Evolution of Glucosinolate Diversity via Whole-Genome Duplications, Gene Rearrangements, and Substrate Promiscuity

2019 ◽  
Vol 70 (1) ◽  
pp. 585-604 ◽  
Author(s):  
Brenden Barco ◽  
Nicole K. Clay
Keyword(s):  
Protein Function ◽  
Higher Plants ◽  
Gene Rearrangements ◽  
Biosynthetic Enzymes ◽  
Whole Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Repeated Evolution ◽  
Substrate Promiscuity

Over several decades, glucosinolates have become a model system for the study of specialized metabolic diversity in plants. The near-complete identification of biosynthetic enzymes, regulators, and transporters has provided support for the role of gene duplication and subsequent changes in gene expression, protein function, and substrate specificity as the evolutionary bases of glucosinolate diversity. Here, we provide examples of how whole-genome duplications, gene rearrangements, and substrate promiscuity potentiated the evolution of glucosinolate biosynthetic enzymes, regulators, and transporters by natural selection. This in turn may have led to the repeated evolution of glucosinolate metabolism and diversity in higher plants.

scholarly journals Vertebrate whole genome duplications shaped the current 3D genome architecture

2021 ◽  
Author(s):  
Caelinn James ◽  
Marco Trevisan-Herraz ◽  
Daniel Rico
Keyword(s):  
Regulatory Networks ◽  
Whole Genome ◽  
3D Genome ◽  
Whole Genome Duplications ◽  
Genome Duplications ◽  
Topologically Associated Domains ◽  
Major Transition ◽  
Evolution Of Gene Regulation ◽  
Evolutionary Success

Topologically associated domains (TADs) are interaction sub-networks of 3D genomes. TAD boundaries frequently coincide with genome breaks while their deletion is under negative selection, suggesting that TADs act as modules facilitating genome rearrangements and metazoan evolution. However, the role of TADs in the evolution of gene regulation and essentiality is not well understood. Here, we show that TADs play a role organising ancestral functions and evolutionary novelty. We discovered that genes co-localise by evolutionary age in the human and mouse genomes, resulting in TADs that have different proportions of younger and older genes. A major transition in the TAD age co-localisation patterns is observed between the genes born as a result of the vertebrate whole genome duplications (WGDs) or before, and those born afterwards. We also found that primate- and rodent-specific genes are more frequently essential when they are located in 'aged' TADs and connected to genes that have not duplicated since the WGD. Our data suggests that evolutionary success of recent genes may increase when located in functionally relevant TADs with established regulatory networks.

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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