ORFanFinder: automated identification of taxonomically restricted orphan genes

MOTIVATION Orphan genes, also known as ORFans, are newly evolved genes in a genome that enable the organism to adapt to specific living environment. The gene content of every sequenced genome can be classified into different age groups, based on how widely/narrowly a gene's homologs are distributed in the context of species taxonomy. Those having homologs restricted to organisms of particular taxonomic ranks are classified as taxonomically restricted ORFans. RESULTS Implementing this idea, we have developed an open source program named ORFanFinder and a free web server to allow automated classification of a genome's gene content and identification of ORFans at different taxonomic ranks. ORFanFinder and its web server will contribute to the comparative genomics field by facilitating the study of the origin of new genes and the emergence of lineage-specific traits in both prokaryotes and eukaryotes. AVAILABILITY AND IMPLEMENTATION http://cys.bios.niu.edu/orfanfinder CONTACT yyin@niu.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

[1]  Ya-Long Guo,et al.  Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. , 2013, The Plant journal : for cell and molecular biology.

[2]  T. Bosch,et al.  More than just orphans: are taxonomically-restricted genes important in evolution? , 2009, Trends in genetics : TIG.

[3]  D. Tautz,et al.  The evolutionary origin of orphan genes , 2011, Nature Reviews Genetics.

[4]  A. Stoltzfus,et al.  Population Diversity of ORFan Genes in Escherichia coli , 2012, Genome biology and evolution.

[5]  César A. Hidalgo,et al.  Proto-genes and de novo gene birth , 2012, Nature.

[6]  Tomislav Domazet-Loso,et al.  A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. , 2007, Trends in genetics : TIG.

[7]  David S. Eisenberg,et al.  Erratum. Finding families for genomic ORFans , 1999, Bioinform..

[8]  Xun Gu,et al.  Comparative analyses reveal distinct sets of lineage-specific genes within Arabidopsis thaliana , 2010, BMC Evolutionary Biology.

[9]  David S. Eisenberg,et al.  Finding families for genomic ORFans , 1999, Bioinform..

[10]  M. Long,et al.  New genes as drivers of phenotypic evolution , 2013, Nature Reviews Genetics.

[11]  M. Long,et al.  Age-dependent chromosomal distribution of male-biased genes in Drosophila. , 2010, Genome research.

[12]  Charles Spillane,et al.  Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana , 2011, BMC Evolutionary Biology.

[13]  Daniel Fischer,et al.  On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer , 2006, BMC Evolutionary Biology.

[14]  H. Ochman,et al.  Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli. , 2004, Genome research.

[15]  Jianzhi Zhang,et al.  Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution. , 2016, Molecular biology and evolution.