Genome-Wide Identification And Expression Analysis Of The IQD Gene Family In Populus Trichocarpa

CaM is one of the most important type of calcium receptor proteins,and it is widespread in eukaryotes.CaM mediates signal transmission that can then regulate cellular physiological functions.Previous researches showed that IQD proteins contain several calmodulin-binding domains,so speculate that IQD proteins participate and coordinate the interactions of CaM and its homologous proteins to regulate the gene expression in transcriptional and post-transcriptional levels,which play important roles in development process and responses to environmental cues in plants.Our study want to get complete information of IQD genes in poplar,based on analyzing the latest poplar genome.Meanwhile,physicochemical property,chromosomal localization,phylogenetic tree analysis,exon/intron organization,gene duplication and gene expression patterns of IQD genes were also investigated to perfect related information about this family.Our results of this research are as follows:1.We first search in poplar whole genome in Phytozome website.All potential candidates were subjected to SMART and Pfam analyses to ensure that the predicted proteins contained IQ sequence motifs.The extensive blastp searches resulted in a total of 40 non-redundant IQD proteins.The 40 putative Populus IQD genes were named PtIQD1 to PtIQD40.Physical parameters including length,molecular mass(kDa),and isoelectric point(pI)for each of the predicted IQD protein were calculated with the online ExPASy programs.WoLF PSORT predicted results told us that 65% of the Populus IQD proteins are localized in the cell nucleus.We used the algorithm of the Calmodulin Target Database to predict the CaM-binding sites in poplar IQD proteins.The search results showed that all of the predicted PtIQD proteins contained at least one CaM-binding site.2.A multiple sequence alignment of the 40 PtIQD domains were performed,then we constructed an unrooted phylogenetic tree.With reference to previous research,this forty IQD members can be divided into four subfamilies(? to ?).Among them,the subfamily I and ? can be further subdivided into I a,I b,I c and ? a,? b,respectively.3.We generated exon/intron organization maps of each Populus IQD gene in order to better understand the structural diversity of PtIQD genes.The 40 members contain different numbers of exons,ranging from two to six.Furthermore,most of the closely related genes within the same subfamily shared similar gene structure in terms of either exon lengths or intron numbers.4.We used the MEME suite of online tools to search for conserved motifs that are shared among related proteins within each subfamily for all 40 PtIQD proteins.We found that motif 1 is a representative IQ CaM-binding motif.It is obvious that some of the closely-related proteins share common motif profiles.5.Chromosomal location images were subsequently produced with MapInspect software.The results show that the 40 PtIQD genes are widely but unevenly distributed on 18 of the 19 chromosomes(excluding chromosome 7).Further analyses in our current study suggest that the retention rate of PtIQD family genes was as high as 80% overall,and all of the duplicated gene pairs were resulting from segmental duplication events.6.The EST expression profiles showed that most of the IQD genes are broadly expressed across different tissues/organs.From the microarray data downloaded from NCBI(accession number GSE13990),we can see that most poplar IQD genes exhibited tissue-specific expression patterns,apparently.Four of the fourteen paralogs we detected had the same or similar patterns of expression accumulation.7.We used qRT-PCR to study the expression levels of subfamily ? members in response to Me JA and PEG-6000 treatments.The results demonstrated that most of the selected PtIQD genes were inducible by the two abiotic stresses.And many genes exhibited significant differences in their expression levels in response to the two different stress treatments.