Dataset Information

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya.

ABSTRACT: MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.

SUBMITTER: Dai Y

PROVIDER: S-EPMC10531014 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya.

Dai Yunsu Y Wang Yu Y Zeng Liwang L Jia Ruizong R He Linwen L Huang Xueying X Zhao Hui H Liu Difa D Zhao Haixu H Hu Shuai S Gao Ling L Guo Anping A Xia Wei W Ji Changmian C

International journal of molecular sciences 20230913 18

MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a w ...[more]

PMID: 37762345

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Project description:BackgroundThe MADS-box gene family is widely distributed in the plant kingdom, and its members typically encoding transcription factors to regulate various aspects of plant growth and development. In particular, the MIKC-type MADS-box genes play a crucial role in the determination of floral organ development and identity recognition. As a type of androdioecy plant, Chionanthus retusus have unique gender differentiation. Manifested as male individuals with only male flowers and female individuals with only bisexual flowers. However, due to the lack of reference genome information, the characteristics of MIKC-type MADS-box genes in C. retusus and its role in gender differentiation of C. retusus remain largely unknown. Therefore, it is necessary to identify and characterize the MADS-box gene family within the genome of the C. retusus.ResultsIn this study, we performed a genome-wide identification and analysis of MIKC-type MADS-box genes in C. retusus (2n = 2x = 46), utilizing the latest reference genome, and studied its expression pattern in individuals of different genders. As a result, we identified a total of 61 MIKC-type MADS-box genes in C. retusus. 61 MIKC-type MADS-box genes can be divided into 12 subfamilies and distributed on 18 chromosomes. Genome collinearity analysis revealed their conservation in evolution, while gene structure, domains and motif analysis indicated their conservation in structure. Finally, based on their expression patterns in floral organs of different sexes, we have identified that CrMADS45 and CrMADS60 may potentially be involved in the gender differentiation of C. retusus.ConclusionsOur studies have provided a general understanding of the conservation and characteristics of the MIKC-type MADS-box genes family in C. retusus. And it has been demonstrated that members of the AG subfamily, CrMADS45 and CrMADS60, may play important roles in the gender differentiation of C. retusus. This provides a reference for future breeding efforts to improve flower types in C. retusus and further investigate the role of MIKC-type MADS-box genes in gender differentiation.

Project description:Late embryogenesis abundant (LEA) proteins comprise a diverse superfamily involved in plant development and stress responses. This study presents a first genome-wide analysis of LEA genes in papaya (Carica papaya L., Caricaceae), an economically important tree fruit crop widely cultivated in the tropics and subtropics. A total of 28 members were identified from the papaya genome, which belong to eight families with defined Pfam domains, i.e., LEA_1 (3), LEA_2 (4), LEA_3 (5), LEA_4 (5), LEA_5 (2), LEA_6 (2), DHN (4), and SMP (3). The family numbers are comparable to those present in Ricinus communis (Euphorbiaceae, 28) and Moringa oleifera (Moringaceae, 29), but relatively less than that found in Moringa oleifera (Cleomaceae, 39) and Arabidopsis thaliana (Brassicaceae, 51), implying lineage-specific evolution in Brassicales. Indeed, best-reciprocal-hit-based sequence comparison and synteny analysis revealed the presence of 29 orthogroups, and significant gene expansion in Tarenaya and Arabidopsis was mainly contributed by whole-genome duplications that occurred sometime after their split with the papaya. Though a role of transposed duplication was also observed, tandem duplication was shown to be a key contributor in gene expansion of most species examined. Further comparative analyses of exon-intron structures and protein motifs supported fast evolution of this special superfamily, especially in Arabidopsis. Transcriptional profiling revealed diverse expression patterns of CpLEA genes over various tissues and different stages of developmental fruit. Moreover, the transcript level of most genes appeared to be significantly regulated by drought, cold, and salt stresses, corresponding to the presence of cis-acting elements associated with stress response in their promoter regions. These findings not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further functional analysis of LEA genes in papaya.

Dataset Information

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya.

Publications

Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in <i>Carica papaya</i>.

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