Abstract
The rubber tree (Hevea brasiliensis Muell. Arg.) is a rubber producing crop and contains specialized laticifers. MADS-box genes are a family of transcription factor genes that regulate plant development, especially floral organ and gametophyte development. 97 MADS-box genes were identified in the rubber tree through transcriptomes and genome mining. 93.8% of the genes were mapped onto the genome scaffolds in correspondence to the coverage (93.8%) of current version of sequenced genome. Phylogenetic analysis indicates that type II MADS-box genes have been more actively duplicated than their orthologous genes in Arabidopsis and rice, so that most (70, 72.2%) of the MADS-box genes in the rubber tree belong to type II subfamily. This is a high percentage compared to those in Arabidopsis (43.7%) and rice (56.8%). Moreover, 69 out of 70 type II genes in the rubber tree are transcribed, and they are mostly predominantly expressed in flowers, but some genes are predominantly expressed in laticifers, suggesting their roles in both flower and laticifer development. The number of type I genes in the rubber tree is only 27 (27.8%), a much smaller number compared to their orthologous genes in Arabidopsis (56.3%) and rice (43.2%). At the same time, most of the type I genes (55.6%, 15) in the rubber tree are silent and are probably pseudogenes. The high birth rate and low death rate of type II genes and low birth rate and high death rate of type I genes may corresponds to special developmental requirements in the rubber tree, e.g. the development of laticifer system for biosynthesis of cis-polyisoprene, the rubber. Moreover, atypical MIKC* factors (e.g. HbMADS1 in S-clade, and HbMADS20 in P-clade) are identified. These genes are diverged to typical MIKC* genes in sequences and facilitate functions required in laticifer development and rubber biosynthesis, which is not necessary in Arabidopsis and rice.
Highlights
MADS-box genes have long evolutionary history and spread widely in plants, animals, and fungi
Homology searches in the microbial database suggested that the MADS domain originated from the DNA binding subunit A of topoisomerases IIA, and gave rise to SERUM RESPONSE FACTOR (SRF)-like and MEF2-like MADS-box genes after gene duplication that occurred in extant eukaryotes [6]
Plant type I genes do not group into a monophyletic cluster [8] and have undergone a faster rate of birth and death during evolution compared with animal type I (SRF) and plant type II (MIKC) genes; early reports concluded that plant type I genes were probably of minor functional importance in comparison to type II genes [9, 10]
Summary
MADS-box genes have long evolutionary history and spread widely in plants, animals, and fungi They were found independently in different organisms and were once named as MINICHROMOSOME MAINTENANCE1 (MCM1) in Saccharomyces cerevisiae [1], AGAMOUS in Arabidopsis thaliana [2], DEFICIENS in Antirrhinum majus [3], and SERUM RESPONSE FACTOR (SRF) in Homo sapiens [4]. All these genes encode a highly conserved N-terminal DNA binding domain of 55–60 amino acids in length and were given the acronym MADS domain using the first letters of the above genes [5]. Arabidopsis type I genes were divided into three subfamilies Mα, Mβ, and Mγ, AGAMOUS LIKE33 was not assigned to any of these [11], while type II MADSbox genes were divided into two main subfamilies MIKCc and MIKC [8]
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