Genome-wide analysis of NIN-like protein (NLP) family in maize (Zea mays L.) by using bioinformatic methods

Abstract

The NIN-like proteins (NLP) belong to RWP-RK transcription factor family and possess the similarity characteristics of NIN (Nodules INception). The NLPs regulate the expression of genes which are involved in nitrate signaling in plants. In this work, we have performed a genome-wide analysis of the NLP gene family in maize (Zea mays L.) through the bioinformatic methods. We identified a total of nine NLP encoding genes in whole genome of maize. The genomic sequences of these genes were from 2855 to 8092 nucleotides in length and contained three or four introns. Their predicted protein sizes ranged in size from 786 to 945 amino acids. The theoretical isoelectric point values of most deduced protein were less than 7. The maize NLP proteins possessed conserved regions of plant NLP at N-terminal as well as at C-terminal including the RWP-RK and PB1 domains. Based on the phylogenic analysis, we detected three current whole-genome gene duplication events which occurred in maize genome apter speciation point. All of NLP genes expressed in tissues at different development stages, from germinating seed to maturation seed were examined. The ZmNLP5, ZmNLP6 and ZmNLP7 were weakly expressed in comparison to others genes in most examined tissues.

The Nin-Like Protein (Nlp) Family in Common Bean: Genome-Wide Identification, Evolution and Expression Analysis

“…Accordingly, the number of exons varies between 3 and 6, while the number of introns varies between 2 and 5. Similar to the Pvul-NIN genes, in a previous report by Cho (2017) on Zea mays, it was observed that the exon and intron structures of 9 NIN genes were found in similar numbers to the ones in this study, the number of exons varied between 4 and 5, while the number of introns varied between 3 and 4 [62]. Phylogenetic analysis was performed to understand and compare the evolutionary relationship between Pvul-NIN and Arabidopsis (non-nodulating) and NIN genes belonging to G. max (Nodulator).…”