Genome-wide identification and expression analysis of the ferritin family in sweetpotato and its two diploid relatives

Abstract

Ferritin (FER), a type of iron-storing proteins, play an essential role in iron storage and in protection against oxidative stress. However, there is limited detailed information regarding FERs in sweetpotato. In this study, a total of 17 putative FER genes, 7, 5 and 5 FERs in sweetpotato (I. batatas, 2n = 6x = 90) and its two diploid relatives I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), located on chromosomes were identified. Phylogenetic analysis revealed that these genes are divided into two different groups. Promoter analysis revealed that IbFER promoters contained a number of abiotic/biotic stress-responsive elements, hormone-responsive element, and iron-dependent regulatory sequence. The structural motif analysis of FER proteins showed that Euk_Ferritin domain was identified near the C-terminus and the structures were relatively conserved in sweetpotato and its two diploid relatives. Transcriptome and RT-qPCR analysis demonstrated that the expression of FERs were detected in different tissues and showed tissue specificity, and they responded to abiotic stresses, such as drought, salt and Fe deficiency. Our results provide a theoretical basis for future genetic research, development of breeding strategies against abiotic stresses and food enrichment with iron in sweetpotato.

Keywords: FER; I. trifida; I. triloba; Abiotic stress; Sweetpotato; Tissue-specific expression.

Fig. 1

Chromosomal localization and distribution of IbFERs (A), ItfFERs (B) and ItbFERs (C). The bars represented chromosomes, the chromosome numbers were displayed on the left side, and the gene names were displayed on the right side

Fig. 2

Phylogenetic analysis of the FERs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, Arabidopsis thaliana, and Oryza saliva. The pink circles, green squares, purple triangles, blue triangles, and orange rhombuses respectively represented the IbFERs, ItfFERs, ItbFERs, AtFERs, and OsFERs

Fig. 3

Collinearity analysis of FER genes between sweetpotato and its two diploid relatives. The gray line represents the syntenic block in plant genomes, and the blue line represents the FER collinear gene pair

Fig. 4

Conserved domains and exon–intron structure of FERs in I. batatas, I. trifida, and, I. triloba. A Phylogenetic tree and conserved domain structures of FERs. The blue box represented the Euk_Ferritin domain. B Exon–intron structures of FERs. The green boxes, yellow boxes, and black lines represented the CDS, UTR, and introns, respectively

Fig. 5

Cis-elements analysis of IbFERs in I. batatas. A Cis-elements distribution of IbFERs. B Cis-elements number of IbFERs. The cis-elements were divided into four categories. The depth of different colors represented the number of cis-elements in IbFERs promoter. C IDRS-like sequences in IbFER promoters. Alignment of promoter regions displaying highest identity to Arabidopsis AtFer1 and maize ZmFer1 IDRS. Fourteen nucleotide long IDRS-like sequences are highlighted in red. Distance of IDRS from ATG is indicated in parentheses

Fig. 6

Gene expression patterns of IbFERs in different tissues. The gene expression patterns of IbFERs in stem tip (ST), stem (S), leaf (L), fibrous root (FR), pencil root (PR), and storage root (SR) of ‘Y25’ were determined by RT-qPCR analysis. Data are presented as the means ± SD (n = 3). Different lowercase letters indicate significant differences (P < 0.05; one-way ANOVA)

Fig. 7

Gene expression patterns of IbFERs in storage roots in ‘X22’ at different periods. FR represented fibrous root (diameter of approximately 1 mm), D1 represented initial SR (diameter of approximately 1 cm), D3 represented SR (diameter of approximately 3 cm), D5 represented SR (diameter of approximately 5 cm) and D10 represented SR (diameter of approximately 10 cm)

Fig. 8

Gene expression patterns of IbFERs under 30% PEG and 200 mM NaCl treatments. A Expression analysis of IbFERs under 30% PEG treatment in a drought-tolerant variety ‘X55-2’. B Expression analysis of IbFERs under 200 mM NaCl treatment in a salt-sensitive variety ‘LZX’ and a salt-tolerant line ‘ND98’. Gene expression level data was determined by RNA-seq

Fig. 9

The expression levels of IbFERs under PEG, NaCl and Fe deficiency treatments by RT-qPCR analysis. A-G IbFERs were measured in ‘X18’ treated with 20% PEG6000. H-N IbFERs were examined in ‘ND98’ plants treated with 200 mM NaCl. O The expression levels of IbFERs under Fe deficiency treatment by RT-qPCR analysis. IbFERs were measured in ‘L9’ treated on -Fe MS medium for 72 h. Data are presented as the means ± SD (n = 3). Data are presented as the means ± SD (n = 3). Different lowercase letters indicate significant differences (P < 0.05; one-way ANOVA). * and ** indicate a significantly difference compared with MS medium (+ Fe) at P < 0.05 and P < 0.01 based on Student’s t-test, respectively