Genome-wide identification of sugar transporter gene family in Brassicaceae crops and an expression analysis in the radish

Abstract

Background: Sugar not only is an important biomacromolecule that plays important roles in plant growth, development, and biotic and abiotic stress tolerance but also provides a skeleton for other macromolecules, such as proteins and nucleic acids. Sugar transporter proteins (STPs) play essential roles in plant sugar transport and ultimately affect the abovementioned life processes. However, the evolutionary dynamics of this important gene family in Brassicaceae crops are still largely unknown, and the functional differentiation of radish STP genes remains unclear.

Results: In the present study, a comparative genomic study of STP genes in five representative Brassicaceae crops was conducted, and a total of 25, 25, 28, 36 and 49 STP genes were individually identified in Raphanus sativus (Rs), Brassica oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj), which were divided into four clades by phylogenetic analysis. The number of STP genes was no direct correlation with genome size and the total number of coding genes in Brassicaceae crops, and their physical and chemical properties showed no significant difference. Expression analysis showed that radish STP genes play vital roles not only in flower and seedpod development but also under heavy metal (cadmium, chromium and lead), NaCl and PEG-6000 stresses, Agrobacterium tumefaciens infection, and exogenous sugar treatment. RsSTP13.2 was significantly upregulated in the resistant radish cultivar by A. tumefaciens infection and induced by heavy metal, NaCl and PEG-6000 stress, indicating that it is involved in resistance to both biotic and abiotic stress in radish.

Conclusions: The present study provides insights into the evolutionary patterns of the STP gene family in Brassicaceae genomes and provides a theoretical basis for future functional analysis of STP genes in Brassicaceae crops.

Keywords: Biotic and abiotic stress; Expression analysis; Gene family; Radish; Sugar transporter proteins (STPs).

Fig. 1

The violin diagram shows the physical and chemical properties of STP proteins in six species. (A) The number of amino acids of STPs. (B) The molecular weight of STPs. (C) The aromaticity of STPs. (D) The instability index of STPs. (E) The isoelectric point of STPs. (F) The gravy of STPs. The ‘ns’ means no significant difference

Fig. 2

An NJ phylogenetic tree of STP protein sequences from A. thaliana (At), R. sativus (Rs), B. oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj). Different colours of branches represent different groups

Fig. 3

The STP gene numbers of four groups among different Brassicaceae species, including A. thaliana (At), R. sativus (Rs), B. oleracea (Bo), B. rapa (Br), B. napus (Bn) and B. juncea (Bj)

Fig. 4

Motif and structural analyses of STPs. (A) Phylogenetic tree of STP proteins. (B) Schematic representation of the conserved motif compositions of STP. (C) Exon/intron structures of STP genes

Fig. 5

Synteny analysis of STP genes between A. thaliana and five Brassicaceae crops. The red lines highlight the syntenic STP gene pairs. (A), (B), (C), (D), and (E) indicate synteny gene pairs between R. sativus, B. oleracea, B. rapa, B. napus, B. juncea and A. thaliana, respectively

Fig. 6

Expression profiles of radish STP genes in various tissues. The fragments per kilobase of transcript per million mapped reads (FPKM) data were log₂ transformed. The color bar is shown at the right

Fig. 7

The expression profiles of RsSTPs 7 d after incubation with Agrobacterium tumefaciens in radish hypocotyls. Lines 18 and 19 are resistance and susceptible radish inbred lines to A. tumefaciens, respectively. CK and T represent 7 d after incubation with LB medium and A. tumefaciens, respectively. The fragments per kilobase of transcript per million mapped reads (FPKM) data were log₂ transformed. The color bar is shown at the right

Fig. 8

Expression profiles of RsSTP responses to cadmium (Cd), chromium (Cr) and lead (Pb) stress in radish. The fragments per kilobase of transcript per million mapped reads (FPKM) data were log₂ transformed. The color bar is shown at the right

Fig. 9

Quantitative real-time PCR analysis of RsSTP expression levels in the roots in response to 1.5% NaCl and 20% PEG stress and 2% glucose, 2% fructose and 2% sucrose treatment. The presented gene expression levels are relative to the expression of the reference gene RsGAPDH. Data are presented as the mean ± standard error of three independent experiments. CK: control treatment with distilled water