Genome-wide Identification,Evolution And Expression Analyses Of NIN Transcription Factors In Soybean

NIN(Nodule inception)transcription factor is widely distributed in the form of multiple gene family in plant which plays important roles in the initiation of bacterial infection and promotion of nodule organogenesis,respectively.Currently,most studies about NIN family mainly focus on model crop Arabidopsis thaliana and Lotus japonicus.However,no systematic study has been performed in other plants.In this study,we performed bioinformatics methods and genome-wide analysis for the first time to identify NIN family members in Glycine max with an aim of finding relatively complete information about NIN family.NIN family members were identified in the genome of Glycine max and a series of comprehensive analyses were performed,including chromosomal location,gene structure,conserved motif,phylogenetic relationships,expression profiling,evolutionary rate and protein-protein interaction network.The main results found were as follows:1.The HMM profile of RWP-RK domain(PF02042)was employed as a query to perform a HMMER search against the soybean genome(http://phytozome.jgi.doe.gov/pz/portal.html).Furthermore,all non-redundant candidate NIN sequences were analyzed to confirm the presence of the conserved RWP-RK domain using the InterproScan program.As a result,a total of 28 family members in soybean were identified.2.Phylogenetic analysis among the NIN family members in Setaria italica,Arabidopsis thaliana,Lotus japonicus,Oryza saliva,Medicago truncatula and Glycine max showed that NIN family members were not evenly distributed in groups.Using analysis of duplicated genes,16 pairs of duplicated genes were identified which accounted for more than 50%of the total NIN members in soybean that indicated gene duplication events were the main causes of the expansion of NIN family in soybean.Besides two pairs of tandem duplication events,14 out of the 16 pairs of duplicated genes were segmental duplication.In addition,most segmental duplication events occurred during the period of recent two WGD events of soybean.Analysis of conserved motif implied that the NIN family members in soybean within the same group may perform similar functions.In addition,motif 1 and motif 3 were the core functional sections which were widely existed in NIN family.Evolutionary rate analysis showed that the ? values were different and less than 1.0 providing a crude indication that the strong purifying selection has been maintained among groups.Moreover,the functional divergence after the gene duplications was seriously restricted.3.The expression profile of NIN family members in the tissues of root?stem?leaf?flower?root hair and nodule shed light on their functional divergence.Furthermore,the expression levels of 15 NIN family members were high in the tissues of root,root hair and nodule related with nodule development,namely GmANIN1,GmNIN2,GmNIN3,GmNIN4,GmNIN9,GmNIN10,GmNIN16,GmNINl7,GmNIN18,GmNIN19,GmNIN20,GmNIN21,GmNIN22,GmNIN23 and GmNIN28.4.Gene annotation and protein-protein interaction network indicated that the six networks with core of NIN family members were mainly associated with the biological process of nitrate transport,cell division and nodulation early signaling transduction.The NIN family members within the same network may perform similar functions.Based on this,we predict the function of Glyma.04G017400 and Glyma.06G017800 in interaction network may be related to the rearrangement of cell wall or the MAPK(Mitogen-activated protein kinase)pathway in nodule nitrogen fixation and also explain function mechanism of NIN transcription factors from molecular network perspective.Our genome-wide analysis improves function and evolution information of NIN family.This study will contribute to future research on the functional characterization of NIN transpcription factors in soybean and also laying a bioinfonnatics foundation aimed at understanding the role of NIN family members.