Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

Hellsten, Uffe; Khokha, Mustafa K.; Grammer, Timothy C.; Harland, Richard M.; Richardson, Paul M.; Rokhsar, Daniel S.

doi:10.1186/1741-7007-5-31

Cited by 106 publications

(136 citation statements)

References 39 publications

(51 reference statements)

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“…Therefore, it is possible that we may have missed some bHLHs or that we may have included a few bHLH domains from some duplicates or pseudogenes (Table 2), such as gene duplicates named Myf3a and Myf3b,Myf4a and Myf4b,Myf5,Myf6a and Myf6b,etc. However, these data are sufficient for the purpose of this study. While a few genes showed detectable asymmetric evolution, the majority of genes analyzed in the Xenopus laevis genome were generally consistent with a hypothesis of symmetric change under purifying selection or strong constraint (Hellsten et al, 2007). In addition, there was only a subtle effect affecting on average only about 1-2 amino acids per peptide for any single gene and the Pak.…”

Section: Bg2348721 Estmentioning

confidence: 60%

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Liu¹,

Li²

2015

Pakistan J. of Biological Sciences

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A B S T R A C TXenopus laevis is a long established model organism for developmental, behavioral and neurological studies. Herein, an updated genome-wide survey was conducted using the ongoing genome project of Xenopus laevis and 106 non-redundant Basic Helix-Loop-Helix (bHLH) genes were identified in the Xenopus laevis genome databases. Gene Ontology (GO) enrichment statistics showed 51 significant GO annotations of biological processes and molecular functions and 5 significant KEGG pathways and a number of Xenopus laevis bHLH genes play significant role in specific development or special physiology processes like the development processes of muscle and eye and other organs. Furthermore, each sub-group of the bHLH family has its special gene functions except for the common GO term categories. Molecular phylogenetic analyses revealed that among these identified bHLH proteins, 105 sequences could classified into 39 families with 46, 25, 10, 5, 16 and 3 members in the corresponding high-order groups A, B, C, D, E and F, respectively with an addition bHLH member categorized as an orphan. The present study provides much useful information for further researches on Xenopus laevis.

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Section: Bg2348721 Estmentioning

confidence: 60%

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Liu¹,

Li²

2015

Pakistan J. of Biological Sciences

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“…In this manner, subfunctionalization will result in duplicate genes with fewer transcripts and more restricted expression profiles. Indeed, shifts in expression after duplication have often been used as evidence for subfunctionalization (Blanc and Wolfe 2004;Casneuf et al 2006;Duarte et al 2006;Hellsten et al 2007;Sémon and Wolfe 2008). To test if gene duplication followed by exon structure divergence results in the partitioning of expression domains, we analyzed the available UniGene (Pontius et al 2003) EST expression profiles, which approximate expression patterns inferred from EST libraries.…”

Section: Exon Divergent Paralogs Are Expressed In Fewer Tissuesmentioning

confidence: 99%

Evidence for widespread subfunctionalization of splice forms in vertebrate genomes

et al. 2015

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Gene duplication and alternative splicing are important sources of proteomic diversity. Despite research indicating that gene duplication and alternative splicing are negatively correlated, the evolutionary relationship between the two remains unclear. One manner in which alternative splicing and gene duplication may be related is through the process of subfunctionalization, in which an alternatively spliced gene upon duplication divides distinct splice isoforms among the newly generated daughter genes, in this way reducing the number of alternatively spliced transcripts duplicate genes produce. Previously, it has been shown that splice form subfunctionalization will result in duplicate pairs with divergent exon structure when distinct isoforms become fixed in each paralog. However, the effects of exon structure divergence between paralogs have never before been studied on a genome-wide scale. Here, using genomic data from human, mouse, and zebrafish, we demonstrate that gene duplication followed by exon structure divergence between paralogs results in a significant reduction in levels of alternative splicing. In addition, by comparing the exon structure of zebrafish duplicates to the co-orthologous human gene, we have demonstrated that a considerable fraction of exon divergent duplicates maintain the structural signature of splice form subfunctionalization. Furthermore, we find that paralogs with divergent exon structure demonstrate reduced breadth of expression in a variety of tissues when compared to paralogs with identical exon structures and singletons. Taken together, our results are consistent with subfunctionalization partitioning alternatively spliced isoforms among duplicate genes and as such highlight the relationship between gene duplication and alternative splicing.

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“…In light of this, we adopted a strategy of selecting probes in conserved sequence regions such that the resulting expression of duplicates may be repre- sented as the sum of their separate expressions. Thus, many interesting patterns of subfunctionalization are potentially masked in our profiles for duplicates, as recently revealed (Hellsten et al, 2007).…”

Section: Introduction Of Transcriptome Profiles To Xenbasementioning

confidence: 65%

“…Sequence identity was determined using blastn between the 11,095 pairs of the previously delineated orthologs (Yanai et al, 2011). Pairs of X. laevis paralogs were retrieved from a recent study (Hellsten et al, 2007) and compared as for the orthologs.…”

Section: Comparison Of the Expression Profiles Of Developmental Genesmentioning

confidence: 99%

“…The two species are easy to distinguish, since X. laevis is characterized by significantly larger embryos and adults, as well as more robust eggs and better husbandry practices. However, X. laevis poses a substantial setback as a genetic system due to an allotetraploid genome with two related paralogues for most genes (Hellsten et al, 2007). X. tropicalis has a shorter generation time of 3-4.5 months, a potential for much greater spawning number (1,000-9,000 vs. 300-1,000), and is the only known Xenopus species with a diploid genome, which is almost half the size of that of X. laevis (Hirsch et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

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Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks

Beer

Wagner

Grishkevich

et al. 2012

Genesis

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Summary: The availability of both the Xenopus tropicalis genome and the soon to be released Xenopus laevis genome provides a solid foundation for Xenopus developmental biologists. The Xenopus community has presently amassed expression data for 2,300 genes in the form of published images collected in the Xenbase, the principal Xenopus research database. A few of these genes have been examined in both X. tropicalis and X. laevis and the cross-species comparison has been proven invaluable for studying gene function. A recently published work has yielded developmental expression profiles for the majority of Xenopus genes across fourteen developmental stages spanning the blastula, gastrula, neurula, and the tail-bud. While this data was originally queried for global evolutionary and developmental principles, here we demonstrate its general use for gene-level analyses. In particular, we present the accessibility of this dataset through Xenbase and describe biases in the characterized genes in terms of sequence and expression conservation across the two species. We further indicate the advantage of examining coexpression for gene function discovery relating to developmental processes conserved across species. We suggest that the integration of additional largescale datasets-comprising diverse functional datainto Xenbase promises to provide a strong foundation for researchers in elucidating biological processes including the gene regulatory programs encoding development. genesis 50:186-191, 2012. V

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Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

Cited by 106 publications

References 39 publications

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

Evidence for widespread subfunctionalization of splice forms in vertebrate genomes

Toward an unbiased evolutionary platform for unraveling Xenopus developmental gene networks

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