ArticleGenome biology and evolution2011
Organ and cell type-specific complementary expression patterns and regulatory neofunctionalization between duplicated genes in Arabidopsis thaliana.
Article in Genome biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed, 57 citations in OpenAlex.
- Genome-Wide Analysis of theInternational journal of molecular sciences · 2025Article
- Dynamics ofProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Evolutionary analysis of the LORELEI gene family in plants reveals regulatory subfunctionalization.Plant physiology · 2022Article
- Dichotomy of the BSL phosphatase signaling spatially regulates MAPK components in stomatal fate determination.Nature communications · 2022Article
- Genome-Wide Identification of GDSL-Type Esterase/Lipase Gene Family inInternational journal of molecular sciences · 2021Article
- Kingdom-wide analysis of the evolution of the plant type III polyketide synthase superfamily.Plant physiology · 2021Article
- Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs.Biochemical Society transactions · 2020Review
- A genome-wide survey of copy number variations reveals an asymmetric evolution of duplicated genes in rice.BMC biology · 2020Article
- Comprehensive analysis of Lon proteases in plants highlights independent gene duplication events.Journal of experimental botany · 2019Article
- Dual-targeting by CRISPR/Cas9 leads to efficient point mutagenesis but only rare targeted deletions in the rice genome.3 Biotech · 2019Article
- Article
- Robust predictions of specialized metabolism genes through machine learning.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Fine-Tuning the Expression of Duplicate Genes by Translational Regulation inFrontiers in plant science · 2019Article
- Rapid and pervasive development- and tissue-specific homeolog expression partitioning in newly formed inter-subspecific rice segmental allotetraploids.BMC genomics · 2018Article
- Analysis of Genes with Alternatively Spliced Transcripts in the Leaf, Root, Panicle and Seed of Rice Using a Long Oligomer Microarray and RNA-Seq.Molecules and cells · 2017Article
- Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes.Plant physiology · 2017Article
- BnDGAT1s Function Similarly in Oil Deposition and Are Expressed with Uniform Patterns in Tissues ofFrontiers in plant science · 2017Article
- Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias.BMC genomics · 2016Article
- Exocyst SEC3 and Phosphoinositides Define Sites of Exocytosis in Pollen Tube Initiation and Growth.Plant physiology · 2016Article
- Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.Plant physiology · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Duplicated genes can contribute to the evolution of new functions and they are common in eukaryotic genomes. After duplication, genes can show divergence in their sequence and/or expression patterns. Qualitative complementary expression, or reciprocal expression, is when only one copy is expressed in some organ or tissue types and only the other copy is expressed in others, indicative of regulatory subfunctionalization or neofunctionalization. From analyses of two microarray data sets with 83 different organ types, developmental stages, and cell types in Arabidopsis thaliana, we determined that 30% of whole-genome duplicate pairs and 38% of tandem duplicate pairs show reciprocal expression patterns. We reconstructed the ancestral state of expression patterns to infer that considerably more cases of reciprocal expression resulted from gain of a new expression pattern (regulatory neofunctionalization) than from partitioning of ancestral expression patterns (regulatory subfunctionalization). Pollen was an especially common organ type for expression gain, resulting in contrasting expression of some duplicates in pollen. Many of the gene pairs with reciprocal expression showed asymmetric sequence rate evolution, consistent with neofunctionalization, and the more rapidly evolving copy often showed a more restricted expression pattern. A gene with reciprocal expression in pollen, involved in brassinosteroid signal transduction, has evolved more rapidly than its paralog, and it shows evidence for a new function in pollen. This study indicates the evolutionary importance of reciprocal expression patterns between gene duplicates, showing that they are common, often associated with regulatory neofunctionalization, and may be a factor allowing for retention and divergence of duplicated genes.
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