teresita M. Porter

Ari Jumpponen

Parag Vaishampayan

Otso Ovaskainen

Nils Hallenberg

Göteborgs universitet

Johan Bengtsson

Göteborgs universitet

Martin Eriksson

Göteborgs universitet

Karl-Henrik Larsson

Ellen Larsson

Göteborgs universitet

Urmas Kõljalg

MycoKeys

1314-4057 (ISSN) 1314-4049 (eISSN)

Vol. 4 37-63

Ämneskategorier

Botanik

Biologisk systematik

Markvetenskap

Ekologi

Mikrobiologi

Mikrobiologi inom det medicinska området

Bioinformatik och systembiologi

DOI

10.3897/mycokeys.4.3606

Mer information

Skapat

2017-10-07