title: Orthograph: a versatile tool for mapping coding nucleotide sequences to clusters of orthologous genes.
abstract: BACKGROUND
  Orthology 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.
  
  
  RESULTS
  We 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.
  
  
  CONCLUSIONS
  With 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.
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany. mpetersen@uni-bonn.de.
authors.forename: Malte
authors.initials: M
authors.lastname: Petersen
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.|Australian National Insect Collection, CSIRO National Research Collections Australia (NRCA), Clunies Ross Street, Canberra, ACT 2601, Australia.|Department for Evolutionary Biology & Ecology, Institute for Biology I (Zoology), University of Freiburg, Hauptstraße 1, Freiburg, 79104, Germany.
authors.forename: Karen
authors.initials: K
authors.lastname: Meusemann
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Donath
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.|Institute of Molecular Biology (IMB), Ackermannweg 4, Mainz, 55128, Germany.
authors.forename: Daniel
authors.initials: D
authors.lastname: Dowling
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen, China.
authors.forename: Shanlin
authors.initials: S
authors.lastname: Liu
authors.affiliation: Arthropod Department, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.
authors.forename: Ralph S
authors.initials: RS
authors.lastname: Peters
authors.affiliation: Institute of Evolutionary Biology and Ecology, Zoology and Evolutionary Biology, University of Bonn, An der Immenburg 1, Bonn, 53121, Germany.
authors.forename: Lars
authors.initials: L
authors.lastname: Podsiadlowski
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.
authors.forename: Alexandros
authors.initials: A
authors.lastname: Vasilikopoulos
authors.affiliation: Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China.|College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
authors.affiliation: Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, Bonn, 53113, Germany. o.niehuis@zfmk.de.|Department for Evolutionary Biology & Ecology, Institute for Biology I (Zoology), University of Freiburg, Hauptstraße 1, Freiburg, 79104, Germany. o.niehuis@zfmk.de.
authors.forename: Oliver
authors.initials: O
authors.lastname: Niehuis
mesh_terms: D000818:Animals; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods*; D005810:Multigene Family / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D059467:Transcriptome / Q000235:genetics; D014863:Wasps / Q000235:genetics
keywords: Crabronidae; Orthology; Paralogy; Sphecidae; Splice variants; Transcriptome