Genome-wide identification of members in the YTH domain-containing RNA-binding protein family in apple and expression analysis of their responsiveness to senescence and abiotic stresses.
YT521-homology (YTH) domain-containing RNA-binding proteins (YTPs) are a small gene family involved in post-transcriptional regulation. We identified 26 putative YTP gene models in the apple genome. Although plant YTPs have been classified into three groups, those in multi-cellular organisms belong only to Groups A and B. The apple genome contains 22 YTP gene models in Group A and four in Group B. Duplication analysis showed that tandem and segmental duplications contributed only partially to an expansion in apple YTP numbers. YTH was the only recognizable domain in apple YTPs; its three-dimensional structure implied possible motifs for RNA-binding. After the assembly of expressed sequence tags (ESTs) and gene-cloning, we were able to identify 14 apple YTPs that were expressed in various tissues, especially senescing leaves. Expression analysis showed that these YTPs also responded to several abiotic stresses. Taken together, our genome-wide evaluation provides new insight for further research on the effects of those stresses.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
Na
N
Wang
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
Zhiyong
Z
Yue
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
Dong
D
Liang
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, PR China. Electronic address: fwm64@nwsuaf.edu.cn.
Fengwang
F
Ma
D002874:Chromosome Mapping; D020224:Expressed Sequence Tags; D020440:Gene Duplication; D015870:Gene Expression; D017343:Genes, Plant; D018745:Genome, Plant; D027845:Malus / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D008958:Models, Molecular; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D013312:Stress, Physiological; D026801:Synteny
D010940:Plant Proteins; D016601:RNA-Binding Proteins
Abiotic stress; Apple; Expression analysis; RNA-binding protein; Senescence; YTH domain