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Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)

Comprehensive analysis of CCCH zinc finger family in poplar (Populus trichocarpa)

Bmc Genomics 13(): 253-253

CCCH zinc finger proteins contain a typical motif of three cysteines and one histidineresidues and serve regulatory functions at all stages of mRNA metabolism. In plants, CCCHtype zinc finger proteins comprise a large gene family represented by 68 members inArabidopsis and 67 in rice. These CCCH proteins have been shown to play diverse roles in plant developmental processes and environmental responses. However, this family has notbeen studied in the model tree species Populus to date. In the present study, a comprehensive analysis of the genes encoding CCCH zinc fingerfamily in Populus was performed. Using a thorough annotation approach, a total of 91 fulllengthCCCH genes were identified in Populus, of which most contained more than oneCCCH motif and a type of non-conventional C-X11-C-X6-C-X3-H motif was unique forPopulus. All of the Populus CCCH genes were phylogeneticly clustered into 13 distinctsubfamilies. In each subfamily, the gene structure and motif composition were relativelyconserved. Chromosomal localization of these genes revealed that most of the CCCHs (81 of9, 9 %) are physically distributed on the duplicated blocks. Thirty-four paralogous pairswere identified in Populus, of which 22 pairs (64.7 %) might be created by the whole genomesegment duplication, whereas 4 pairs seem to be resulted from tandem duplications. In 91CCCH proteins, we also identified 63 putative nucleon-cytoplasm shuttling proteins and 3typical RNA-binding proteins. The expression profiles of all Populus CCCH genes have beendigitally analyzed in six tissues across different developmental stages, and under variousdrought stress conditions. A variety of expression patterns of CCCH genes were observedduring Populus development, of which 34 genes highly express in root and 22 genes show thehighest level of transcript abundance in differentiating xylem. Quantitative real-time RT-PCR(RT-qPCR) was further performed to confirm the tissue-specific expression and responses todrought stress treatment of 12 selected Populus CCCH genes. This study provides the first systematic analysis of the Populus CCCH proteins.Comprehensive genomic analyses suggested that segmental duplications contributesignificantly to the expansion of Populus CCCH gene family. Transcriptome profilingprovides first insights into the functional divergences among members of Populus CCCHgene family. Particularly, some CCCH genes may be involved in wood development whileothers in drought tolerance regulation. Our results presented here may provide a starting pointfor the functional dissection of this family of potential RNA-binding proteins.

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Accession: 052269675

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PMID: 22708723

DOI: 10.1186/1471-2164-13-253

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