Retention, Molecular Evolution and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica rapa Shed Light on the Evolution of Increasing Morphotypes in Plants

IAAs and ARFs, major components of the auxin signaling network, are involved in many developmental processes in plants. Investigating their evolution will shed light on the relationship between these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion and expression patterns of IAAs and ARFs in Brassica rapa and their evolution in 8 other plant species, including algae, bryophytes, lycophytes and angiosperms. All 33 of the ARFs, including 1 AL (a type of ARF-like protein), and 53 IAAs were identified in the B. rapa genome. The genes mainly diverged approximately 13 million years ago. After the split, no IAAs were completely lost, and they were more preferentially retained than ARFs. In land plants, compared to ARFs, which increased in stability, IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants increase their morphotypes and adapt to their complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both IAAs and ARFs.