ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2019
Landscape of gene transposition-duplication within the Brassicaceae family.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Dynamic and non-additive gene regulation shapes maize responses to simultaneous salt and cold stress.Functional & integrative genomics · 2026Article
- Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots.Nature communications · 2026Article
- Evolutionary diversity of cell-type-specific expression and stress response in Brassicaceae roots.bioRxiv : the preprint server for biology · 2026Article
- Article
- Genome-wide identification and analysis of phosphate utilization related genes (PURs) reveal their roles involved in low phosphate responses in Brassica napus L.BMC plant biology · 2025Article
- Genome-wide identification ofFrontiers in plant science · 2025Article
- Local cryptic diversity in salinity adaptation mechanisms in the wild outcrossingProceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.Genome biology and evolution · 2024Article
- Acquisition of new function through gene duplication in the metallocarboxypeptidase family.Scientific reports · 2023Article
- Living with high potassium: Balance between nutrient acquisition and K-induced salt stress signaling.Plant physiology · 2023Article
- Divergence in the ABA gene regulatory network underlies differential growth control.Nature plants · 2022Article
- Novel genome characteristics contribute to the invasiveness of Phragmites australis (common reed).Molecular ecology · 2022Article
- Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice.Scientific reports · 2021Article
- Halophytism: What Have We Learnt FromPlant physiology · 2018Review
- Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species.Applications in plant sciencesArticle
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed the CLfinder-OrthNet pipeline that detects co-linearity among multiple closely related genomes, finds orthologous gene groups, and encodes the evolutionary history of each orthologue group into a representative network (OrthNet). Using a search based on network topology, we identified 1,394 OrthNets that included gene transposition-duplication (tr-d) events, out of 17,432 identified in six Brassicaceae genomes. Occurrences of tr-d shared by subsets of Brassicaceae genomes mirrored the divergence times between the genomes and their repeat contents. The majority of tr-d events resulted in truncated open reading frames (ORFs) in the duplicated loci. However, the duplicates with complete ORFs were significantly more frequent than expected from random events. These were derived from older tr-d events and had a higher chance of being expressed. We also found an enrichment of tr-d events with complete loss of intergenic sequence conservation between the original and duplicated loci. Finally, we identified tr-d events uniquely found in two extremophytes among the six Brassicaceae genomes, including tr-d of SALT TOLERANCE 32 and ZINC TRANSPORTER 3 that relate to their adaptive evolution. CLfinder-OrthNet provides a flexible toolkit to compare gene order, visualize evolutionary paths among orthologues as networks, and identify gene loci that share an evolutionary history.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.