Plant gene duplicates after polyploidy cycles

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Across plant genomes, WGD and other duplication modes leave distinct, lineage-biased duplicate landscapes.

Source

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants

Qiao X, Li Q, Yin H, et al. · Genome biology · 2019

doi.org/10.1186/s13059-019-1650-2 Read the full paper ↗770 citationscc by

Study at a glance

Design: Computational / modelling — Classified duplicate genes across sequenced plant genomes into WGD and single-gene modes
N: N=141 · 141 sequenced plant genomes
Population: Sequenced plant genomes across the plant kingdom
Outcome: Modes of gene duplication after polyploidization–diploidization cycles

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Plant gene duplicates after polyploidy cycles

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141 sequenced plant genomes.

The otherwise compact ciliate ( Paramecium tetraurelia ) genome (72 Mb) has nonetheless retained a high number of gene sets (40,000) after at least three successive whole-genome duplications [–].

WGD, tandem, proximal, transposed, dispersed.

D (defined as 1R and 2R) at least ~ 450 million years ago (Mya) [–]—about 20–30% of human genes are thought to be paralogs produced by these two WGDs, and these “ohnologs” have a strong association with human disease [,

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What they did

Classified duplicates in 141 plant genomes into WGD, tandem, proximal, transposed, and dispersed classes.

What they found

Recent WGDs retain more WGD pairs; Brassicas show frequent WGT; modes vary by clade.

The limits

What it doesn't show

Classification depends on algorithms/parameters; not every pair’s function is tested.

Key terms

WGD: Whole-genome duplication.
WGT: Whole-genome triplication.
Tandem duplicate: Adjacent gene copies.
Diploidization: Return toward diploid-like state.
Ohnolog: WGD-derived paralog.
DupGen_finder: Duplicate classification tool.

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Common questions

Genomes?

141 plants.

Modes?

Five duplicate classes.

Focus?

Polyploidy cycles.

Clade note?

Brassicaceae WGTs.