Journey through the past: 150 million years of plant genome evolution

Proost, Sebastian; Pattyn, Pedro; Geräts, Tom; Peer, Yves Van de

doi:10.1111/j.1365-313x.2011.04521.x

Cited by 89 publications

(85 citation statements)

References 74 publications

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“…Like many other plant genomes sequenced thus far [24][25][26][27] , the orchid genome harbored the remnants of one or more large-scale duplication events. Although only a small fraction of the genome (3.51%) showed collinearity (conservation of gene order and content) with other regions in the genome, this proportion most likely constitutes a substantial underestimate.…”

Section: Genome Evolutionmentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers

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Section: Genome Evolutionmentioning

confidence: 99%

The genome sequence of the orchid Phalaenopsis equestris

et al. 2014

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“…There are 21 Hsfs in Arabidopsis and 25 Hsfs in rice and apple, 30 Hsfs in maize, and 52 Hsfs in soybean, generated through gene duplication and whole-genome duplications (Proost et al, 2011). Nearly all Hsfs belong to 3 classes, and the numbers in each class are similar in various plant species.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis)

Huang¹,

Peng²,

Li³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. Chinese cabbage (Brassica rapa ssp. pekinensis) is one of the most important vegetable crops grown worldwide, and various methods exist for selection, propagation, and cultivation. The entire Chinese cabbage genome has been sequenced, and the heat shock transcription factor family (Hsfs) has been found to play a central role in plant growth and development and in the response to biotic and abiotic stress conditions, particularly in acquired thermotolerance. We analyzed heat tolerance mechanisms in Chinese cabbage. In this study, 30 Hsfs were identified from the Chinese cabbage genome database. The classification, phylogenetic reconstruction, chromosome distribution, conserved motifs, expression analysis, and interaction networks of the Hsfs were predicted and analyzed. Thirty BrHsfs were classified into 3 major classes (class A, B, and C) according to their structural characteristics and phylogenetic comparisons, and class A was further subdivided into 8 subclasses. Distribution mapping results showed that Hsf genes were located on 10 Chinese cabbage chromosomes. The expression profile indicated that Hsfs play differential roles in 5 organs in Chinese cabbage, and likely participate in the development of underground parts and regulation of reproductive growth. An orthologous gene interaction network was constructed, and included MBF1C, ROF1, TBP2, CDC2, and HSP70 5 genes, which are closely related to heat stress. Our results contribute to the understanding of the complexity of Hsfs in Chinese cabbage and provide a basis for further functional gene research.

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“…Comparative genome analyses have revealed at least two whole-genome duplication (WGD) events during the early evolution of angiosperms: The first occurred before the monocoteudicot split and the second predated the divergence of major core eudicot lineages (De Bodt et al, 2005;Soltis et al, 2007;Van de Peer et al, 2009a, 2009bProost et al, 2011). Following these WGD events, the genomes of early angiosperms became greatly enlarged with a dramatically increased number of genes.…”

Section: Evolutionary Significance Of the Autoregulatory Loops In Cycmentioning

confidence: 99%

Evolution of Double Positive Autoregulatory Feedback Loops in CYCLOIDEA2 Clade Genes Is Associated with the Origin of Floral Zygomorphy

et al. 2012

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Members of the CYCLOIDEA2 (CYC2) clade of the TEOSINTE BRANCHED1, CYCLOIDEA, and PCF transcription factor genes are widely involved in controlling floral zygomorphy, a key innovation in angiosperm evolution, depending on their persistently asymmetric expression in the corresponding floral domains. However, it is unclear how this asymmetric expression is maintained throughout floral development. Selecting Primulina heterotricha as a model, we examined the expression and function of two CYC2 genes, CYC1C and CYC1D. We analyzed the role of their promoters in protein-DNA interactions and transcription activation using electrophoresis mobility shift assays, chromatin immunoprecipitation, and transient gene expression assays. We find that CYC1C and CYC1D positively autoregulate themselves and cross-regulate each other. Our results reveal a double positive autoregulatory feedback loop, evolved for a pair of CYC2 genes to maintain their expression in developing flowers. Further comparative genome analyses, together with the available expression and function data of CYC2 genes in the core eudicots, suggest that this mechanism might have led to the independent origins of floral zygomorphy, which are associated with plant-insect coevolution and the adaptive radiation of angiosperms.

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Journey through the past: 150 million years of plant genome evolution

Cited by 89 publications

References 74 publications

The genome sequence of the orchid Phalaenopsis equestris

The genome sequence of the orchid Phalaenopsis equestris

Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis)

Evolution of Double Positive Autoregulatory Feedback Loops in CYCLOIDEA2 Clade Genes Is Associated with the Origin of Floral Zygomorphy

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