SNORKEL1 (
SK1) and
SNORKEL2 (
SK2) are ethylene responsive factors that regulate the internode elongation of deepwater rice in response to submergence. We previously reported that normal cultivated rice lacks
SK genes because the Chromosome 12 region containing
SK genes was deleted from its genome. However, no study has analyzed how the genome defect occurred in that region by comparing normal cultivated rice and deepwater rice. In this study, comparison of the sequence of the end of Chromosome 12, which contains
SK genes, between normal and deepwater rice showed that complicated genome changes such as insertions, deletions, inversions, substitutions, and translocation occurred frequently in this region. In addition to
SK1 and
SK2 of deepwater rice, gene prediction analysis identified four genes containing AP2/ERF domains in normal cultivated rice and six in deepwater rice; we called these genes
SK-LIKE (
SKL) genes.
SKs and
SKLs were present in close proximity to each other, and the
SKLs in normal cultivated rice were in tandem. These predicted genes belong to the same AP2/ERF subfamily and were separated into four types: SK1, SK2, SKL3, and SKL4. Sequence comparison indicated that normal cultivated rice possesses a gene with high homology to
SK2, which we named
SKL1. However, none of the predicted
SKLs except for
SKL3s were expressed during submergence. Although
SKL3s were expressed in both normal and deepwater rice, normal rice does not undergo internode elongation, suggesting that its expression does not contribute to internode elongation. Plants overexpressing
SKL1, which showed the most homology to
SK2, underwent internode elongation similar to plants overexpressing
SK1 and
SK2 under normal growth conditions. A yeast one-hybrid assay showed that the C-end of SKL1 has transcription activity, as do the C-ends of SK1 and SK2. Our results suggested that
SKLs were derived via gene duplication, but were not expressed and pseudogenized in normal cultivated rice during sequence evolution.
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