Correlated expression of retrocopies and parental genes in zebrafish

Zhong, Zaixuan; Yang, Liandong; Zhang, Yong E.; Xue, Yu; He, Shunping

doi:10.1007/s00438-015-1140-5

Cited by 7 publications

(5 citation statements)

References 80 publications

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“…2D). This pattern has been discovered for retrogene and parental gene pairs in rice and zebrafish (Sakai et al 2011;Zhong et al 2015). The Genotype-Tissue Expression (GTEx) data (The GTEx Consortium 2015) show similar correlation (Supplemental Fig.…”

Section: Gentree Is An Integrated Database For New Genes In the Humansupporting

confidence: 57%

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

et al. 2019

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Section: Gentree Is An Integrated Database For New Genes In the Humansupporting

confidence: 57%

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

et al. 2019

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“…To identify sex-biased genes in zebrafish ( Danio rerio ), paired-end RNA-seq datasets from zebrafish adult testis, adult ovary, male head, female head, whole male body without head or testis, whole female body without head or ovary were collected from NCBI’s SRA database (Collins et al 2012) and one testis sample was generated by our lab at Novogene (Beijing, China) (Zhong et al 2016). Detailed information about these RNA-seq data can be found in supplementary table S1, Supplementary Material online.…”

Section: Methodsmentioning

confidence: 99%

Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes

Yang

Zhang

2016

Genome Biol Evol

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Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level. In order to differentiate between adaptive and nonadaptive causes, we tested for codon usage bias and signatures of different selective regimes in our sequence data. Our results show that both male- and female-biased genes show signatures consistent with adaptive evolution. In order to test the generality of our findings across fish, we also analyzed publicly available data on sticklebacks, and found results consistent with our findings in zebrafish.

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“…While this evolutionary pathway has not been directly tested in retrogenes, it has been noticed that many retrogenes maintain the parental gene expression pattern in rice (Sakai et al 2011) and zebrafish (Zhong et al 2016), a possible result of selection for increase dosage of the cognate gene product. This hypothesis could be further tested by determining whether retrogene-parental gene pairs with overlapping expression show a higher combined transcription level compared with parental genes in multiple close outgroup species lacking those retrogenes.…”

Section: Retrocopy Evolutionary Dynamics and Pathways To Biological Fmentioning

confidence: 99%

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

Casola

Betrán

2017

Genome Biology and Evolution

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Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene’s transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different “life cycle” stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.

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Correlated expression of retrocopies and parental genes in zebrafish

Cited by 7 publications

References 80 publications

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

Both Male-Biased and Female-Biased Genes Evolve Faster in Fish Genomes

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

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