Record Details
Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus
ScholarsArchive at Oregon State University
| Field | Value |
|---|---|
| Title | Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus |
| Names |
Vukašinović, Nemanja
(creator) Cvrčková, Fatima (creator) Eliáš, Marek (creator) Cole, Rex A. (creator) Fowler, John E. (creator) et al. (creator) |
| Date Issued | 2014-04-11 (iso8601) |
| Note | This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Public Library of Science. The published article can be found at: http://www.plosone.org/. |
| 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. |
| Genre | Article |
| Access Condition | http://creativecommons.org/licenses/by/3.0/us/ |
| Identifier | Vukašinović, N., Cvrčková, F., Eliáš, M., Cole, R., Fowler, J. E., et al. (2014) Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus. PLoS ONE 9(4): e94077. doi:10.1371/journal.pone.0094077 |
