ABSTRACT
SQUAMOSA promoter-binding protein-like (SPL) proteins play crucial roles in plant growth, development, and responses to environmental stressors. The peanut (Arachis hypogaea L.) is a globally important oil crop. In this study, we cloned the full-length cDNA of 15 SPLs in the peanut by transcriptome sequencing and rapid amplification of cDNA ends, and analyzed their genomic DNA sequences. cDNA lengths varied significantly, from 369 to 3102 bp. The SBP domain of the peanut SPL proteins was highly conserved compared to SPLs in other plant species. Based on their sequence similarity to SPLs from other plant species, the peanut SPLs could be grouped into five subgroups. In each subgroup, lengths of individual genes, conserved motif numbers, and distribution patterns were similar. Seven of the SPLs were predicted to be targets of miR156. The SPLs were ubiquitously expressed in the roots, leaves, flowers, gynophores, and seeds, with different expression levels and accumulation patterns. Significant differences in the expression of most of the SPLs were observed between juvenile and adult leaves, suggesting that they are involved in developmental regulation. Dynamic changes occurred in transcript levels at stage 1 (aerial grown green gynophores), stage 2 (gynophores buried in soil for about three days), and stage 3 (gynophores buried in soil for about nine days with enlarged pods). Possible roles that these genes play in peanut pod initiation are discussed.
Subject(s)
Arachis/metabolism , Cloning, Molecular , Gene Expression Regulation, Plant , Plant Proteins/genetics , Transcription Factors/genetics , Arachis/genetics , Base Sequence , Gene Expression Regulation, Developmental , Genes, Plant , MicroRNAs , Organ Specificity , Phylogeny , Plant Components, Aerial/genetics , Plant Components, Aerial/metabolism , Plant Proteins/chemistry , Plant Proteins/metabolism , Plant Roots/genetics , Plant Roots/metabolism , RNA, Messenger , Sequence Alignment , Sequence Analysis, DNA , Sequence Analysis, RNA , Transcription Factors/chemistry , Transcription Factors/metabolismABSTRACT
Nucleotide-binding site (NBS) disease resistance genes play a crucial role in plant defense responses against pathogens and insect pests. Many NBS-encoding genes have been detected in Lotus japonicus, an important forage crop in many parts of the world. However, most NBS genes identified so far in L. japonicus were only partial sequences. We identified 45 full-length NBS-encoding genes in the L. japonicus genome, and analyzed gene duplications, motifs, and the molecular phylogeny to further understand the NBS gene family. We found that gene duplication events rarely occur in L. japonicus NBS-encoding (LjNBS) genes. In addition, LjNBS genes were subjected to selection pressure, and codon usage bias was evident. We tested for purifying selection (specifically in the CC-NBS-LRR and TIR-NBS-LRR groups), and found strong purifying selection in the TIR-domain-containing sequences, indicating that the CC-NBS-LRR group is more likely to undergo expansion than the TIR-NBS-LRR group. Moreover, our results showed that both selection and mutation contributed to LjNBS codon usage bias, but mutational bias was the major influence on codon usage.