Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa

Abstract

Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.

Keywords: SRS gene family; evolutionary analysis; expression pattern; genome-wide analysis; quinoa.

FIGURE 1

Phylogenetic relationships of SRS proteins from Arabidopsis, Zea mays L, Solanum lycopersicum, Spinacia oleracea L, Nicotiana sylvestris, Selaginella moellendorffii, Physcomitrella patens and quinoa. The proteins clustered into four subgroups, denoted with different colors to represent subfamilies as follows: Group1 (red), Group 2 (blue), Group 3 (purple), Group 4 (green). The information of the SRS family members from Arabidopsis, Zea mays L, Solanum lycopersicum, Spinacia oleracea L, Nicotiana sylvestris, Selaginella moellendorffii, Physcomitrella patens and quinoa was listed in the supporting information (Supplementary Table S1). A phylogenetic tree was constructed using the maximum likelihood method, bootstrap values based on 1,000 replications were calculated.

FIGURE 2

Chromosome mapping of CqSRS genes in quinoa.

FIGURE 3

Structural analysis of CqSRS genes in quinoa. An unrooted phylogenetic tree was constructed based on the full-length sequences of CqSRS proteins using the N-J method in MEGA7. Bootstrap values based on 1,000 replications were calculated. (A) The distribution of motifs in SRS proteins. (B) The exon-intron structure of the SRS genes. (C) The amino acid composition of each motif, motif sequences in Supplementary Table S2.

FIGURE 4

Cis-acting components of quinoa SRS genes. All promoter sequences (2000 bp) were analyzed. Cis-acting element names and functions can be found in Supplementary Table S3.

FIGURE 5

The potential interaction network of CqSRS based on the Arabidopsis and quinoa.

FIGURE 6

Tertiary Structure Prediction of SRS genes in quinoa.

FIGURE 7

The expression profiles of SRS genes in different treatments, developmental stages and tissues of quinoa. (A) CqSRS expression patterns under different treatments, including Root-CK, Root-dry, Root-heat, Root-low_P Root-salt, Shoot-CK, Shoot-dry, Shoot-heat, Shoot-low_P and Shoot-salt. (B) CqSRS expression patterns under different developmental stages and tissues, Inflo, Apical meristems, Flowers and immature seeds, Leaves petioles, Stems, Internode stems, Seedling, Inflorescences, Leaves Dry, seeds, Flowers of white sweet quinoa, Fruit of white sweet quinoa, Flowers of yellow bitter quinoa, Fruit of yellow bitter quinoa. Gene expression was calculated by FPKM. RNA-sequencing (RNA-seq) data (PRJNA394651 and PRJNA306026) were downloaded from NCBI. We standardized the data using the Log2 method.

FIGURE 8

Expression profiles of 10 SRS genes using qRT-PCR analysis in quinoa. Values represented the mean ± standard error of the mean (SEM) of three biological replicates with three technical replicates at different treatments. Error bars indicated the SEM among the three experiments. Different lowercase letters represent significant levels of difference (p < 0.05).

FIGURE 9

RT-qPCR analysis of the 10 CqSRS genes under drought in leaf and root. Values represented the mean ± standard error of the mean (SEM) of three biological replicates with three technical replicates at different treatments. Error bars indicated the SEM among the three experiments. Different lowercase letters represent significant levels of difference (p < 0.05).