Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Sep 21;12(18):3334.
doi: 10.3390/plants12183334.

Identification and Expression of the MADS-box Gene Family in Different Versions of the Ginkgo biloba Genome

Pengyan Zhou  1   2 , Zesen Wang  2 , Yingang Li  1 , Qi Zhou  1
Affiliations

Identification and Expression of the MADS-box Gene Family in Different Versions of the Ginkgo biloba Genome

Pengyan Zhou et al. Plants (Basel). .

Abstract

MADS-box transcription factors play important roles in many organisms. These transcription factors are involved in processes such as the formation of the flower organ structure and the seed development of plants. Ginkgo biloba has two genome versions (version 2019 and version 2021), and there is no analysis or comparison of the MADS-box gene family in these two genomes. In this study, 26 and 20 MADS-box genes were identified from the two genomes of Ginkgo, of which 12 pairs of genes reached more than 80% similarity. According to our phylogenetic analysis results, we divided these genes into type I (Mα and Mγ subfamilies) and type II (MIKC and Mδ subfamilies) members. We found that both sets of genomes lacked the Mβ gene, while the MIKC gene was the most numerous. Further analysis of the gene structure showed that the MIKC genes in the two genomes had extralong introns (≥20 kb); these introns had different splicing patterns, and their expression might be more abundant. The gene expression analysis proved that GbMADS genes were expressed to varying degrees in eight Ginkgo biological tissues. Type II GbMADS genes not only were found to be related to female flower bud differentiation and development but also are important in seed development. Therefore, MADS-box genes may play important roles in the development of Ginkgo reproductive organs, which may suggest a genetic role in sexual differentiation. This study further contributes to the research on MADS-box genes and provides new insights into sex determination in Ginkgo.

Keywords: Ginkgo genome; MADS-box; expression; gene structure.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
A phylogenetic tree was constructed with the ML method, which is composed of homologous MADS protein sequences in Ginkgo, A. thaliana, and Populus L. The red circle represents MADS in Ginkgo and the white square represents MADS in A. thaliana. Version2019 represents the MADS proteins identified from the 2019 version of the genome. Version2021 represents the MADS proteins identified from the 2021 version of the genome. For version2019, the light green represents MIKC subfamily, the dark pink represents Mα subfamily, the light pink represents Mβ subfamily, the light purple represents Mγ subfamily, and the orange represents Mδ subfamily. For version2021, the green represents MIKC subfamily, the blue represents Mα subfamily, the light pink represents Mβ subfamily, the light purple represents Mγ subfamily, and the light orange represents Mδ subfamily.
Figure 2
Figure 2
Gene structure of GbMADS genes. Version2019 represents the MADS genes identified from the 2019 version of the genome. Version2021 represents the MADS genes identified from the 2021 version of the genome. Green lines are exons, and black lines are introns.
Figure 3
Figure 3
Interaction network analysis of GbMADS proteins. Version2019 represents the MADS proteins interaction in the 2019 version of the genome, and Version2021 represents the MADS proteins interaction in the 2021 version of the genome.
Figure 4
Figure 4
GbMADS gene expression analysis. Orange to blue represent expression from high to low.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Messenguy F., Dubois E. Role of MADS-box proteins and their cofactors in combinatorial control of gene expression and cell development. Gene. 2003;316:1–21. doi: 10.1016/S0378-1119(03)00747-9. - DOI - PubMed
    1. Krizek B.A., Fletcher J.C. Molecular mechanisms of flower development: An armchair guide. Nat. Rev. Genet. 2005;6:688–698. doi: 10.1038/nrg1675. - DOI - PubMed
    1. Parenicova L., de Folter S., Kieffer M., Horner D.S., Favalli C., Busscher J., Cook H.E., Ingram R.M., Kater M.M., Davies B., et al. Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: New openings to the MADS world. Plant Cell. 2003;15:1538–1551. doi: 10.1105/tpc.011544. - DOI - PMC - PubMed
    1. Leseberg C.H., Li A., Kang H., Duvall M., Mao L. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. Gene. 2006;378:84–94. doi: 10.1016/j.gene.2006.05.022. - DOI - PubMed
    1. Arora R., Agarwal P., Ray S., Singh A.K., Singh V.P., Tyagi A.K., Kapoor S. MADS-box gene family in rice: Genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genom. 2007;8:242. doi: 10.1186/1471-2164-8-242. - DOI - PMC - PubMed

LinkOut - more resources