ArticlePloS one2014
Dissecting a hidden gene duplication: the Arabidopsis thaliana SEC10 locus.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 48 citations in OpenAlex.
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Unveiling the functional fate of duplicated genes through expression profiling and structural analysis.Genome research · 2025Article
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Rab GTPases, tethers, and SNAREs work together to regulateFrontiers in plant science · 2023Review
- The host exocyst complex is targeted by a conserved bacterial type-III effector that promotes virulence.The Plant cell · 2022Article
- Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis.BMC genomics · 2021Article
- Functional Specialization within the EXO70 Gene Family in Arabidopsis.International journal of molecular sciences · 2021Article
- Impact of short-read sequencing on the misassembly of a plant genome.BMC genomics · 2021Article
- EXO70A2 Is Critical for Exocyst Complex Function in Pollen Development.Plant physiology · 2020Article
- AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome.The Plant cell · 2020Article
- Integrating Molecular Biology and Bioinformatics Education.Journal of integrative bioinformatics · 2019Article
- A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.PloS one · 2019Article
- CSI1, PATROL1, and exocyst complex cooperate in delivery of cellulose synthase complexes to the plasma membrane.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Solanaceous exocyst subunits are involved in immunity to diverse plant pathogens.Journal of experimental botany · 2018Article
- Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence.BMC research notes · 2017Article
- EXO70C2 Is a Key Regulatory Factor for Optimal Tip Growth of Pollen.Plant physiology · 2017Article
- Evolution of Gene Duplication in Plants.Plant physiology · 2016Review
- Unconventional protein secretion in plants: a critical assessment.Protoplasma · 2016Review
- Article
- RNA Silencing of Exocyst Genes in the Stigma Impairs the Acceptance of Compatible Pollen in Arabidopsis.Plant physiology · 2015Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation.
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