Land-plant Phylogenomic and Pomegranate Transcriptomic Analyses Reveal an Evolutionary Scenario of CYP75 Genes Subsequent to Whole Genome Duplications

Abstract Pervasive hybridization and whole genome duplications (WGDs) influenced genome evolution in several eukaryotic lineages. While frequent and recurrent hybridizations may result in reticulate phylogenies, the evolutionary events underlying these reticulations, including detailed structure of the ancestral diploid and polyploid genomes, were only rarely reconstructed. Here, we elucidate the complex genomic history of a monophyletic clade from the mustard family (Brassicaceae), showing contentious relationships to the early-diverging clades of this model plant family. Genome evolution in the crucifer tribe Biscutelleae (c. 60 species, 5 genera) was dominated by pervasive hybridizations and subsequent genome duplications. Diversification of an ancestral diploid genome into several divergent but crossable genomes was followed by hybridizations between these genomes. Whereas a single genus (Megadenia) remained diploid, the four remaining genera originated by allopolyploidy (Biscutella, Lunaria, Ricotia) or autopolyploidy (Heldreichia). The contentious relationships among the Biscutelleae genera, and between the tribe and other early diverged crucifer lineages, are best explained by close genomic relatedness among the recurrently hybridizing ancestral genomes. By using complementary cytogenomics and phylogenomics approaches, we demonstrate that the origin of a monophyletic plant clade can be more complex than a parsimonious assumption of a single WGD spurring post-polyploid cladogenesis. Instead, recurrent hybridization among the same and/or closely related parental genomes may phylogenetically interlink diploid and polyploid genomes despite the incidence of multiple independent WGDs. Our results provide new insights into evolution of early-diverging Brassicaceae lineages and elucidate challenges in resolving the contentious relationships within and between land plant lineages with pervasive hybridization and WGDs.

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No evidence for the radiation time lag model after whole genome duplications in Teleostei

10.1101/099663 ◽

2017 ◽

Author(s):

Sacha Laurent ◽

Nicolas Salamin ◽

Marc Robinson-Rechavi

Keyword(s):

Time Lag ◽

Land Plant ◽

Plant Evolution ◽

Whole Genome ◽

Long Term Effects ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Lag Model ◽

Evolutionary Success ◽

Radiation Time

AbstractThe short and long term effects of polyploidization on the evolutionary fate of lineages is still unclear despite much interest. First recognized in land plants, it has become clear that polyploidization is widespread in eukaryotes, notably at the origin of vertebrates and teleost fishes. Many hypotheses have been proposed to link the evolutionary success of lineages and whole genome duplications. For instance, the radiation time lag model suggests that paleopolyploidy would favour the apparition of key innovations, although the evolutionary success would not become apparent until a later dispersion event. Some results indicate that this model may be observed during land plant evolution. In this work, we test predictions of the radiation time lag model using both fossil data and molecular phylogenies in ancient and more recent teleost whole genome duplications. We fail to find any evidence of delayed evolutionary success after any of these events and conclude that paleopolyploidization still remains to be unambiguously linked to evolutionary success in fishes.

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

Cell Reports ◽

10.1016/j.celrep.2012.09.034 ◽

2012 ◽

Vol 2 (5) ◽

pp. 1387-1398 ◽

Cited By ~ 34

Author(s):

Param Priya Singh ◽

Séverine Affeldt ◽

Ilaria Cascone ◽

Rasim Selimoglu ◽

Jacques Camonis ◽

...

Keyword(s):

Whole Genome ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Early Vertebrates

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Significance of whole-genome duplications on the emergence of evolutionary novelties

Briefings in Functional Genomics ◽

10.1093/bfgp/ely007 ◽

2018 ◽

Vol 17 (5) ◽

pp. 329-338 ◽

Cited By ~ 21

Author(s):

Yuuta Moriyama ◽

Kazuko Koshiba-Takeuchi

Keyword(s):

Whole Genome ◽

Whole Genome Duplications ◽

Genome Duplications ◽

Evolutionary Novelties

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Case Studies of Seven Gene Families with Unusual High Retention Rate Since the Vertebrate and Teleost Whole-Genome Duplications

Evolutionary Biology: Self/Nonself Evolution, Species and Complex Traits Evolution, Methods and Concepts ◽

10.1007/978-3-319-61569-1_19 ◽

2017 ◽

pp. 369-396 ◽

Cited By ~ 1

Author(s):

Frédéric G. Brunet ◽

Thibault Lorin ◽

Laure Bernard ◽

Zofia Haftek-Terreau ◽

Delphine Galiana ◽

...

Keyword(s):

Case Studies ◽

Retention Rate ◽

Gene Families ◽

Whole Genome ◽

Whole Genome Duplications ◽

Genome Duplications

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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 ◽

10.3390/genes9110563 ◽

2018 ◽

Vol 9 (11) ◽

pp. 563 ◽

Cited By ~ 6

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.

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