Genome-wide identification, expression profiling, and functional analysis of ammonium transporter 2 (AMT2) gene family in cassava (Manihot esculenta crantz)

Abstract

Background: Nitrogen (N), absorbed primarily as ammonium (NH4+) from soil by plant, is a necessary macronutrient in plant growth and development. Ammonium transporter (AMT) plays a vital role in the absorption and transport of ammonium (NH4+). Cassava (Manihot esculenta Crantz) has a strong adaptability to nitrogen deprivation. However, little is known about the functions of ammonium transporter AMT2 in cassava.Methods: The cassava AMT2-type genes were identified and their characteristics were analyzed using bioinformatic techniques. The spatial expression patterns were analyzed based on the public RNA-seq data and their expression profiles under low ammonium treatment were studied using Real-time quantitative PCR (RT-qPCR) method. The cassava AMT2 genes were transformed into yeast mutant strain TM31019b by PEG/LiAc method to investigate their functions.Results: Seven AMT2-type genes (MeAMT2.1-2.7) were identified in cassava and they were distributed on 6 chromosomes and included two segmental duplication events (MeAMT2.2/MeAMT2.4 and MeAMT2.3/MeAMT2.5). Based on their amino acid sequences, seven MeAMT2 were further divided into four subgroups, and each subgroup contained similar motif constitution and protein structure. Synteny analysis showed that two and four MeAMT2 genes in cassava were collinear with those in the Arabidopsis and soybean genomes, respectively. Sixteen types of cis-elements were identified in the MeAMT2 promoters, and they were related to light-, hormone-, stress-, and plant growth and development-responsive elements, respectively. Most of the MeAMT2 genes displayed tissue-specific expression patterns according to the RNA-seq data, of them, three MeAMT2 (MeAMT2.3, MeAMT2.5, and MeATM2.6) expressions were up-regulated under ammonium deficiency. Complementation experiments showed that yeast mutant strain TM31019b transformed with MeAMT2.3, MeAMT2.5, or MeATM2.6 grew better than untransgenic yeast cells under ammonium deficiency, suggesting that MeAMT2.3, MeAMT2.5, and MeATM2.6 might be the main contributors in response to ammonium deficiency in cassava.Conclusion: This study provides a basis for further study of nitrogen efficient utilization in cassava.

Genome-Wide Analysis of Sweet Potato Ammonium Transporter (AMT): Influence on Nitrogen Utilization, Storage Root Development and Yield

“…Sweet potato prefer ammonium over nitrate [44,45], and the ammonium transporter (AMT) plays crucial roles in ammonium transport [18]. The AMT gene family has been identified in many plants such as Arabidopsis, tomato, rice, and cassava [23,27,28,46,47] but not sweet potato. We performed a genome-wide analysis to identify 12 AMT family genes that belong to two subfamilies in sweet potato.…”

“…AMT proteins from Arabidopsis, rice (Oryza sativa), soybean (Glycine max) [55], maize (Zea mays) [56], cassava (Manihot esculenta Crantz) [23,28], and tomato (Solanum lycopersicum) [27] were downloaded from the TAIR (http://www.arabidopsis.org/ (accessed on 25 April 2022)), NCBI (https://www.ncbi.nlm.nih.gov/ (accessed on 25 April 2022)), and Phytozome (https://phytozome-next.jgi.doe.gov/ (accessed on 25 April 2022)) databases. Sequence similarity analysis was performed using the CLUSTALW website (https://www.…”

“…The nucleotide substitution parameters Ks (synonymous) and Ka (nonsynonymous) of the duplicated genes were assessed using TBtools v1.098669 [54], and then the Ka/Ks ratio was calculated [23]. The gene duplication events of sweet potato AMT and collinearity analysis with six other species were assessed and performed, respectively, according to the method of Yao et al [58].…”

“…Subsequently, several AMT genes have been identified in Arabidopsis, rice, tomato, and other plant species [20][21][22]. Plant AMT genes form a polygenic family, divided into AMT1s and AMT2s subfamilies according to gene homology [23]. For example, there are five AMT1 genes and one AMT2 gene in Arabidopsis thaliana [24].…”