MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.
OBJECTIVE
MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms.


METHODS
The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes.


RESULTS
Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes.


CONCLUSIONS
The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.
Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany.
Lydia
L
Gramzow
Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany.
Lisa
L
Weilandt
Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, 07743 Jena, Germany guenter.theissen@uni-jena.de.
Günter
G
Theißen
D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D032462:Cycadopsida / Q000235:genetics*; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D026161:MADS Domain Proteins / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D028222:Picea / Q000235:genetics; D041603:Pinus taeda / Q000235:genetics; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D012639:Seeds / Q000235:genetics; D016415:Sequence Alignment; D064028:Tracheophyta / Q000235:genetics; D059467:Transcriptome
D026161:MADS Domain Proteins; D010940:Plant Proteins
MADS-box gene; MRCA; Picea; Pinus; ancestral gene set; conifer; flower development; gymnosperm; most recent common ancestor; pine; seed plant; spruce