Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes

Dai, Hongzheng; Yoshimatsu, Toshio F.; Long, Manyuan

doi:10.1016/j.gene.2006.04.033

Cited by 60 publications

(80 citation statements)

References 24 publications

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“…Likewise, these duplicated SKP genes appear to be functional based on expression analysis and their ability to encode proteins that retain their interaction with CUL1 and F-box proteins to form SCF E3 complexes (Gagne et al, 2002;Risseeuw et al, 2003;Takahashi et al, 2004;Wang et al, 2004b). The results with SKP and expanded MATH-BTB proteins together with recent studies demonstrating that apparent retrogenes are actively transcribed (Boschan et al, 2002;Marques et al, 2005;Dai et al, 2006;Vinckenbosch et al, 2006;Zhao et al, 2007) suggests this type of gene expansion does not a priori synthesize nonfunctional loci, in contrast with previous assumptions (Graur and Li, 2000). For several of the obvious MATH-BTB pseudogenes in rice, several types of expression studies (ESTs/cDNAs, MPSS, and microarrays) indicate that they are still transcribed.…”

Section: Discussionmentioning

confidence: 53%

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

et al. 2007

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Selective ubiquitination of proteins is directed by diverse families of ubiquitin-protein ligases (or E3s) in plants. One important type uses Cullin-3 as a scaffold to assemble multisubunit E3 complexes containing one of a multitude of bric-a-brac/tramtrack/ broad complex (BTB) proteins that function as substrate recognition factors. We previously described the 80-member BTB gene superfamily in Arabidopsis thaliana. Here, we describe the complete BTB superfamily in rice (Oryza sativa spp japonica cv Nipponbare) that contains 149 BTB domain-encoding genes and 43 putative pseudogenes. Amino acid sequence comparisons of the rice and Arabidopsis superfamilies revealed a near equal repertoire of putative substrate recognition module types. However, phylogenetic comparisons detected numerous gene duplication and/or loss events since the rice and Arabidopsis BTB lineages split, suggesting possible functional specialization within individual BTB families. In particular, a major expansion and diversification of a subset of BTB proteins containing Meprin and TRAF homology (MATH) substrate recognition sites was evident in rice and other monocots that likely occurred following the monocot/dicot split. The MATH domain of a subset appears to have evolved significantly faster than those in a smaller core subset that predates flowering plants, suggesting that the substrate recognition module in many monocot MATH-BTB E3s are diversifying to ubiquitinate a set of substrates that are themselves rapidly changing. Intriguing possibilities include pathogen proteins attempting to avoid inactivation by the monocot host.

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Section: Discussionmentioning

confidence: 53%

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

et al. 2007

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“…The abundance is lower than that of root and mature leaf (28.1% for both). In contrast, .50% of retrogenes express in testis for both human (Emerson et al, 2004) and fly (Dai et al, 2006). These data indicate that the incipient Z/W chromosomes do not play a significant role with respect to retrogene origination.…”

Section: There Is No Retrogene Traffic Out Of the Sex Chromosome In Pmentioning

confidence: 83%

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome

2009

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Retroposition, as an important copy mechanism for generating new genes, was believed to play a negligible role in plants. As a representative dicot, the genomic sequences of Populus (poplar; Populus trichocarpa) provide an opportunity to investigate this issue. We identified 106 retrogenes and found the majority (89%) of them are associated with functional signatures in sequence evolution, transcription, and (or) translation. Remarkably, examination of gene structures revealed extensive structural renovation of these retrogenes: we identified 18 (17%) of them undergoing either chimerization to form new chimerical genes and (or) intronization (transformation into intron sequences of previously exonic sequences) to generate new intron-containing genes. Such a change might occur at a high speed, considering eight out of 18 such cases occurred recently after divergence between Arabidopsis (Arabidopsis thaliana) and Populus. This pattern also exists in Arabidopsis, with 15 intronized retrogenes occurring after the divergence between Arabidopsis and papaya (Carica papaya). Thus, the frequency of intronization in dicots revealed its importance as a mechanism in the evolution of exon-intron structure. In addition, we also examined the potential impact of the Populus nascent sex determination system on the chromosomal distribution of retrogenes and did not observe any significant effects of the extremely young sex chromosomes.

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“…Betrán et al (2002) found an excess of retrogenes transposing from the X chromosome to the autosomes in D. melanogaster, but not the reverse. More recent studies have confirmed this excess of retrogenes moving off the X and neo-X chromosomes in multiple Drosophila species (Dai et al 2006;Bai et al 2007;Meisel et al 2009;Vibranovski et al 2009). Unlike retrogenes, DNA-based transpositions do not appear to consistently move in excess from the X to autosomes: while there is an excess found for DNAbased relocations in Drosophila (Bhutkar et al 2007;Meisel et al 2009;Vibranovski et al 2009;Moyle et al 2010), there is not an excess of DNA-based duplicative transpositions (Meisel et al 2009).…”

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confidence: 86%

Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony

Han

Hahn

2012

Genetics

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Gene transposition puts a new gene copy in a novel genomic environment. Moreover, genes moving between the autosomes and the X chromosome experience change in several evolutionary parameters. Previous studies of gene transposition have not utilized the phylogenetic framework that becomes possible with the availability of whole genomes from multiple species. Here we used parsimonious reconstruction on the genomic distribution of gene families to analyze interchromosomal gene transposition in Drosophila. We identified 782 genes that have moved chromosomes within the phylogeny of 10 Drosophila species, including 87 gene families with multiple independent movements on different branches of the phylogeny. Using this large catalog of transposed genes, we detected accelerated sequence evolution in duplicated genes that transposed when compared to the parental copy at the original locus. We also observed a more refined picture of the biased movement of genes from the X chromosome to the autosomes. The bias of X-to-autosome movement was significantly stronger for RNA-based movements than for DNA-based movements, and among DNAbased movements there was an excess of genes moving onto the X chromosome as well. Genes involved in female-specific functions moved onto the X chromosome while genes with male-specific functions moved off the X. There was a significant overrepresentation of proteins involving chromosomal function among transposed genes, suggesting that genetic conflict between sexes and among chromosomes may be a driving force behind gene transposition in Drosophila.

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Retrogene movement within- and between-chromosomes in the evolution of Drosophila genomes

Cited by 60 publications

References 24 publications

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

Large-Scale, Lineage-Specific Expansion of a Bric-a-Brac/Tramtrack/Broad Complex Ubiquitin-Ligase Gene Family in Rice

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome

Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n-Dimensional Parsimony

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