Genome-Wide Analysis of the SNARE Family in Cultivated Peanut (Arachis hypogaea L.) Reveals That Some Members Are Involved in Stress Responses

Abstract

The superfamily of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediates membrane fusion during vesicular transport between endosomes and the plasma membrane in eukaryotic cells, playing a vital role in plant development and responses to biotic and abiotic stresses. Peanut (Arachis hypogaea L.) is a major oilseed crop worldwide that produces pods below ground, which is rare in flowering plants. To date, however, there has been no systematic study of SNARE family proteins in peanut. In this study, we identified 129 putative SNARE genes from cultivated peanut (A. hypogaea) and 127 from wild peanut (63 from Arachis duranensis, 64 from Arachis ipaensis). We sorted the encoded proteins into five subgroups (Qa-, Qb-, Qc-, Qb+c- and R-SNARE) based on their phylogenetic relationships with Arabidopsis SNAREs. The genes were unevenly distributed on all 20 chromosomes, exhibiting a high rate of homolog retention from their two ancestors. We identified cis-acting elements associated with development, biotic and abiotic stresses in the promoters of peanut SNARE genes. Transcriptomic data showed that expression of SNARE genes is tissue-specific and stress inducible. We hypothesize that AhVTI13b plays an important role in the storage of lipid proteins, while AhSYP122a, AhSNAP33a and AhVAMP721a might play an important role in development and stress responses. Furthermore, we showed that three AhSNARE genes (AhSYP122a, AhSNAP33a and AhVAMP721) enhance cold and NaCl tolerance in yeast (Saccharomyces cerevisiae), especially AhSNAP33a. This systematic study provides valuable information about the functional characteristics of AhSNARE genes in the development and regulation of abiotic stress responses in peanut.

Keywords: SNARE; gene family; peanut; stress; vesicular transport.

Figure 1

Phylogenetic tree of the SNARE family in A. hypogaea, A. duranensis, A. ipaensis and Arabidopsis. Maximum-likelihood tree based on full-length SNARE proteins sequences reconstructed using the nearest-neighbor-interchange model. SNARE protein sequences from A. hypogaea, A. duranensis, A. ipaensis and Arabidopsis are marked with gray, blue, green and red circles, respectively. Qa-, Qb-, Qc-, Qb+c and R-SNARE are marked with red, yellow, green, orange and blue backgrounds, respectively. The ribbon in the outer ring indicates different subfamilies.

Figure 2

Number of SNARE genes identified per SNARE-type subfamily. (A) A. ipaensis; (B) A. duranensis; (C) A. hypogaea. The sum of genes in A. ipaensis and A. duranensis (green–yellow) is also shown (C).

Figure 3

Phylogenetic relationships, gene structures and conserved motifs of AhSNARE genes in cultivated peanut. (A) Phylogenetic relationships; (B) conversed motifs; (C) exon–intron structures. Yellow boxes represent exons; gray lines represent introns.

Figure 4

Chromosomal location and distribution of 129 AhSNARE genes. Chromosome size is indicated by relative length. Scale bar represents megabases (Mb). Physical locations of AhSNARE genes are indicated on each chromosome.

Figure 5

Collinearity analysis of SNARE genes. (A) Synteny analysis of SNARE genes in A. hypogaea–A. duranensis and A. hypogaea–A. ipaensis. Green lines indicate syntenic genes between A. duranensis and A. hypogaea. Blue lines indicate syntenic genes between A. duranensis and A. hypogaea. Black boxes represent A. hypogaea chromosomes. Colored boxes represent chromosomes of A. duranensis and A. ipaensis. Ad, A. duranensis; Ai, A. ipaensis; Ah, A. hypogaea. (B) Synteny analysis of SNARE genes within A. hypogaea. Colored lines represent syntenic relationships between different type of SNAREs. Red, Qa-SNARE; green, Qb-SNARE; blue, Qb+c-SNARE; purple, R-SNARE. Scale bar represents megabases (Mb). Chromosome numbers are indicated on the top of each bar. Green boxes represent A genome; yellow boxes represent B genome.

Figure 6

Expression profiles of SNARE genes in seven peanut tissues and at 12 different developmental stages of peanut. The heatmap was generated using TBtools software, and fragments per kilobase of transcript per million fragments (FPMK) values for SNARE genes were Log2-transformed. The color box represents lower values (blue) to higher values (red).

Figure 7

Expression of AhSNARE genes in response to salt and chilling stress. Relative expression levels of 10 AhSNARE genes in roots (red) and leaves (green) after 0 h, 3 h, 6 h, 12 h and 24 h of salt (A) or low-temperature treatment (B) as determined by RT-qPCR. Data were calculated from three biological replicates. The error bars show the standard deviation of the three biological replicates.

Figure 8

Growth of transformed yeast harboring pESC-AhSYP122a, pESC-AhVAMP721a, pESC-AhSNAP33a, pESC-AhSYP122a/AhSNAP33a or pESC-AhVAMP721a/AhSNAP33a vectors under −20 °C for 1 h, and 0.5 M or 0.8 M NaCl for 5 h. The experiment was repeated three times.