Genome-Wide Identification MIKC-Type MADS-Box Gene Family and Their Roles during Development of Floral Buds in Wheel Wingnut (Cyclocarya paliurus).

Yinquan Qu,Weilong Kong,Xiangxiang Fu,Qian Wang

doi:10.3390/ijms221810128

Abstract

MADS-box transcription factors (TFs) have fundamental roles in regulating floral organ formation and flowering time in flowering plants. In order to understand the function of MIKC-type MADS-box family genes in Cyclocarya paliurus (Batal.) Iljinskaja, we first implemented a genome-wide analysis of MIKC-type MADS-box genes in C. paliurus. Here, the phylogenetic relationships, chromosome location, conserved motif, gene structure, promoter region, and gene expression profile were analyzed. The results showed that 45 MIKC-type MADS-box were divided into 14 subfamilies: BS (3), AGL12 (1), AP3-PI (3), MIKC* (3), AGL15 (3), SVP (5), AGL17 (2), AG (3), TM8 (1), AGL6 (2), SEP (5), AP1-FUL (6), SOC1 (7), and FLC (1). The 43 MIKC-type MADS-box genes were distributed unevenly in 14 chromosomes, but two members were mapped on unanchored scaffolds. Gene structures were varied in the same gene family or subfamily, but conserved motifs shared similar distributions and sequences. The element analysis in promoters’ regions revealed that MIKC-type MADS-box family genes were associated with light, phytohormone, and temperature responsiveness, which may play important roles in floral development and differentiation. The expression profile showed that most MIKC-type MADS-box genes were differentially expressed in six tissues (specifically expressed in floral buds), and the expression patterns were also visibly varied in the same subfamily. CpaF1st24796 and CpaF1st23405, belonging to AP3-PI and SEP subfamilies, exhibited the high expression levels in PA-M and PG-F, respectively, indicating their functions in presenting heterodichogamy. We further verified the MIKC-type MADS-box gene expression levels on the basis of transcriptome and qRT-PCR analysis. This study would provide a theoretical basis for classification, cloning, and regulation of flowering mechanism of MIKC-type MADS-box genes in C. paliurus.

Highlights

MIKC-type MADS-box genes were identified from the C. paliurus genome using the HMM program for the K-box domain search and the local BLASTP search with Arabidopsis
MIKC-type MADS-box transcription factors are one of the notable protein families in flowering plants involved in flower induction, floral initiation, and floral morphogenesis [11]
The identified 45 C. paliurus MIKC-type MADS-box proteins were classified into 14 distinct subfamilies, which is consistent with the classification and identified results of A. thaliana [12]

Summary

Introduction

MADS-box gene family, one of the most extensively studied transcription factors (TFs), have fundamental roles in developmental control and signal transduction in plants, animals, and fungi [1]. According to the sequence structure, MADS-box gens have been divided into two super clades: type I and type II. MADS domain with a simple structure, containing only 1 to 2 exons, whereas type II constitutes MIKCC and MIKC∗ in plants encodes a MEF2-like and MIKC type MADS domain with semi-conservative K-box (keratin-like domain) and poorly conservative I-box (intervening domain) and variable C-terminal domain (C-terminal region) [2,3]. MIKCtype MADS-box genes are best known for their functions: regulating the development of floral organs and fruits, and controlling flowering time and gametophytic cell division, photosynthesis, and nutrient metabolism [4]. The MIKCC -type genes have been subdivided into 13 groups, namely, AG (class C genes), AGL6, AGL12, AP3-PI (class B genes), Bs, SOC1, SVP, SEP (class E genes), AGL17, AP1-FUL (class A genes), AGL15, FLC, and TM8 [5]

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Conclusion