ORFanFinder: automated identification of taxonomically restricted orphan genes

Alex Ekstrom1
and
Yanbin Yin*,2

+ Author Affiliations
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.
http://cys.bios.niu.edu/orfanfinder/

Introduction

Definition: Orphan genes are new protein-coding genes that are restricted to taxonomically closely related genomes. A synonymous term ORFan (orphan Open Reading Frames) was introduced by (Fischer and Eisenberg, 1999) and is more commonly used in the microbial literature.Orphan genes are new inventions of a genome: Orphan genes are also known as new genes or ORFans that enable the organism to adapt to its specific living environment (Khalturin et al., 2009; Chen et al., 2013). In the past decade, elucidating the origin, evolution and function of orphan genes has become a highly interesting research topic in the evolutionary genomics field (Tautz and Domazet-Loso, 2011; Carvunis et al., 2012; Long et al., 2013).Relevance to pathogenesis: In the microbial genomics field, recent pan-genome analyses of numerous bacterial pathogens and their closely related laboratory strains have suggested that each genome of a same species may have a significant fraction of its gene content to be unique (Medini et al., 2005; Medini et al., 2008; Bentley, 2009). Many of the unique genes are lineage-specific ORFans that are shown to reside in pathogenic islands or prophages (phages incorporated into the host genomes) and thus may contribute to pathogenesis (Raskin et al., 2006; Pallen and Wren, 2007).ORFans of different ages: From the evolutionary genomics perspective any genome is a gene pool that has been dynamically changing throughout its evolution. As a result, some genes of a genome may have emerged very recently only in the studied genome (genome-specific ORFans), while some others may have firstly appeared in the most recent common ancestor of an entire genus of species (genus-specific ORFans). Hence to understand how ORFans have contributed to the niche-specific adaptation and pathogenesis, computer tools are desired to automatically identify, classify, annotate and present ORFans of different ages, which will assist further evolutionary and functional analyses.

sra 高通量数据压缩文件

circRNA
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