Abstract
Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mβ, Mγ) and type II (MIKC*, MIKCC) groups, and MIKCC genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKCC genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKCC genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.
Highlights
The MADS-box genes, widely distributed in fungi, plants, and animals, encode a large transcription factor family
To identify the MADS-box gene family, both the hidden Markov model (HMM) profile (PF00319) and 107 Arabidopsis MADS-box protein sequences were used as queries to perform HMMER and BLASTP against the “SX” longan genome
Our analysis showed that expression patterns of MIKCC genes in longan tissues were classified into four clusters (Figure 7A)
Summary
The MADS-box genes, widely distributed in fungi, plants, and animals, encode a large transcription factor family. In Arabidopsis MADS-box genes were separated into five groups including Mα, Mβ, Mγ, Mδ, and MIKC based on the phylogenetic analysis (Parenicova et al, 2003) These MIKC type transcription factors, only found in the plant, can be subdivided into MIKCC and MIKC∗ groups based on differences in I and K domains and have been characterized functionally in the regulation of growth and development (Theissen et al, 2000; Becker and Theissen, 2003). These type II genes may be separated from the ancestor of extant land plants (Becker and Theissen, 2003)
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