Analysis of the Maternally Expressed gene1 Family Provides Novel Insight into the Evolution and Expression of Tandem Gene Duplicates in Maize

Maternally expressed gene1 (Meg1) encodes a small cysteine-rich peptide that is required for the normal development of the basal endosperm transfer cells (BETCs) in maize. Twelve copies of Meg1-like genes were identified to be a gene cluster near the Meg1 gene. Here we analyzed the genomic organization, gene structure, expression, and chromatin status of the Meg family. Except Meg1 and Meg13, all the other members are flanked by homologous sequences varying in lengths from a few hundred bp to >5 kb, indicating that the gene family expanded through unequal crossing-over. Eight Meg genes have intact gene structures and they are transcribed specifically in the BETC. Chromatin immunoprecipitation analysis revealed that the BETC-specific Meg genes are associated with activating and repressive epigenetic marks in BETC and in non-BETC samples, respectively, indicating that regulation of chromatin structure is involved in their cell type-specific expression. Phylogenetic analysis and synteny mapping suggest that the major duplication events took place after the maize allotetraploidy at 4.8 million years ago (mya) but prior to the emergence of teosinte. Meg13, the oldest member displays a tissue expression pattern different from rest of the members and this indicates that Meg genes acquired new functions as they expand and evolve. A strong signature of positive selection in the youngest members suggests that further functional diversification occurred during the evolution of the Meg family.