Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato
Genome-wide identification, phylogeny and expression analysis of SUN, OFP and YABBY gene family in tomato
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DOI：
10.1007/s00438-013-0733-0
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发表时间：
2013-04-01
影响因子：
3.1
通讯作者：
van der Knaap, Esther
中科院分区：
文献类型：
--
作者：
Huang, Zejun;Van Houten, Jason;van der Knaap, Esther
植物特异性基因家族IQD/SUN、OFP和YABBY的成员被认为在植物生长发育中起重要作用。YABBY家族成员参与侧器官极性和生长; OFP成员编码转录抑制因子，而IQD/SUN成员的作用不太清楚。番茄果形基因SUN、OVATE和FASCIATED分别属于IQD/SUN、OFP和YABBY基因家族。基因重复导致SUN的高表达导致果实伸长，而OVATE中的过早终止密码子和FASCIATED内的大倒位分别控制果实伸长和扁平的果实形状。在本研究中，我们在番茄中鉴定了34个SlSUN，31个SlOFP和9个SlYABBY基因，并确定了它们在12条染色体上的位置。基因组定位分析表明，SlSUN，SlOFP和SlYABBY基因富集在几条染色体的顶部和底部片段。特别地，在染色体10上，发现一簇SlOFP起源于串联重复事件。我们还构建了三个系统发育树的基础上的IQ 67，OVATE和YABBY结构域的蛋白质序列，分别从这些家庭的成员在拟南芥和番茄。拟南芥和番茄基因的最接近的推定直系同源物由系统发育树上的位置和序列相似性确定。此外，表达分析表明，一些家庭成员表现出组织特异性表达，而其他人更普遍表达。另外，某些家族成员与茄科植物中已知的控制果实形状的QTL重叠。这些结果有助于阐明SUN、OFP和YABBY家族成员在植物生长发育中的作用。
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.