Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus Public Deposited

http://ir.library.oregonstate.edu/concern/articles/6h440v44f

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  • 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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  • 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
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  • description.provenance : Approved for entry into archive by Erin Clark(erin.clark@oregonstate.edu) on 2014-07-15T18:19:08Z (GMT) No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene.pdf: 720279 bytes, checksum: a48a2b438e72c237e48e947c4b33c24c (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene_SupportingInformation.zip: 794642 bytes, checksum: daf1562bbf9dbd85ffee250918673ce3 (MD5)
  • description.provenance : Submitted by Erin Clark (erin.clark@oregonstate.edu) on 2014-07-15T18:18:47Z No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene.pdf: 720279 bytes, checksum: a48a2b438e72c237e48e947c4b33c24c (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene_SupportingInformation.zip: 794642 bytes, checksum: daf1562bbf9dbd85ffee250918673ce3 (MD5)
  • description.provenance : Made available in DSpace on 2014-07-15T18:19:08Z (GMT). No. of bitstreams: 3 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene.pdf: 720279 bytes, checksum: a48a2b438e72c237e48e947c4b33c24c (MD5) ColeRexBotanyPlantPathologyDissectingHiddenGene_SupportingInformation.zip: 794642 bytes, checksum: daf1562bbf9dbd85ffee250918673ce3 (MD5) Previous issue date: 2014-04-11

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