Abstract
Dianthus is a large genus containing many species with high ornamental economic value. Extensive breeding strategies permitted an exploration of an improvement in the quality of cultivated carnation, particularly in flowers. However, little is known on the molecular mechanisms of flower development in carnation. Here, we report the identification and description of MADS-box genes in carnation (DcaMADS) with a focus on those involved in flower development and organ identity determination. In this study, 39 MADS-box genes were identified from the carnation genome and transcriptome by the phylogenetic analysis. These genes were categorized into four subgroups (30 MIKCc, two MIKC*, two Mα, and five Mγ). The MADS-box domain, gene structure, and conserved motif compositions of the carnation MADS genes were analysed. Meanwhile, the expression of DcaMADS genes were significantly different in stems, leaves, and flower buds. Further studies were carried out for exploring the expression of DcaMADS genes in individual flower organs, and some crucial DcaMADS genes correlated with their putative function were validated. Finally, a new expression pattern of DcaMADS genes in flower organs of carnation was provided: sepal (three class E genes and two class A genes), petal (two class B genes, two class E genes, and one SHORT VEGETATIVE PHASE (SVP)), stamen (two class B genes, two class E genes, and two class C), styles (two class E genes and two class C), and ovary (two class E genes, two class C, one AGAMOUS-LIKE 6 (AGL6), one SEEDSTICK (STK), one B sister, one SVP, and one Mα). This result proposes a model in floral organ identity of carnation and it may be helpful to further explore the molecular mechanism of flower organ identity in carnation.
Highlights
The MADS-box gene family playing an important role in the regulation of plant growth and development is well known as a key transcription factor (TF)
The Hidden Markov Model (HMM) profile for the MADS-box domain (Pfam accession number: PF00319) was used to search (e-value 1e-7, score 30) against the genome protein sequences by using HMM search tool to ensure the completeness of MADS-box genes as far as possible
To define the candidate MADS-box genes, carnation genome and transcriptome protein sequences were searched by using a HMM profile in the Pfam database
Summary
The MADS-box gene family playing an important role in the regulation of plant growth and development is well known as a key transcription factor (TF). MADS-box genes identified as floral homeotic genes contain a highly-conserved MADS box DNA-binding domain of approximately. MADS-box genes were classified into two major types: type I and type II genes, based on the phylogenetic relation of the conserved MADS box domain [5,6]. Type I genes can be further divided into three subgroups, Mα, Mβ, and Mγ, while type II, known as M-type, can be classified into two subgroups, MIKCc and MIKC*, based on their structural characteristics [8,9]. It has been reported that type I MADS-box genes encode SRF-like domain proteins, that type II group genes encode MEF2-like genes of animals and yeast, and that MIKC-type genes are found only in plants [10,11]. The MIKCc proteins contain four common domains, including MADS (M), weakly-conserved intervening (I), conserved keratin (K), and the highly-variable C-terminal (C)
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