title: Genome-wide investigation and expression analyses of the pentatricopeptide repeat protein gene family in foxtail millet.
abstract: Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants.
  
  
  
  Here, a genome-wide identification and comparison of the PPR genes from 5 organisms was performed, including the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the eudicot Arabidopsis, and the monocots rice and foxtail millet. It appears that the expansion of this gene family prior to the divergence of the euphyllophytes and the lycophytes in land plants. The duplication and divergence rates of the foxtail millet PPR genes (SiPPRs) showed that the expansion period of this gene family around 400 Mya, and indicated that genome segmental duplication was very likely the primary mechanism underlying the expansion of the PPR gene family in vascular plants. An analysis of a complete set of SiPPR genes/proteins that included classification, chromosomal location, orthologous relationships, duplication analysis, and auxiliary motifs is presented. Expression analysis of the SiPPR genes under stress conditions revealed that the expression of 24 SiPPR genes was responsive to abiotic stress. Subcellular localization analysis of 11 PPR proteins indicated that 5 proteins were localized to chloroplasts, that 4 were localized to mitochondria, and that 2 were localized to the cytoplasm.
  
  
  
  Our results contribute to a more comprehensive understanding the roles of PPR proteins and will be useful in the prioritization of particular PPR proteins for subsequent functional validation studies in foxtail millet.
authors: Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors: Jia-Ming
authors: JM
authors: Liu
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China. xuzhaoshi@caas.cn.
authors: Zhao-Shi
authors: ZS
authors: Xu
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors: Pan-Pan
authors: PP
authors: Lu
authors: Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China.|Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors: Wei-Wei
authors: WW
authors: Li
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors: Ming
authors: M
authors: Chen
authors: Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin, 150025, China. kaku3008@126.com.
authors: Chang-Hong
authors: CH
authors: Guo
authors: Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Beijing, 100081, China.
authors: You-Zhi
authors: YZ
authors: Ma
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant; D024101:Mitochondrial Proteins / Q000235:genetics*; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D010641:Phenotype; D021381:Protein Transport; D032983:Setaria Plant / Q000235:genetics* / Q000378:metabolism
chemical_list: D024101:Mitochondrial Proteins
keywords: Foxtail millet; Genome segmental duplication; Pentatricopeptide repeat (PPR) proteins; Phylogenesis; Responsive mechanism; Subcellular localization