Shandong Lvdu Bio technique Industry

Binzhou, China

Shandong Lvdu Bio technique Industry

Binzhou, China
SEARCH FILTERS
Time filter
Source Type

Cao J.,Jiangsu University | Shi F.,Shandong Lvdu Bio technique Industry
Evolutionary Bioinformatics | Year: 2012

Rapid alkalinization factors (RALFs) are plant small peptides that could induce a rapid pH increase in the medium of plant cell suspension culture and play a critical role in plant development. The evolutionary process of the RALF gene family remains unclear. To obtain details of the phylogeny of these genes, this study characterized RALF genes in Arabidopsis, rice, poplar and maize. Phylogenetic trees, evolutionary patterns and molecular evolutionary rates were used to elucidate the evolutionary process of this gene family. In addition, the different signatures of selection, expression patterns, and subcellular localization of RALFs were also analyzed. We found that the RALF gene family had a rapid birth process after the separation of the eudicot and monocot species about 145 million years ago, that tandem duplication played a dominant role in the expansion of Arabidopsis and rice RALF gene family, and that RALFs were under purifying selection according to estimations of the substitution rates of these genes. We also identified a diverse expression pattern of RALF genes and predominant extracellular localization feature of RALF proteins. Our findings shed light on several key differences in RALF gene family evolution among the plant species, which may provide a scaffold for future functional analysis of this family. © the author(s), publisher and licensee Libertas Academica Ltd.


Cao J.,Jiangsu University | Shi F.,Shandong Lvdu Bio technique Industry | Liu X.,Jiangsu University | Jia J.,Jiangsu University | And 2 more authors.
Journal of Biomolecular Structure and Dynamics | Year: 2011

Sm proteins are members of a family of small proteins that are widespread in biosphere and found associated with RNA metabolism. To date, to our knowledge, only Arabidopsis SAD1 gene has been studied functionally in plant. In this study, 42 Sm genes are identified through comprehensive analysis in Arabidopsis. And a complete overview of this gene family is presented, including the gene structures, phylogeny, chromosome locations, selection pressure and expression. The results reveal that gene duplication contributes to the expansion of the Sm gene family in Arabidopsis genome, diverse expression patterns suggest their functional differentiation and divergence analysis indicates purifying selection as a key role in evolution. Our comparative genomics analysis of Sm genes will provide the first step towards the future experimental research on determining the functions of these genes. ©Adenine Press (2011).


Cao J.,Jiangsu University | Shi F.,Shandong Lvdu Bio Technique Industry
Journal of Integrative Agriculture | Year: 2012

This study is performed to investigate the mitochondrial carrier gene family in silkworm genome. In total, 30 genes are identified and claded into eight well-conserved groups. Gene duplication contributes to the expansion and complexity of this family. Diverse expression patterns suggest their functional differentiation. Analyses of the sitespecific profiles reveal critical amino acid residues for functional divergence. This study highlights the molecular evolution of the mitochondrial carrier gene family in silkworm and may provide a starting point for further experimental verification. © 2012 Chinese Academy of Agricultural Sciences.


Cao J.,Jiangsu University | Shi F.,Shandong Lvdu Bio Technique Industry
Journal of Biomolecular Structure and Dynamics | Year: 2012

In the present study, a comprehensive analysis of the arginase gene family in metazoans was performed. A total of 126 arginase genes have been identified in 44 species. Phylogenetic analyses indicate that arginase genes consist of four groups. Conservative and divergent gene structures are found among the groups. The syntenies also exist in distantly related genomes among multiple species. Adaptive evolution shows that, while purifying selection may have been the main force driving the evolution of the arginases, some of critical sites responsible for the functional divergence may have been under positive selection. Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the arginase gene family and of the function and evolution of this family in metazoans. Copyright © 2012 Taylor and Francis.


Cao J.,Jiangsu University | Shi F.,Shandong Lvdu Bio technique Industry | Liu X.,Jiangsu University | Huang G.,Jiangsu University | Zhou M.,Jiangsu University
FEBS Letters | Year: 2010

A study was performed to investigate the phylogenetic relationship among AAAH members and to statistically evaluate sequence conservation and functional divergence. In total, 161 genes were identified from 103 species. Phylogenetic analysis showed that well-conserved subfamilies exist. Exon-intron structure analysis showed that the gene structures of AAAH were highly conserved across some different lineage species, while some species-specific introns were also found. The dynamic distribution of ACT domain suggested one gene fusion event has occurred in eukaryota. Significant functional divergence was found between some subgroups. Analysis of the site-specific profiles revealed critical amino acid residues for functional divergence. This study highlights the molecular evolution of this family and may provide a starting point for further experimental verifications. © 2010.

Loading Shandong Lvdu Bio technique Industry collaborators
Loading Shandong Lvdu Bio technique Industry collaborators