AUTHOR=Xiong Wei , Risse Judith , Berke Lidija , Zhao Tao , van de Geest Henri , Oplaat Carla , Busscher Marco , Ferreira de Carvalho Julie , van der Meer Ingrid M. , Verhoeven Koen J. F. , Schranz M. Eric , Vijverberg Kitty 

TITLE=Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion (Taraxacum officinale)

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1198909

DOI=10.3389/fpls.2023.1198909

ISSN=1664-462X

ABSTRACT=<p>The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that <italic>MADS-box</italic> and <italic>TCP</italic> transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of <italic>MADS-box</italic> and <italic>TCP</italic> genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our <italic>de novo</italic> assembly of diploid sexual dandelion (<italic>Taraxacum officinale</italic>) and 11 other Asteraceae to investigate the lineage-specific evolution of <italic>MADS-box</italic> and <italic>TCP</italic> genes in the Asteraceae. We compared the phylogenomic results of <italic>MADS-box</italic> and <italic>TCP</italic> genes with their expression in <italic>T. officinale</italic> floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that <italic>MADS-box MIKC</italic><sup>c</sup> and <italic>TCP-CYCLOIDEA</italic> (<italic>CYC</italic>) genes have expanded in the Asteraceae. The phylogenomic analysis identified <italic>AGAMOUS</italic>-like (<italic>AG</italic>-like: <italic>SEEDSTICK</italic> [<italic>STK</italic>]-like), <italic>SEPALATA</italic>-like (<italic>SEP</italic>3-like), and <italic>TCP-PROLIFERATING CELL FACTOR</italic> (<italic>PCF</italic>)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named “<italic>Asteraceae-Specific MADS-box</italic> genes (<italic>AS-MADS</italic>).” Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that <italic>AS-MADS</italic> is paralogous to <italic>FLOWERING LOCUS C</italic> (<italic>FLC</italic>) as demonstrated by the shared ancient duplication of <italic>FLC</italic> and <italic>SEP</italic>3.</p>