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Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato

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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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Correspondence to Esther van der Knaap.

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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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