Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation

Abstract

MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS.

Keywords: MADS-box gene; Taraxacum kok-saghyz; Taraxacum mongolicum; biomass; collinearity; natural rubber biosynthesis.

Figure 1

Phylogenetic relationships of Taraxacum and Arabidopsis MADS-box transcription factors. Phylogenetic analyses were conducted on MADS-box transcription factors from Arabidopsis thaliana (black), Taraxacum kok-saghyz (TKS, red), and Taraxacum mongolicum (TM, blue). ClustalW was used for multiple sequence alignment. The phylogenetic tree was constructed using the neighbor-joining (NJ) method with 1000 bootstrap repeats. Type I proteins are shown in cyan, and type II proteins are shown in purple.

Figure 2

Phylogenetic analyses of the type I and type II MADS-box transcription factors. Phylogenetic analyses were performed on the type I (A) and type II (B) MADS-box transcription factors from Arabidopsis thaliana (black), TKS (red), and TM (blue). ClustalW was used for multiple sequence alignment. The phylogenetic tree was constructed using the NJ method with 1000 bootstrap repeats. Each subclade is represented by a specific color.

Figure 3

Gene structures of TkMADS and TmMADS. Analyses of gene structures of TkMADS (A) and TmMADS (B). Exon–intron structure analyses were performed using the Gene Structure Display Server (GSDS) database. The lengths of the exons and introns of each gene are shown on the scale of lines. The blue areas represent the UTR, the yellow areas represent the exons, and the black lines represent the introns.

Figure 4

Conserved motifs of TkMADS and TmMADS proteins. Analyses of conserved motifs of TkMADS (A) and TmMADS (B) proteins. The conserved motifs were identified using the MEME database and are indicated by different colors. Motif 1 and motif 2 represent the MADS domain and K domain, respectively.

Figure 5

Chromosomal locations of MADS-box genes in the genomes of TKS and TM. Physical mapping of the TkMADS (A) and TmMADS (B) genes was conducted via MapChart based on the genomic data of TKS and TM. Eight chromosomes of TKS and TM are numbered Chr1~8, and Chr0 is a pseudochromosome that failed to assemble with the other eight chromosomes [28].

Figure 6

Duplication and synteny analysis of TkMADS and TmMADS genes. The red lines indicate duplications within the genomes of TKS (A) and TM (B). (C) All the collinear TkMADS and TmMADS genes are shown in red lines in the genomes of TKS and TM. The grey lines indicate collinear genes.

Figure 7

Expression profiles of TkMADS genes in different tissues of TKS. The expression levels of TkMADS genes were determined via qRT-PCR. TkActin was used as an internal standard. The gray bar indicates that no expression was detected, while the red, black, and green bars represent high, moderate, and low expression levels, respectively.

Figure 8

Expression of TkMADS genes related to biomass formation in tetraploid and diploid TKS. Phenotypes of tetraploid 4X and diploid 1151 plants cultured in a growth chamber (A) and non–temperature-controlled greenhouses (B) for 6 months. Differentially expressed TkMADS genes were identified by comparisons between the RNA-seq data of 4XL and 1151L (C) and between those of 4XR and 1151R (E) and further verified via qRT-PCR (D,F).

Figure 9

Expression of TkMADS genes related to NR biosynthesis in different lines of TKS verified via qRT-PCR. The high NR content (HNR) group includes X51, X52, and X53, and the low NR content (LNR) group includes 166, 615, and 619.