Genome-wide identification and expression analysis of the GRAS family proteins in <Emphasis Type="Italic">Medicago truncatula</Emphasis>

The GRAS gene family performs a variety of functions in plant growth and development processes, and they also play essential roles in plant response to environmental stresses. Medicago truncatula is a diploid plant with a small genome used as a model organism. Despite the vital role of GRAS genes in plant growth regulation, few studies on these genes in M. truncatula have been conducted to date. Using the M. truncatula reference genome data, we identified 68 MtGRAS genes, which were classified into 16 groups by phylogenetic analysis, located on eight chromosomes. The structure analysis indicated that MtGRAS genes retained a relatively constant exon–intron composition during the evolution of the M. truncatula genome. Most of the closely related members in the phylogenetic tree had similar motif compositions. Different motifs distributed in different groups of the MtGRAS genes were the sources of their functional divergence. Twenty-eight MtGRAS genes were expressed in six tissues, namely root, bud, blade, seedpod, nodule, and flower tissues, suggesting their putative function in many aspects of plant growth and development. Nine MtGRAS genes were upregulated under cold, freezing, drought, ABA, and salt stress treatments, indicating that they play vital roles in the response to abiotic stress in M. truncatula. Our study provides valuable information that can be utilized to improve the quality and agronomic benefits of M. truncatula and other plants.     

Genome-wide dissection of the chalcone synthase gene family in <Emphasis Type="Italic">Oryza sativa</Emphasis>

Enzymes of the chalcone synthase (CHS) family catalyze the generation of multiple secondary metabolites in fungi, plants, and bacteria. These metabolites have played key roles in antimicrobial activity, UV protection, flower pigmentation, and pollen fertility during the evolutionary process of land plants. We performed a genome-wide investigation about CHS genes in rice (Oryza sativa). The phylogenetic relationships, gene structures, chromosomal locations, and functional predictions of the family members were examined. Twenty-seven CHS family genes (OsCHS01–27) were identified in the rice genome and were found to cluster into six classes according to their phylogenetic relationships. The 27 OsCHS genes were unevenly distributed on six chromosomes, and 17 genes were found in the genome duplication zones with two segmental duplication and five tandem duplication events that may have played key roles in the expansion of the rice CHS gene family. In addition, the OsCHS genes exhibited diverse expression patterns under salicylic acid treatment. Our results revealed that the OsCHS genes exhibit both diversity and conservation in many aspects, which will contribute to further studies of the function of the rice CHS gene family and provide a reference for investigating this family in other plants.     

Genome-wide survey and expression analysis of the stress-associated protein gene family in desert poplar, <Emphasis Type="Italic">Populus euphratica</Emphasis>

Stress-associated proteins (SAPs) are a novel class of zinc finger proteins that extensively participate in abiotic stress responses. To date, no overall analysis and expression profiling of SAP genes in woody plants have been reported. Populus euphratica is distributed in desert regions and is extraordinarily adaptable to abiotic stresses. Thus, it is regarded as a promising candidate for studying abiotic stress resistance mechanisms of woody plants. In this study, 18 non-redundant SAP genes were identified from the genome of P. euphratica using basic local alignment search tool algorithms and functional domain verification. Among these 18 PeuSAP genes, 15 were intronless. To investigate the evolutionary relationships of SAP genes in P. euphratica and other Salicaceae plants, phylogenetic analyses were performed. Subsequently, the expression profiles of the 18 PeuSAP genes were analyzed in different tissues and under various stresses (drought, salt, heat, cold, and abscisic acid (ABA) treatment) using quantitative real-time PCR. Tissue expression analysis indicated that PeuSAPs showed no tissue specificity. PeuSAPs were induced by multiple abiotic stresses, especially drought, salt, and heat stresses, perhaps because of abundant cis-acting heat shock elements and drought-inducible elements in the promoter regions of the PeuSAPs. Moreover, single nucleotide polymorphisms (SNPs) variant analysis revealed many synonymous and non-synonymous SNPs in PeuSAP genes, but the zinc finger structure was conserved during evolution. These results provide an overview of the SAP gene family in P. euphratica and a reference for further functional research on PeuSAP genes.     

Genome-wide analysis and characterization of molecular evolution of the <Emphasis Type="Italic">HCT</Emphasis> gene family in pear (<Emphasis Type="Italic">Pyrus bretschneideri</Emphasis>)

Lignin is a major component of stone cells in pear fruit, which significantly affects fruit quality. Hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT), a recently discovered enzyme in plants, is an important gene that participates in the formation of lignin. Although HCT gene cloning and expression patterns have been studied in several species, including pear, there is still no extensive genome-wide bioinformatics analysis on the whole gene family, and the evolutionary history of HCT gene family is still unknown. A total of 82 HCT genes were identified in pear, most of which have one or two exons, and all with the conserved HXXXD motif and transferase domains. Based on the structural characteristics and phylogenetic analysis of these sequences, the HCT gene family genes could be classified into four main groups. Structural analysis also revealed that 25 % of HCT genes share a MYB binding site. Expansion of the HCT gene family mostly occurred before the divergence between Arabidopsis and Rosaceae, with whole-genome duplication or segmental duplication events playing the most important role in the expansion of the HCT gene family in pear. At the same time, purifying selection also played a critical role in the evolution of HCT genes. Five of the 82 HCT genes were verified by qRT-PCR to correspond to the pattern of stone cell formation during pear fruit development. The genome-wide identification, chromosome localization, gene structures, synteny, and expression analyses of pear HCT genes provide an overall insight into HCT gene family and their potential involvement in growth and development of stone cells.     

Identification,characterization, and expression of the <Emphasis Type="Italic">SWEET</Emphasis> gene family in <Emphasis Type="Italic">Phalaenopsis equestris</Emphasis> and <Emphasis Type="Italic">Dendrobium officinale</Emphasis>

Sugars are important molecules that function not only as primary metabolites, but also as nutrients and signal molecules in plants. The sugar transport protein genes family SWEET has been recently identified. The availability of the Dendrobium officinale and Phalaenopsis equestris genome sequences offered the opportunity to study the SWEET gene family in this two orchid species. We identified 22 and 16 putative SWEET genes, respectively, in the genomes of D. officinale and P. equestris using comprehensive bioinformatics analysis. Based on phylogenetic comparisons with SWEET proteins from Arabidopsis and rice, the DoSWEET and PeSWEET proteins could be divided into four clades; among these, clade II specifically lacked PeSWEETs and clade IV specifically lacked DoSWEETs, and there were orthologs present between D. officinale and P. equestris. Protein sequence alignments suggest that there is a predicted serine phosphorylation site in each of the highly conserved MtN3/saliva domain regions. Gene expression analysis in four tissues showed that three PeSWEET genes were most highly expressed in the flower, leaf, stem, and root, suggesting that these genes might play important roles in growth and development in P. equestris. Analysis of gene expression in different floral organs showed that five PeSWEET genes were highly expressed in the column (gynostemium), implying their possible involvement in reproductive development in this species. The expression patterns of seven PeSWEETs in response to different abiotic stresses showed that three genes were upregulated significantly in response to high temperature and two genes were differently expressed at low temperature. The results of this study lay the foundation for further functional analysis of SWEET genes in orchids.     

Molecular characterization and expression profiling of the phosphoenolpyruvate carboxylase genes in peanut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Phosphoenolpyruvate carboxylase (PEPC) is a tightly controlled enzyme located at the core of plant carbohydrate metabolism. Plant PEPCs belong to a small multigene family encoding several plant-type PEPC genes, along with at least one distantly related bacterial-type PEPC gene. The PEPC genes have been intensively studied in Arabidopsis, but not in peanut (Arachis hypogaea L.). Previously, we isolated five PEPC genes (AhPEPC1, AhPEPC2, AhPEPC3, AhPEPC4 and AhPEPC5) from peanut. Here, due to the sequencing of the peanut genome, we analyzed the complexity of its PEPC gene family, including phylogenetic relationships, gene structure and chromosome mapping. The results showed that AhPEPC1, AhPEPC2, AhPEPC3 and AhPEPC4 encoded typical plant-type enzymes, while AhPEPC5 was a bacterial-type PEPC. The recombinant proteins of these genes were expressed in Escherichia coli, and the calculated molecular weights of the recombinant proteins were 110.8 kD (AhPEPC1), 110.7 kD (AhPEPC2), 110.3 kD (AhPEPC3), 110.8 kD (AhPEPC4), and 116.4 kD (AhPEPC5). The expression patterns of AhPEPC1-5 were analyzed under cold, salt and drought conditions. Our results indicated that the expression of AhPEPC3 was rapidly and substantially enhanced under abiotic stress, whereas the expression of AhPEPC1 and AhPEPC2 was slightly enhanced under certain stress conditions. Some genes were down-regulated in leaves under stress: AhPEPC1, AhPEPC4 and AhPEPC5 under salt stress and AhPEPC4 and AhPEPC5 under drought stress. These results suggest that peanut PEPC proteins may differ in their functions during acclimation to abiotic stresses.