Abstract
Auxin response factors (ARFs) are recently discovered transcription factors that bind with auxin response elements (AuxRE, TGTCTC) to regulate the expression of early auxin-responsive genes. To our knowledge, the ARF gene family has never been characterized in cotton, the most important fiber crop in the world. In this study, a total of 35 ARF genes, named as GrARFs, were identified in a diploid cotton species Gossypium raimondii. The 35 ARF genes were located in 12 of the 13 cotton chromosomes; the intron/exon distribution of the GrARF genes was similar among sister pairs, whereas the divergence of some GrARF genes suggests the possibility of functional diversification. Our results show that the middle domains of nine GrARF proteins rich in glutamine (Q) are activators, while 26 other GrARF proteins rich in proline (P), serine (S), and threonine (T) are repressors. Our results also show that the expression of GrARF genes is diverse in different tissues. The expression of GrARF1 was significantly higher in leaves, whereas GrARF2a had higher expression level in shoots, which implicates different roles in the tested tissues. The GrARF11 has a higher expression level in buds than that in leaves, while GrARF19.2 shows contrasting expression patterns, having higher expression in leaves than that in buds. This suggests that they play different roles in leaves and buds. During long-term evolution of G. raimondii, some ARF genes were lost and some arose. The identification and characterization of the ARF genes in G. raimondii elucidate its important role in cotton that ARF genes regulate the development of flower buds, sepals, shoots, and leaves.
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Acknowledgment
This project is partially support by grants from US NIFA (to BZ) and Cotton Incorporated (to BZ) and a grant from the National Natural Science Foundation of China (31170263 to QW).
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The authors have declared that no competing interests exist.
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Supplementary 1
DNA sequence of GrARF genes. (DOCX 74 kb)
Supplementary 2
Protein sequence of GrARF genes. (DOCX 24 kb)
Supplementary 3
Primers of GrARF genes. (XLS 22 kb)
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Sun, R., Wang, K., Guo, T. et al. Genome-wide identification of auxin response factor (ARF) genes and its tissue-specific prominent expression in Gossypium raimondii . Funct Integr Genomics 15, 481–493 (2015). https://doi.org/10.1007/s10142-015-0437-0
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DOI: https://doi.org/10.1007/s10142-015-0437-0