Surprising Complexity of MADS-Box Genes in Ferns and Their Allies Revealed By the 1000 Plant Transcriptome Project

Transcript sequences from more than 1000 plant species, ranging from algae, via bryophytes (liverworts, hornworts and mosses), lycophytes and monilophytes (ferns and their allies), to flowering plants, was acquired in the course of the 1000 plant transcriptome (1kp) project (www.onekp.com). Using this data, the genetic basis for transitions during plant evolution like body plan changes during the colonization of land and the origin of seeds and flowers, can now be studied in unprecedented detail.

MADS-domain proteins encoded by MADS-box genes are crucial transcription factors for plant development. Hence, changes in numbers and origin of clades of MADS-domain proteins have been associated with transitions in plant evolution. Here, we identify more than 21,500 genes encoding MADS-domain proteins in the 1kp data using Hidden Markov Model approaches. The average number of MADS-box genes increases from around two in the transcriptomes of algae to around 30 in flowering plants. Surprisingly, the average number of MADS-box genes in ferns and their allies (such as horsetails) is about as high as in flowering plants even though ferns appear to have a more simple body plan lacking seeds, fruits and flowers. We further classify the MADS-domain transcription factors into clades by reconstructing Maximum Likelihood phylogenies using RAxML. We find that the MADS-box genes of ferns form separate clades to the ones of flowering plants, indicating independent expansions of these genes in ferns and flowering plants. Our analyses provide a starting point for studying the genetic basis of the evolutionary transition from ferns to seed plants.