Fig 1.
Phylogenetic tree (A), conserved protein motifs (B), and gene structures (C) of HAD genes from rice and Arabidopsis. The phylogenetic tree of the HAD protein family in rice and Arabidopsis was constructed using MEGA-X software based on the maximum likelihood method and a JTT matrix-based model. Different colours represent different subgroups. The conserved motifs of the protein were analysed with MEME software and marked with different colours. For the gene structures, green represents untranslated 5′- and 3′-regions, and yellow represents exons.
Table 1.
Information of the 20 motifs in HAD proteins.
Fig 2.
Graphical sequence logo representation of the four conserved motifs in plant HAD proteins.
Signatures of the motif were motif I: DXD; motif II: S/T; motif III: K; motif IV: GDXXXD.
Fig 3.
Simulated three-dimensional structures of typical HAD proteins in rice by SWISS-MODEL.
(A) The three-dimensional structure of the OsHAD25 protein, which represents the C0 cap domain. The template accession No. is 3 pgl.1. A for OsHAD25. (B) The three-dimensional structure of the OsHAD14 protein, which represents the C1 cap domain. The template accession No. is 3 l5k.1. A for OsHAD14. (C) The three-dimensional structure of the OsHAD24 protein, which represents the C2 cap domain. The template accession No. is 1rkq.1. A for OsHAD24. The β strands are coloured blue, while the α helices are coloured red. The special flap and squiggle structures are coloured pink and yellow, respectively. Cap domains are marked in green. Two conserved aspartic acid residues of motif I are marked orange.
Fig 4.
Chromosomal distribution and interchromosomal relationship between HAD family genes in rice and Arabidopsis.
The transparent lines indicate all the collinear blocks in the rice and Arabidopsis genomes. The red lines indicate duplicated HAD gene pairs. The chromosome names are marked on the outermost edge of the circle.
Fig 5.
Distribution of the cis-element P1BS and W-box in the 1.5-kb regions upstream of ATG in the HAD genes of rice.
Fig 6.
The expression profiles of HAD genes in roots and shoots of rice under Pi deficiency conditions.
The RNA-seq data were downloaded from the DRYAD database (https://datadryad.org). 3d, 7d, 21d and 22d represent the seedlings that were treated under Pi-deficient conditions for 3, 7, 21 and 22 days. 21+1d and 21+3d represent the seedlings that were treated under Pi-deficient conditions for 21 days, followed by 1 and 3 days of recovery under normal conditions.
Fig 7.
qRT-PCR analysis of the selected HAD genes in rice during a period of P starvation followed by resupply.
Germinated seeds were grown in normal nutrient solution for 10 d and then transferred to a solution without Pi for 10 d, followed by 2 d recovery (R) in normal solution. RNA was extracted for quantitative RT-PCR, and the expression of HAD genes was normalized to that of OsACTIN. Data are means (±SEM) of three replicates. Significant differences compared with the control (0 d) were determined using Tukey’s test (*P<0.05; **P<0.01).