Asymmetric evolution of duplicate genes encoding the CCAAT‐binding factor NF‐Y in plant genomes

Abstract

Summary• NF-Y is a ubiquitous CCAAT-binding factor composed of NF-YA, NF-YB and NF-YC. Multiple genes encoding NF-Y subunits have been identified in plant genomes. It remains unclear whether the duplicate genes underwent different evolutionary patterns.• Likelihood-ratio tests were used to examine whether the amino acid substitution rates are the same between duplicate genes. The influences of selection on evolution were evaluated by comparing the conservative and radical amino acid substitution rates, as well as maximum-likelihood analysis.• Some NF-YB and NF-YC duplicates showed significant evidence of asymmetric evolution but not the NF-YA duplicates. Most amino acid replacements in the NF-YB and NF-YC duplicates result in changes in hydropathy, polar requirement and polarity. The physicochemical changes in the sequences of NF-YB seem to be coupled to asymmetric divergence in gene function.• Plant NF-Y genes have evolved in different patterns. Relaxed selective constraints following gene duplication are most likely responsible for the unequal evolutionary rates and distinct divergence patterns of duplicate NF-Y genes. Positive selection may have promoted amino acid hydropathy changes in the NF-YC duplicates.

A C Subunit of the Plant Nuclear Factor NF-Y Required for Rhizobial Infection and Nodule Development Affects Partner Selection in the Common Bean–Rhizobium etliSymbiosis

“…NF-YC1 was not only required for nodule organogenesis and rhizobia infection, but also influences partner selection in common bean-R. etli symbiosis. NF-YCs constitute a gene family in plants (Yang et al, 2005;Stephenson et al, 2007;Siefers et al, 2009), and common bean is not an exception, with three members identified based on the current EST data set. Both NF-YC1 and NF-YC2 were upregulated by rhizobium infection, but only NF-YC1 was found to be specifically upregulated by highly efficient R. etli strains at 24 HAI (Figure 1).…”

“…Based on the current EST and genomic sequence information available for this legume, this analysis indicates that, as described for other plant species (Gusmaroli et al, 2001(Gusmaroli et al, , 2002Yang et al, 2005;Stephenson et al, 2007;Siefers et al, 2009), NF-YC is a gene family, with at least three members in common bean.…”

The Promiscuous Life of Plant NUCLEAR FACTOR Y Transcription Factors

“…The comprehensive search for NF-Y genes in Arabidopsis thaliana (Gusmaroli et al, 2001(Gusmaroli et al, , 2002Yang et al, 2005;Siefers et al, 2009) was followed by similar ones in other plant species, including rice (Oryza sativa), wheat (Triticum aestivum), and Brachypodium distachyon (Stephenson et al, 2007;Thirumurugan et al, 2008;Cao et al, 2011b). It became clear that each plant NF-Y gene family has undergone significant amplification (e.g., seven NF-YC genes in rice [Thirumurugan et al, 2008] and 14 in wheat [Stephenson et al, 2007]).…”

A Putative CCAAT-Binding Transcription Factor Is a Regulator of Flowering Timing in Arabidopsis

“…There is seemingly only one gene for each HAP factor in yeast and animals (Mantovani, 1999). In plants, however, these factors are all encoded in a gene family (Edwards et al, 1998;Yang et al, 2005). There are at least 10 annotated members in each family in Arabidopsis and also multiple members in each HAP family in rice (Oryza sativa; Kwong et al, 2003;Yang et al, 2005).…”