Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes

BMC Bioinformatics

Software

Ralph S. Peters¹  Xin Zhou²  Malte Petersen³  Alexander Donath³  Alexandros Vasilikopoulos³  Bernhard Misof³  Karen Meusemann⁴  Oliver Niehuis⁵  Daniel Dowling⁶  Shanlin Liu⁷  Lars Podsiadlowski⁸ 

[1] Arthropod Department, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany;Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, 100193, Beijing, China;College of Food Science and Nutritional Engineering, China Agricultural University, 100083, Beijing, China;Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany;Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany;Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Clunies Ross Street, ACT 2601, Canberra, Australia;Department for Evolutionary Biology & Ecology, Institute for Biology I (Zoology), University of Freiburg, Hauptstraße 1, 79104, Freiburg, Germany;Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany;Department for Evolutionary Biology & Ecology, Institute for Biology I (Zoology), University of Freiburg, Hauptstraße 1, 79104, Freiburg, Germany;Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany;Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany;China National GeneBank, BGI-Shenzhen, Shenzhen, China;Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany;

关键词: Orthology;    Paralogy;    Splice variants;    Sphecidae;    Crabronidae;    Transcriptome;   

DOI  :  10.1186/s12859-017-1529-8

 received in 2016-08-25, accepted in 2017-02-06,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundOrthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms’ gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e.g., RNA sequencing). Here, identification of orthologous nucleotide or amino acid sequences can be achieved using a graph-based approach that maps nucleotide sequences to genes of known orthology. Existing implementations of this approach, however, suffer from algorithmic issues that may cause problems in downstream analyses.ResultsWe present a new software pipeline, Orthograph, that addresses and solves the above problems and implements useful features for a wide range of comparative genomic and transcriptomic analyses. Orthograph applies a best reciprocal hit search strategy using profile hidden Markov models and maps nucleotide sequences to the globally best matching cluster of orthologous genes, thus enabling researchers to conveniently and reliably delineate orthologs and paralogs from transcriptomic and genomic sequence data. We demonstrate the performance of our approach on de novo-sequenced and assembled transcript libraries of 24 species of apoid wasps (Hymenoptera: Aculeata) as well as on published genomic datasets.ConclusionWith Orthograph, we implemented a best reciprocal hit approach to reference-based orthology prediction for coding nucleotide sequences such as RNAseq data. Orthograph is flexible, easy to use, open source and freely available at https://mptrsen.github.io/Orthograph. Additionally, we release 24 de novo-sequenced and assembled transcript libraries of apoid wasp species.

【 授权许可】

CC BY   
© The Author(s) 2017