Table 5B. Reports of retrogenes in plant and animal genomes.[1]

 

Organism

Genomic results

Reference

Arabidopsis

15 intronized retrogenes after divergence from Papaya

(Zhu, Zhang et al. 2009)

Rice (Oryzae sativa)

27 LTR retrotransposition retrogenes

1208 primary non-LTR retrogenes, 42% chimeric; OsDR10 retrogene taxonomically restricted, encodes pathogen resistance

(Wang, Zheng et al. 2006; Xiao, Liu et al. 2009)

Poplar (Populus trichocarpa)

106 retrogenes, 18 chimeric (8/18 formed after divergence from Arabidopsis)

(Zhu, Zhang et al. 2009)

Zebrafish

652 retrocopies, 440 intact retrogenes (437 transcribed), 212 pseudogenes, 10 chimerical retrogenes

(Fu, Chen et al. 2010)

Tetrapods

Ankyrin-repeat-containing Sowah retrogene has distinct cis-regulation restricted to tetrapods

(Maeso, Irimia et al. 2012)

Mosquitos

133 retrogenes common to Aedes aegypti, Anopheles gambiae, 57 specific to A. gambiae

(Toups and Hahn 2010)

Silkworm (Bombyx mori)

68 functional inter-chromosomal retrogenes; 57% excess beyond expectation from Z sex chromosome to autosomes

(Wang, Long et al. 2012)

Drosophila (X to autosomes)

Nuclear transport genes (Ntf-2 and ran) generated autosomal retroposed copies three independent times (in D. melanogaster, D. ananassae, and D. grimshawi lineages)

(Tracy, Rio et al. 2010)

Vertebrates and insects

Retrogenes reported: 163 Human, 199 Chimp, 275 Macaca, 154 Mouse, 202 Rat, 95 Dog, 163 Cow, 232 Opossum, 99 Chicken, 140 Zebrafish, 212 Fruitfly, 108 Anopheles

(Pan and Zhang 2009)

Non-mammalian chordates

Intact retrogenes: 235 Amphioxus, 96 sea squirt, 151 zebrafish, 66 Tetraodon, 148 Fugu, 159 Medaka, 119 stickleback, 216 Xenopus, 217 lizard, 57 chicken, 146 Platypus, 565 human

(Chen, Zou et al. 2011)

Vertebrates

Retrogene origin of TM1 domain in ZIP prion proteins unique to vertebrates

(Ehsani, Tao et al. 2011)

Rat

26 putative TDPOZ family retrogenes in a 2.5 Mb cluster on chromosome 2

(Choo, Hsu et al. 2007)

Rat

LINE1 and ERV sequences exonized in chimeric T1, T2 TDPOZ retrogene transcripts

(Huang, Lin et al. 2009)

Mus musculus

Imprinted expression of four retrogenes in mouse: Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1.

(McCole, Loughran et al. 2011)

Primates and rodents

Intronization in primate specific retrogene RNF113B; and independent "intronization" in retrogene DCAF12L2, one common to primates and rodents, one rodent-specific.

(Szczesniak, Ciomborowska et al. 2011)

Homo sapiens

Identified nine intron-containing retrogenes; intronizations by cryptic splice sites, silent in parental genes but active in the retrogenes

(Kang, Zhu et al. 2012)

Homo sapiens

Up to 202 retrogenes derived from snoRNAs (small nucleolar RNAs)

(Luo and Li 2007)

Homo sapiens

81 chimeric retrogenes with LINE-1 signatures

(Buzdin, Gogvadze et al. 2003)

Homo sapiens

Differential epigenetic marking of imprinted retrogenes derived from non-imprinted parental loci

(Monk, Arnaud et al. 2011)

Homo sapiens

NANOGP8 is a human-specific retro-oncogene

(Fairbanks, Fairbanks et al. 2012)

Homo sapiens

At least 18,046 “processed pseudogene” retrogene candidates identified by ENCODE

(Pei, Sisu et al. 2012)

Mice and humans

Functionality of retro-“processed pseudogenes” as siRNAs and molecular decoys for regulatory RNAs controlling the parental locus (PTEN and KRAS oncogenes)

(Muro, Mah et al. 2011; Tutar 2012)

Homo sapiens

Evidence that the beta-globin HBBP1 retro-“processed pseudogene” is functional and subject to selective maintenance equal to globin coding sequences

(Moleirinho, Seixas et al. 2013)

 

REFERENCES

 

Buzdin, A., E. Gogvadze, et al. (2003). "The human genome contains many types of chimeric retrogenes generated through in vivo RNA recombination." Nucleic Acids Res 31(15): 4385-4390. http://www.ncbi.nlm.nih.gov/pubmed/12888497.

Chen, M., M. Zou, et al. (2011). "Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates." PLoS One 6(7): e21466. http://www.ncbi.nlm.nih.gov/pubmed/21779328.

Choo, K. B., M. C. Hsu, et al. (2007). "Testis-specific expression and genomic multiplicity of the rat Rtdpoz genes that encode bipartite TRAF- and POZ/BTB-domain proteins." Gene 387(1-2): 141-149. http://www.ncbi.nlm.nih.gov/pubmed/17071022.

Ehsani, S., R. Tao, et al. (2011). "Evidence for retrogene origins of the prion gene family." PLoS One 6(10): e26800. http://www.ncbi.nlm.nih.gov/pubmed/22046361.

Fairbanks, D. J., A. D. Fairbanks, et al. (2012). "NANOGP8: evolution of a human-specific retro-oncogene." G3 (Bethesda) 2(11): 1447-1457. http://www.ncbi.nlm.nih.gov/pubmed/23173096.

Fu, B., M. Chen, et al. (2010). "The rapid generation of chimerical genes expanding protein diversity in zebrafish." BMC Genomics 11: 657. http://www.ncbi.nlm.nih.gov/pubmed/21106061.

Huang, C. J., W. Y. Lin, et al. (2009). "Transcription of the rat testis-specific Rtdpoz-T1 and -T2 retrogenes during embryo development: co-transcription and frequent exonisation of transposable element sequences." BMC Mol Biol 10: 74. http://www.ncbi.nlm.nih.gov/pubmed/19630990.

Kang, L. F., Z. L. Zhu, et al. (2012). "Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles." BMC Evol Biol 12: 128. http://www.ncbi.nlm.nih.gov/pubmed/22839428.

Luo, Y. and S. Li (2007). "Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs." Nucleic Acids Res 35(2): 559-571. http://www.ncbi.nlm.nih.gov/pubmed/17175533.

Maeso, I., M. Irimia, et al. (2012). "An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement." Genome Res 22(4): 642-655. http://www.ncbi.nlm.nih.gov/pubmed/22234889.

McCole, R. B., N. B. Loughran, et al. (2011). "A case-by-case evolutionary analysis of four imprinted retrogenes." Evolution 65(5): 1413-1427. http://www.ncbi.nlm.nih.gov/pubmed/21166792.

Moleirinho, A., S. Seixas, et al. (2013). "Evolutionary constraints in the beta-globin cluster: the signature of purifying selection at the delta-globin (HBD) locus and its role in developmental gene regulation." Genome Biol Evol 5(3): 559-571. http://www.ncbi.nlm.nih.gov/pubmed/23431002.

Monk, D., P. Arnaud, et al. (2011). "Human imprinted retrogenes exhibit non-canonical imprint chromatin signatures and reside in non-imprinted host genes." Nucleic Acids Res 39(11): 4577-4586. http://www.ncbi.nlm.nih.gov/pubmed/21300645.

Muro, E. M., N. Mah, et al. (2011). "Functional evidence of post-transcriptional regulation by pseudogenes." Biochimie 93(11): 1916-1921. http://www.ncbi.nlm.nih.gov/pubmed/21816204.

Pan, D. and L. Zhang (2009). "Burst of young retrogenes and independent retrogene formation in mammals." PLoS One 4(3): e5040. http://www.ncbi.nlm.nih.gov/pubmed/19325906.

Pei, B., C. Sisu, et al. (2012). "The GENCODE pseudogene resource." Genome Biol 13(9): R51. http://www.ncbi.nlm.nih.gov/pubmed/22951037.

Szczesniak, M. W., J. Ciomborowska, et al. (2011). "Primate and rodent specific intron gains and the origin of retrogenes with splice variants." Mol Biol Evol 28(1): 33-37. http://www.ncbi.nlm.nih.gov/pubmed/20889727.

Toups, M. A. and M. W. Hahn (2010). "Retrogenes reveal the direction of sex-chromosome evolution in mosquitoes." Genetics 186(2): 763-766. http://www.ncbi.nlm.nih.gov/pubmed/20660646.

Tracy, C., J. Rio, et al. (2010). "Convergently recruited nuclear transport retrogenes are male biased in expression and evolving under positive selection in Drosophila." Genetics 184(4): 1067-1076. http://www.ncbi.nlm.nih.gov/pubmed/20065068.

Tutar, Y. (2012). "Pseudogenes." Comp Funct Genomics 2012: 424526. http://www.ncbi.nlm.nih.gov/pubmed/22611337.

Wang, J., M. Long, et al. (2012). "Retrogenes moved out of the z chromosome in the silkworm." J Mol Evol 74(3-4): 113-126. http://www.ncbi.nlm.nih.gov/pubmed/22535494.

Wang, W., H. Zheng, et al. (2006). "High rate of chimeric gene origination by retroposition in plant genomes." Plant Cell 18(8): 1791-1802. http://www.ncbi.nlm.nih.gov/pubmed/16829590%22.

Xiao, W., H. Liu, et al. (2009). "A rice gene of de novo origin negatively regulates pathogen-induced defense response." PLoS One 4(2): e4603. http://www.ncbi.nlm.nih.gov/pubmed/19240804.

Zhu, Z., Y. Zhang, et al. (2009). "Extensive structural renovation of retrogenes in the evolution of the populus genome." Plant Physiol 151(4): 1943-1951. http://www.ncbi.nlm.nih.gov/pubmed/19789289.

 

 


[1] Note that almost all of these reported cases involve retrogenes or segments of retrogene chimeras where the parental sequence is clearly present in the same genome. Retrogenes from highly processed or horizontal transferred transcripts would not have been included in these studies.