Chance and Necessity: Emerging Introns in Intronless Retrogenes Shengjun Tan, State Key Laboratory of Integrated Management of Pest Insects and Rodents and Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China Zhenglin Zhu, School of Life Sciences, Chongqing University, Chongqing, China Tao Zhu, MOE Key Laboratory for Biodiversity Science and Ecological Engineering and Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China Rigen Te, State Key Laboratory of Integrated Management of Pest Insects and Rodents and Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China Yong E Zhang, State Key Laboratory of Integrated Management of Pest Insects and Rodents and Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China Retrogenes are duplicated genes generated via retro- position, which were conventionally believed to contain no introns. However, emerging data showed that a significant number of retrogenes do have introns. Thus, these genes represent an attractive system to study how new genes evolve exon–intron structure. Comparison between par- ental genes and retrogenes revealed that retrogenes mainly evolve chimeric structures by fusing with local host genes or recruiting pre-existing intergenic sequences. Additionally, retrogenes could gain introns by inheriting introns of parental genes or by transforming parental exonic sequences. The functional necessity on intron gain in retrogenes remains largely elusive although limited data suggest that newborn introns play regulatory roles, enable exon shuffling and alternative splicing. Accumulation of population genomic data may help to understand which evolutionary force shapes the fixation of introns in both retrogenes and de novo originated genes given the same intron birth process acts on both type of new genes. Introduction New gene origination attracted the interest of biologists back to the 1930s (Muller, 1936) and emerging evidence in the era of genomics showed that new gene acts as one major driver of phenotypic evolution (Chen et al., 2013). Among various mechanisms leading to the birth of new genes, retroposition or reverse transcription of messenger RNA (mRNA) of parental genes is special in that the loss of introns could serve as a natural hallmark to differentiate old parental genes and newly derived retrogenes (Brosius, 2003; Cardoso-Moreira and Long, 2012). This is possibly the most important reason why many early characterised new genes such as jingwei (Long and Langley, 1993) or sphinx (Wang et al., 2002) are all retroposed duplicated genes or retrogenes. See also: Processed Pseudogenes and Their Functional Resurrection in the Human and Mouse Genomes; Pseudogenes and Their Evolution Since retrogenes were generally believed to be intronless, screening of paralogous pairs including both multi-exonic gene and single-exon gene becomes a standard routine in the identification of retrogenes (Meisel et al., 2009; Zhang et al., 2011). However, after carefully examining the structure of retrogenes, numerous reports (e.g. Fablet et al., 2009; Zhu et al., 2009; Zhang et al., 2014) discovered a surprising fact that an appreciable proportion of retro- genes do have introns. Considering that most extensively studied retrogenes are often quite young, the origination mechanism of newly evolved introns could be reliably inferred because sequence features surrounding them do Advanced article Article Contents . Introduction . General Mechanisms and Causes of Intron Gain . Retrogenes Evolve New Exon–Intron Structures Mainly through Chimerism . Chimeric Retrogenes are Widespread in both Plants and Animals . Inheritance of Parental Introns . Intronization . Sequence Insertion . Functional Necessity of Intron Gain for Retrogenes . Conclusion and Open Question . Acknowledgements Online posting date: 15 th August 2014 eLS subject area: Evolution & Diversity of Life How to cite: Tan, Shengjun; Zhu, Zhenglin; Zhu, Tao; Te, Rigen; and Zhang, Yong E (August 2014) Chance and Necessity: Emerging Introns in Intronless Retrogenes. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0022886 eLS & 2014, John Wiley & Sons, Ltd. www.els.net 1