Fig 1.
Phylogenetic tree constructed using the sequences of bHLH proteins from both peach and Arabidopsis.
The small red circles represent the peach bHLH proteins; the small green triangles represent the bHLH proteins from Arabidopsis. The Roman numeral outside the large red circle indicates the name of each subfamily of the peach bHLH superfamily. The black dotted line represents the initial or final boundary of each subfamily of the peach bHLH superfamily.
Fig 2.
Motif distribution of peach bHLH superfamily proteins.
The motifs of the bHLH superfamily proteins were analyzed using the MEME web server. The red, blue, and green blocks represent motifs 1, 2 and 3, respectively. The length of the gray line indicates the length of a sequence relative to all the other sequences. The position of each block indicates the location of a motif with a matching sequence. The phylogenetic tree on the right was constructed using only the sequences of bHLH proteins from peach.
Fig 3.
Motif composition and logos of peach bHLH proteins.
A. The logos of motifs 1 and 2, which together constitute the bHLH domain in peach. The overall height of each stack represents the conservation of the sequence at that position. The capital letters indicate over 50% conservation of amino acids among the bHLH domains. The Arabic numerals under the colored capital letters indicate the width of the motif. Each color of the English letters represents a type of amino acid residue. B. The logo of motif 3, which constitutes another conserved motif, is present only in eight members of subfamily III e.
Fig 4.
Multiple sequence alignment of the peach bHLH proteins.
Amino acids with more than 50% identity are labeled with colored boxes. The ID order of 95 peach bHLH proteins is the same as in Fig 3.
Fig 5.
Distribution of bHLH superfamily genes on the eight chromosomes of peach.
Fig 6.
Syntenic relationships of bHLH superfamily genes in peach and Arabidopsis.
Eight chromosomes of peach (Pp01–Pp08) and five chromosomes of Arabidopsis (A01–A05) are mapped in different colors. The red lines connect the orthologous bHLH genes between peach and Arabidopsis. The blue and green lines connect the paralogous bHLH genes in peach and Arabidopsis, respectively.
Fig 7.
Locations and lengths of the exons and introns of peach bHLH superfamily genes.
Exons and introns are presented as filled yellow sticks and thin gray single lines, respectively. UTRs are represented by dark blue bars at the ends. The red dotted line separates each subfamily and clearly presents the member conservation of each subfamily. The phylogenetic tree on the right was constructed using only the sequences of bHLH proteins in peach.
Fig 8.
Relative expression levels of selected bHLH genes in fruits of the two peach cultivars.
Error bars represent standard errors from three independent replicates.