Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

By

Nilsson, R. Henrik
Tedersoo, Leho
Abarenkov, Kessy
Ryberg, Martin
Kristiansson, Erik
Hartmann, Martin
Schoch, Conrad L.
Nylander, Johan A. A.
Bergsten, Johannes
Porter, Teresita M.
Jumpponen, Ari
Vaishampayan, Parag
Ovaskainen, Otso
Hallenberg, Nils
Bengtsson-Palme, Johan
Eriksson, K. Martin
Larsson, Karl-Henrik, 1948-
Larsson, Ellen
Kõljalg, Urmas, 1961-

Type

Article

Date of Publication

2012

Original Publication

MycoKeys

Volume

4

Pages

37-63

Subjects

Barcoding , Databases , Fungi , ITS , sequence quality control , sequence reliability

Contributed by

Pensoft Publishers

Language

English

Published by

Sofia, Bulgaria Pensoft Publishers 2011-

Identifiers

DOI: https://doi.org/10.3897/mycokeys.4.3606

 

Abstract

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.