Abstract
BackgroundPineapple is the most important crop with CAM photosynthesis, but its molecular biology is underexplored. MADS-box genes are crucial transcription factors involving in plant development and several biological processes. However, there is no systematic analysis of MADS-box family genes in pineapple (Ananas comosus).ResultsForty-eight MADS-box genes were identified in the pineapple genome. Based on the phylogenetic studies, pineapple MADS-box genes can be divided into type I and type II MADS-box genes. Thirty-four pineapple genes were classified as type II MADS-box genes including 32 MIKC-type and 2 Mδ-type, while 14 type I MADS-box genes were further divided into Mα, Mβ and Mγ subgroups. A majority of pineapple MADS-box genes were randomly distributed across 19 chromosomes. RNA-seq expression patterns of MADS-box genes in four different tissues revealed that more genes were highly expressed in flowers, which was confirmed by our quantitative RT-PCR results. There is no FLC and CO orthologs in pineapple. The loss of FLC and CO orthologs in pineapple indicated that modified flowering genes network in this tropical plant compared with Arabidopsis. The expression patterns of MADS-box genes in photosynthetic and non-photosynthetic leaf tissues indicated the potential roles of some MADS-box genes in pineapple CAM photosynthesis. The 23% of pineapple MADS-box genes showed diurnal rhythm, indicating that these MADS-box genes are regulated by circadian clock.ConclusionsMADS-box genes identified in pineapple are closely related to flowering development. Some MADS-box genes are involved in CAM photosynthesis and regulated by the circadian clock. These findings will facilitate research on the development of unusual spiral inflorescences on pineapple fruit and CAM photosynthesis.
Highlights
Pineapple is the most important crop with Crassulacean Acid Metabolism (CAM) photosynthesis, but its molecular biology is underexplored
Forty-eight MADS-box genes were identified in the pineapple genome
The expression patterns of MADS-box genes in photosynthetic and nonphotosynthetic leaf tissues indicated the potential roles of some MADS-box genes in pineapple CAM photosynthesis
Summary
Whole-genome identification of MADS-box genes in pineapple. The protein sequences of pineapple, rice and Arabidopsis were obtained from Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html), RGAP (http://rice.plantbiology.msu.edu/) and TAIR (http://www.arabidopsis.org/) databases, respectively. To identify the MADS-box genes in pineapple, the Hidden Markov Model (HMM) profiles of the SFR (type I) domain (PF00319) and the MEF2 (type II) domain (PF09047), downloaded from Pfam database (http://pfam.xfam.org, Pfam 31.0), were used to search the pineapple genome database[43, 44]. All of the proteins with an E-value lower than 0.01 were selected. Using all Arabidopsis and rice MADS-box genes as queries, the predicted pineapple MADS genes were checked by BLASTP searches (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The predicted MADS models detected were examined manually. The retrieved pineapple MADS genes were further verified by the NCBI Conserved Domain Database (https://www.ncbi.nlm.nih.gov/cdd)
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