Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

Paterson, Andrew H.; Chapman, Brad; Kissinger, Jessica C.; Bowers, John E.; Feltus, F. Alex; Estill, James C.

doi:10.1016/j.tig.2006.09.003

Cited by 170 publications

(179 citation statements)

References 32 publications

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“…(2) Genes in some specific functional categories tend to be retained after duplication. Several gene functional groups are preferentially preserved in duplicate [58,[76][77][78].…”

Section: Palaeopolyploidy and Gene Family Numbersmentioning

confidence: 99%

Polyploidy-associated genome modifications during land plant evolution

Jiao

Paterson

2014

Phil. Trans. R. Soc. B

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The occurrence of polyploidy in land plant evolution has led to an acceleration of genome modifications relative to other crown eukaryotes and is correlated with key innovations in plant evolution. Extensive genome resources provide for relating genomic changes to the origins of novel morphological and physiological features of plants. Ancestral gene contents for key nodes of the plant family tree are inferred. Pervasive polyploidy in angiosperms appears likely to be the major factor generating novel angiosperm genes and expanding some gene families. However, most gene families lose most duplicated copies in a quasi-neutral process, and a few families are actively selected for single-copy status. One of the great challenges of evolutionary genomics is to link genome modifications to speciation, diversification and the morphological and/or physiological innovations that collectively compose biodiversity. Rapid accumulation of genomic data and its ongoing investigation may greatly improve the resolution at which evolutionary approaches can contribute to the identification of specific genes responsible for particular innovations. The resulting, more ‘particulate’ understanding of plant evolution, may elevate to a new level fundamental knowledge of botanical diversity, including economically important traits in the crop plants that sustain humanity.

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“…(2) Genes in some specific functional categories tend to be retained after duplication. Several gene functional groups are preferentially preserved in duplicate [58,[76][77][78].…”

Section: Palaeopolyploidy and Gene Family Numbersmentioning

confidence: 99%

Polyploidy-associated genome modifications during land plant evolution

Jiao

Paterson

2014

Phil. Trans. R. Soc. B

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“…Arabidopsis thaliana genes (Paterson et al, 2006) were tblastn-aligned to 2081 Tragopogon, 227 016 Lactuca and 146 701 Helianthus expressed sequence tags (ESTs), with a minimum criterion of Eo0.001. After filtering for p50% identity, 807 Lactuca, 0 Tragopogon and 262 Helianthus ESTs matched at the translated protein level.…”

Section: Homoeologue Identificationmentioning

confidence: 99%

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

et al. 2009

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Whole-genome duplication (polyploidisation) is a widespread mechanism of speciation in plants. Over time, polyploid genomes tend towards a more diploid-like state, through downsizing and loss of duplicated genes (homoeologues), but relatively little is known about the timing of gene loss during polyploid formation and stabilisation. Several studies have also shown gene transcription to be affected by polyploidisation. Here, we examine patterns of gene loss in 10 sets of homoeologues in five natural populations of the allotetraploid Tragopogon miscellus that arose within the past 80 years following independent whole-genome duplication events. We also examine 44 first-generation synthetic allopolyploids of the same species. No cases of homoeologue loss arose in the first allopolyploid generation, but after 80 years, 1.6% of homoeologues were lost in natural populations. For seven homoeologue sets we also examined transcription, finding that 3.4% of retained homoeologues had been silenced in the natural populations, but none in the synthetic plants. The homoeologue losses and silencing events found were not fixed within natural populations and did not form a predictable pattern among populations. We therefore show haphazard loss and silencing of homoeologues, occurring within decades of polyploid formation in T. miscellus, but not in the initial generation.

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“…For example, how does diploidization shape a polyploid genome to restore bivalent chromosome behavior and plant fertility, and how does a newly formed polyploid cope with sudden changes in gene dosage across an entire genome? In yeast, it has been shown that diploidization and rescue of dosage may affect certain classes of genes (Scannell et al, 2007), and in plants, fractionation and selective elimination of genes in duplicated segments may play a role in diploidization (Paterson et al, 2006;Thomas et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

Cited by 170 publications

References 32 publications

Polyploidy-associated genome modifications during land plant evolution

Polyploidy-associated genome modifications during land plant evolution

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

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