A parsimonious model of lineage-specific expansion of MADS-box genes in Physcomitrella patens.

KEY MESSAGE: The MADS-box gene family expanded in the lineage leading to the moss, Physcomitrella patens , mainly as a result of polyploidisations and/or large-scale segmental duplication events and to a lesser extent by tandem duplications. Plant MADS-box genes comprise a large family best known for the roles of type II MIKC (C) genes in floral organogenesis, but also including type II MIKC* genes, some of which have been implicated in male gametophytic development, and type I genes, a few of which are involved in ontogeny of female gametophytes, seeds and embryos. Genome-wide analyses of the MADS-box family in angiosperms have revealed numeric predominance of type I and MIKC (C) genes and cross-species phylogenetic clustering of the Mα, Mβ and Mγ subtypes of type I genes and of 12 major subgroups of MIKC (C) genes. The genome sequence of Physcomitrella patens has facilitated investigation of its full complement of 26 MADS-box genes, including 6 MIKC (C) genes, 11 MIKC* genes, seven type I genes and two pseudogenes. A much higher degree of similarity in sequence and architecture within the MIKC (C) and MIKC* gene subtypes exists in Physcomitrella than in Arabidopsis. Furthermore, MADS-box and K-box sequence is highly conserved between the MIKC (C) and MIKC* subgroups in Physcomitrella. Nine MIKC* genes and two MIKC (C) genes are located in pairs or triplets on individual DNA scaffolds. Phylogenetic gene clustering, gene architectures and gene linkages (directly determined from examination of the genome sequence) underpin a parsimonious model of two tandem duplications and three segmental duplication events, which can account for lineage-specific expansion of the MADS-box gene family in Physcomitrella from 4 members to 26. Two of these segmental duplication events may be indicative of polyploidisations, one of which has been postulated previously.