The dynamics of functional classes of plant genes in rediploidized ancient polyploids.

Eric C H Chen, Carlos Buen Abad Najar, Chunfang Zheng, Alex Brandts, Eric H Lyons, Haibao Tang, Lorenzo Carretero-Paulet, Victor A. Albert, David Sankoff

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

We measure the simultaneous dynamics of duplicate orthologous gene loss in rosids, in asterids, and in monocots, as influenced by biological functional class. This pan-angiosperm view confirms common tendencies and consistency through time for both ancient and more recent whole genome polyploidization events. The gene loss analysis represents an assessment of post-polyploidization evolution, at the level of individual gene families within and across sister genomes. Functional analysis confirms universal trends previously reported for more recent plant polyploidy events: genes involved with regulation and responses were retained in multiple copies, while genes involved with metabolic and catalytic processes tended to lose copies, across all three groups of plants.To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of retention of duplicate, triplicate, etc. genes.

Original languageEnglish (US)
JournalBMC Bioinformatics
Volume14 Suppl 15
StatePublished - 2013
Externally publishedYes

Fingerprint

Plant Genes
Polyploidy
Genes
Gene
Genome
Duplicate Genes
Plant Genome
Angiosperms
Functional Analysis
Class
Functional analysis

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

Chen, E. C. H., Buen Abad Najar, C., Zheng, C., Brandts, A., Lyons, E. H., Tang, H., ... Sankoff, D. (2013). The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinformatics, 14 Suppl 15.

The dynamics of functional classes of plant genes in rediploidized ancient polyploids. / Chen, Eric C H; Buen Abad Najar, Carlos; Zheng, Chunfang; Brandts, Alex; Lyons, Eric H; Tang, Haibao; Carretero-Paulet, Lorenzo; Albert, Victor A.; Sankoff, David.

In: BMC Bioinformatics, Vol. 14 Suppl 15, 2013.

Research output: Contribution to journalArticle

Chen, ECH, Buen Abad Najar, C, Zheng, C, Brandts, A, Lyons, EH, Tang, H, Carretero-Paulet, L, Albert, VA & Sankoff, D 2013, 'The dynamics of functional classes of plant genes in rediploidized ancient polyploids.', BMC Bioinformatics, vol. 14 Suppl 15.
Chen ECH, Buen Abad Najar C, Zheng C, Brandts A, Lyons EH, Tang H et al. The dynamics of functional classes of plant genes in rediploidized ancient polyploids. BMC Bioinformatics. 2013;14 Suppl 15.
Chen, Eric C H ; Buen Abad Najar, Carlos ; Zheng, Chunfang ; Brandts, Alex ; Lyons, Eric H ; Tang, Haibao ; Carretero-Paulet, Lorenzo ; Albert, Victor A. ; Sankoff, David. / The dynamics of functional classes of plant genes in rediploidized ancient polyploids. In: BMC Bioinformatics. 2013 ; Vol. 14 Suppl 15.
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