Abstract
The MADS-box gene family is an important transcription factor family involved in floral organogenesis. The previously proposed ABCDE model suggests that different floral organ identities are controlled by various combinations of classes of MADS-box genes. The five-class ABCDE model cannot cover all the species of angiosperms, especially the orchid. Thus, we developed a two-stage approach for MADS-box gene classification to advance the study of floral organogenesis of angiosperms. First, eight classes of reference datasets (A, AGL6, B12, B34, BPI, C, D, and E) were curated and clustered by phylogenetic analysis and unsupervised learning, and they were confirmed by the literature. Second, feature selection and multiple prediction models were curated according to sequence similarity and the characteristics of the MADS-box gene domain using support vector machines. Compared with the BindN and COILS features, the local BLAST model yielded the best accuracy. For performance evaluation, the accuracy of Phalaenopsis aphrodite MADS-box gene classification was 93.3%, which is higher than 86.7% of our previous classification prediction tool, iMADS. Phylogenetic tree construction – the most common method for gene classification yields classification errors and is time-consuming for analysis of massive, multi-species, or incomplete sequences. In this regard, our new system can also confirm the classification errors of all the random selection that were incorrectly classified by phylogenetic tree analysis. Our model constitutes a reliable and efficient MADS-box gene classification system for angiosperms.
Highlights
Angiosperms, i.e., flowering plants, have evolved a most remarkable flower to ensure fertilization and reproduction
M-type MADS-box genes are involved in reproduction, especially female gametophyte, embryo, and endosperm development (Masiero et al, 2011), and MIKCtype MADS-box genes participate in meristem differentiation, flowering, fruit development, and the determination of floral organ identity according to the ABCDE model (Callens et al, 2018)
Basic Local Alignment Search Tool (BLAST) expressed the highest accuracy with whole sequences and I, K, and C domains, but BindN had the best accuracy with the M domain
Summary
Angiosperms, i.e., flowering plants, have evolved a most remarkable flower to ensure fertilization and reproduction. Flowering processes and floral organ determination are controlled by MADS-box genes (Theissen et al, 2000). Type I, named the M-type, contains the conserved M domain and the large variability region at the C-terminus (Masiero et al, 2011). The M domain has the DNA binding activity, the I domain influences the DNAbinding dimerization, and the K domain can form amphipathic helices that mediate dimerization of MADS-box proteins and are involved in the formation of other complexes (EgeaCortines et al, 1999; Yang et al, 2003). M-type MADS-box genes are involved in reproduction, especially female gametophyte, embryo, and endosperm development (Masiero et al, 2011), and MIKCtype MADS-box genes participate in meristem differentiation, flowering, fruit development, and the determination of floral organ identity according to the ABCDE model (Callens et al, 2018)
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