Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus

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/.Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may\ud disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and\ud non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst\ud tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual\ud assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the\ud reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence\ud segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are\ud concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by\ud substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying\ud transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type\ud phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we\ud demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A.\ud thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence\ud assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation