The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

By Steven B. Cannon, A. Mitra, A. Baumgarten, Nevin D. Young, G. May. BMC Plant Biology, 2004

1,838 citations recorded by the source corpus.

BackgroundMost genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses.ResultsOur approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions.ConclusionsCombining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/608adb5f9f2d7e2d152b84492db5d9523c48b38f

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Citations in the corpus

Genomic Survey and Gene Expression Analysis of the Basic Leucine Zipper Transcription Factor Family in Rice1[W][OA] (2007, background): “In the case of plants, during the course of its evolution, a gene family has generally undergone either tandem duplication or large-scale segmental duplication to maintain the high number of family members (Cannon et al., 2004).”
Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. (2011, background): “Further segmental tandem duplication of large chromosome regions has been shown to play a prominent role in the evolution of Arabidopsis MYB genes, in particular sub-groups 6 and 7 (Cannon et al., 2004; Stracke et al., 2007; Matus et al., 2008), and also in poplar (Populus trichocarpa), in which mor”
Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice (2006, background): “Moreover, a study of 50 Arabidopsis gene families showed that the two families with the strongest bias toward tandem organization encoded plant defense functions [31].”
Widespread genome duplications throughout the history of flowering plants. (2006, background): “…Harbor Laboratory Press; ISSN 1088-9051/06; www.genome.org genome duplications from segmental and tandem duplications by mapping chromosomal locations of duplicate genes or blocks of genes (Simillion et al. 2002; Blanc et al. 2003; Bowers et al. 2003; Cannon et al. 2004; Paterson et al. 2004b).”
Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition. (2009, methodology): “GO terms using the word ubiquitin, a term related to the very complicated proteasome, a selective protein degradation machine (67), were particularly overretained posttetraploidy and underretained post–tandem duplication (12, 88).”
Root-to-shoot Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice (2009, positive): “The three GSTTs in Arabidopsis have clearly arisen through gene duplication (Cannon et al., 2004), with the enzymes showing conservation in both sequence and enzyme activity.”
Genome-Wide Comparative Analysis and Expression Pattern of TCP Gene Families in Arabidopsis thaliana and Oryza sativa (2007, neutral): “Genome duplication events are thought to have occurred during angiosperm evolution (Kent et al. 2003; Cannon et al. 2004; Mehan et al. 2004; Li et al. 2006).”
Genome-wide analysis of NAC transcription factor family in rice. (2010, background): “During evolution, both segmental duplication and tandem duplication have contributed to the large number of gene families in plants (Cannon et al., 2004).”