ArticleGenome research2012
Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- Functional Diversification and the Plant Secondary Cell Wall.Journal of molecular evolution · 2023Review
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- Genome-Wide Identification and Expression Analysis of the RADIALIS-like Gene Family inPlants (Basel, Switzerland) · 2023Article
- Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.Molecular biology and evolution · 2023Article
- The G2-Like gene family in Populus trichocarpa: identification, evolution and expression profiles.BMC genomic data · 2023Article
- Genomic imbalance modulates transposable element expression in maize.Plant communications · 2023Article
- Identification and characterization of lipoxygenase (LOX) genes involved in abiotic stresses in yellow horn.PloS one · 2023Article
- The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation.The Plant cell · 2022Article
- Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum.BMC genomics · 2022Article
- Genome-wide identification and analysis ofFrontiers in genetics · 2022Article
24 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions.
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