Comprehensive Phylogenetic Analysis of MADS-box Family in Citrus

MADS-box genes comprise a large family of transcription factors that are known as key regulators of important processes during plant development. The completion of the two citrus genome sequences (mandarin and sweet orange) has allowed the genomic survey and analysis of many gene families. Here, a comprehensive phylogenetic analysis of the MADS-box gene family in citrus was performed using the latest version of the sweet orange (citrus.hzau.edu.cn/orange/, version 1.1) and mandarin (Phytozome, version 1.0) genomes. Using a combination of batch BLAST and Hidden Markov Model (HMM) searches, 95 non-redundant MADS-box genes each were identified in sweet orange and mandarin. Bayesian trees built based on the alignment of the MADS domain from Arabidopsis and citrus protein sequences grouped these MADS-box into Type I (Mα, Mβ and Mγ) and Type II (MIKC^c and MIKC*) groups, and the MIKC^c and MIKC* were further divided into 11 and 2 subgroups (clades). Most of the Type II MADS-box citrus orthologs can be grouped together with their Arabidopsis counterparts with high posterior probability, whereas in Type I MADS-box genes, lineage-specific expansions in citrus were evident. Chromosomal location of sweet orange MADS-box genes reveals four tandemly duplicated regions, containing two regions each from MIKC^cor Mα genes. Furthermore, Bayesian trees were generated using MADS-box orthologs from citrus and four species (Arabidopsis, eucalyptus, grapevine and poplar). Detailed discussions about similarities and differences in the evolutionary patterns of Type I and Type II genes between citrus and these plant genomes will be presented.

Financial support: FAPESP (Process: 2008/02248-1)