Abstract
Members of the plant-specific gene families IQD/SUN, OFP and YABBY are thought to play important roles in plant growth and development. YABBY family members are involved in lateral organ polarity and growth; OFP members encode transcriptional repressors, whereas the role of IQD/SUN members is less clear. The tomato fruit shape genes SUN, OVATE, and FASCIATED belong to IQD/SUN, OFP and the YABBY gene family, respectively. A gene duplication resulting in high expression of SUN leads to elongated fruit, whereas a premature stop codon in OVATE and a large inversion within FASCIATED control fruit elongation and a flat fruit shape, respectively. In this study, we identified 34 SlSUN, 31 SlOFP and 9 SlYABBY genes in tomato and identified their position on 12 chromosomes. Genome mapping analysis showed that the SlSUN, SlOFP, and SlYABBY genes were enriched on the top and bottom segments of several chromosomes. In particular, on chromosome 10, a cluster of SlOFPs were found to originate from tandem duplication events. We also constructed three phylogenetic trees based on the protein sequences of the IQ67, OVATE and YABBY domains, respectively, from members of these families in Arabidopsis and tomato. The closest putative orthologs of the Arabidopsis and tomato genes were determined by the position on the phylogenetic tree and sequence similarity. Furthermore, expression analysis showed that some family members exhibited tissue-specific expression, whereas others were more ubiquitously expressed. Also, certain family members overlapped with known QTLs controlling fruit shape in Solanaceous plants. Combined, these results may help elucidate the roles of SUN, OFP and YABBY family members in plant growth and development.
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Abbreviations
- AtIQD:
-
IQ67 domain protein in Arabidopsis thaliana
- AtOFP:
-
Arabidopsis thaliana OVATE family proteins
- AtYABBY:
-
YABBY protein in Arabidopsis thaliana
- CaOvate :
-
OVATE-like gene of Capsicum annuum
- DBA:
-
Days before anthesis
- DPA:
-
Days post anthesis
- DUF623:
-
Domain-of-unknown-function 623, Pfam accession PF04844
- FAS:
-
FASCIATED
- IQD/SUN:
-
IQ67 domain protein, SUN-like protein
- ITAG:
-
International Tomato Annotation Group
- KaFTom:
-
Kazusa Full-Length Tomato cDNA Database
- Myr:
-
Million years
- NCBI:
-
National Center for Biotechnology Information
- QTL:
-
Quantitative Trait Locus
- RPKM:
-
Reads per kilobase of exon model per million mapped reads
- SGN:
-
Sol Genomics Network
- SlOFP:
-
Solanum lycopersicum OVATE family proteins
- SlSUN:
-
Solanum lycopersicum SUN-like proteins
- SlYABBY:
-
Solanum lycopersicum YABBY proteins
- TAIR:
-
The Arabidopsis Information Resource
- TALE:
-
3-Amino acid loop extension
- WGS:
-
Whole Genome Shotgun Sequencing
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Acknowledgments
We thank Dr. Zhangjun Fei from Boyce Thompson Institute for Plant Research for assistance with the RNA-seq analysis, the Molecular and Cellular Imaging Center with depositing the RNA-seq data in the small read archive, and Dr. Dean Fraga for assistance with the phylogenetic analysis. This work was supported by the National Science Foundation grant (IOS 0922661).
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Communicated by C. Gebhardt.
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Huang, Z., Van Houten, J., Gonzalez, G. et al. Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato. Mol Genet Genomics 288, 111–129 (2013). https://doi.org/10.1007/s00438-013-0733-0
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DOI: https://doi.org/10.1007/s00438-013-0733-0