scholarly journals Whole‐genome duplications followed by tandem duplications drive diversification of the protein modifier SUMO in Angiosperms

2016 ◽  
Vol 211 (1) ◽  
pp. 172-185 ◽  
Author(s):  
Valentin Hammoudi ◽  
Georgios Vlachakis ◽  
M. Eric Schranz ◽  
Harrold A. den Burg
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Tandem Duplications

scholarly journals Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution

2020 ◽  
Author(s):  
Akihiro Ezoe ◽  
Kazumasa Shirai ◽  
Kousuke Hanada
Keyword(s):  
Gene Duplication ◽  
Related Species ◽  
Plant Evolution ◽  
Whole Genome ◽  
Duplicated Genes ◽  
Closely Related Species ◽  
Whole Genome Duplications ◽  
New Genes ◽  
Genome Duplications ◽  
Tandem Duplications

Abstract Gene duplication is a major mechanism to create new genes. After gene duplication, some duplicated genes undergo functionalization, whereas others largely maintain redundant functions. Duplicated genes comprise various degrees of functional diversification in plants. However, the evolutionary fate of high and low diversified duplicates is unclear at genomic scale. To infer high and low diversified duplicates in Arabidopsis thaliana genome, we generated a prediction method for predicting whether a pair of duplicate genes was subjected to high or low diversification based on the phenotypes of knock-out mutants. Among 4,017 pairs of recently duplicated A. thaliana genes, 1,052 and 600 are high and low diversified duplicate pairs, respectively. The predictions were validated based on the phenotypes of generated knock-down transgenic plants. We determined that the high diversified duplicates resulting from tandem duplications tend to have lineage-specific functions, whereas the low diversified duplicates produced by whole-genome duplications are related to essential signaling pathways. To assess the evolutionary impact of high and low diversified duplicates in closely related species, we compared the retention rates and selection pressures on the orthologs of A. thaliana duplicates in two closely related species. Interestingly, high diversified duplicates resulting from tandem duplications tend to be retained in multiple lineages under positive selection. Low diversified duplicates by whole-genome duplications tend to be retained in multiple lineages under purifying selection. Taken together, the functional diversities determined by different duplication mechanisms had distinct effects on plant evolution.

scholarly journals On the Expansion of “Dangerous” Gene Repertoires by Whole-Genome Duplications in Early Vertebrates

Cell Reports ◽  
2012 ◽  
Vol 2 (5) ◽  
pp. 1387-1398 ◽  
Author(s):  
Param Priya Singh ◽  
Séverine Affeldt ◽  
Ilaria Cascone ◽  
Rasim Selimoglu ◽  
Jacques Camonis ◽  
...  
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Early Vertebrates

scholarly journals Legume Cytosolic and Plastid Acetyl-Coenzyme—A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 563 ◽  
Author(s):  
Anna Szczepaniak ◽  
Michał Książkiewicz ◽  
Jan Podkowiński ◽  
Katarzyna Czyż ◽  
Marek Figlerowicz ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Coenzyme A ◽  
Phylogenetic Inference ◽  
Whole Genome ◽  
Evolutionary Patterns ◽  
Acetyl Coenzyme A ◽  
Acetyl Coenzyme ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Acetyl Coenzyme A Carboxylase

Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

scholarly journals Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

2018 ◽  
Vol 221 (1) ◽  
pp. 565-576 ◽  
Author(s):  
Liming Cai ◽  
Zhenxiang Xi ◽  
André M. Amorim ◽  
M. Sugumaran ◽  
Joshua S. Rest ◽  
...  
Keyword(s):  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications

scholarly journals Synteny-Guided Resolution of Gene Trees Clarifies the Functional Impact of Whole-Genome Duplications

2020 ◽  
Vol 37 (11) ◽  
pp. 3324-3337
Author(s):  
Elise Parey ◽  
Alexandra Louis ◽  
Cédric Cabau ◽  
Yann Guiguen ◽  
Hugues Roest Crollius ◽  
...  
Keyword(s):  
Gene Families ◽  
Sequence Evolution ◽  
Whole Genome ◽  
Gene Trees ◽  
Ensembl Database ◽  
Whole Genome Duplications ◽  
Gene Copies ◽  
Genome Duplications ◽  
Phenotypic Robustness ◽  
New Gene

Abstract Whole-genome duplications (WGDs) have major impacts on the evolution of species, as they produce new gene copies contributing substantially to adaptation, isolation, phenotypic robustness, and evolvability. They result in large, complex gene families with recurrent gene losses in descendant species that sequence-based phylogenetic methods fail to reconstruct accurately. As a result, orthologs and paralogs are difficult to identify reliably in WGD-descended species, which hinders the exploration of functional consequences of WGDs. Here, we present Synteny-guided CORrection of Paralogies and Orthologies (SCORPiOs), a novel method to reconstruct gene phylogenies in the context of a known WGD event. WGDs generate large duplicated syntenic regions, which SCORPiOs systematically leverages as a complement to sequence evolution to infer the evolutionary history of genes. We applied SCORPiOs to the 320-My-old WGD at the origin of teleost fish. We find that almost one in four teleost gene phylogenies in the Ensembl database (3,394) are inconsistent with their syntenic contexts. For 70% of these gene families (2,387), we were able to propose an improved phylogenetic tree consistent with both the molecular substitution distances and the local syntenic information. We show that these synteny-guided phylogenies are more congruent with the species tree, with sequence evolution and with expected expression conservation patterns than those produced by state-of-the-art methods. Finally, we show that synteny-guided gene trees emphasize contributions of WGD paralogs to evolutionary innovations in the teleost clade.

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