Effect of colchicine-induced polyploidy on morphological characteristics and essential oil composition of ajowan (<Emphasis Type="Italic">Trachyspermum ammi</Emphasis> L.)

Cyclophilins (CYPs) belong to the immunophilin superfamily, having the peptidyl prolyl cis/trans isomerase activity that can catalyze the cis/trans isomerisation process of proline residues. Previous studies have shown their importance in plants, but no comprehensive analysis of maize CYP family has been reported. In the present study, a whole-genome-wide analysis of maize CYP family was performed and 39 ZmCYP genes (ZmCYP1 to ZmCYP39) were identified from maize genome, which were unequally distributed on maize ten chromosomes. Phylogenetic analysis revealed a weak relationship among these ZmCYP genes. Furthermore, their gene structure and motif patterns also displayed variant within the gene family. Four segmental and one tandem duplicated gene pairs were found from 39 ZmCYP genes, respectively, indicating their roles in the expansion of maize CYP family. Expression analysis of 39 ZmCYP genes in maize tissues showed their differential tissue specific expression patterns. Quantitative real-time PCR analysis of 19 selected ZmCYP genes under salinity stress indicated their stress-inducible expression profile. Heterologous expression of ZmCYP15 in E. coli enhanced tolerance against abiotic stress. Subcellular localization analysis indicated ZmCYP15 was located in nucleus and cytoplasm. Our study describes the importance of the maize CYP gene family in stress response, and provides a reference for future study and application for maize genetic improvement.     

Genomewide analysis of <Emphasis Type="Italic">MATE</Emphasis>-type gene family in maize reveals microsynteny and their expression patterns under aluminum treatment

Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro–exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The K_a/ K_s ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.     

Genome-wide identification,systematic analysis and characterization of <Emphasis Type="Italic">SRO</Emphasis> family genes in maize (<Emphasis Type="Italic">Zea mays</Emphasis> L.)

SIMILAR TO RCD ONE (SRO) is a small plant-specific gene family, which play essential roles in plant growth and development as well as in abiotic stresses. However, the function of SROs in maize is still unknown. In our study, six putative SRO genes were isolated from the maize genome. A systematic analysis was performed to characterize the ZmSRO gene family. The ZmSRO gene family was divided into two groups according to the motif and intron/exon analysis. Phylogenetic analysis of them with other plants showed that the clades of SROs along with the divergence of monocot and dicot and ZmSROs were more closely with OsSROs. Many abiotic stress response and hormone-induced cis-regulatory elements were identified from the promoter region of ZmSROs. Furthermore, RNA-seq analysis indicated that SRO genes were widely expressed in different tissues and development stages in maize, and the expression divergence was also obviously observed. Analyses of expression in response to PEG6000 and NaCl treatment, in addition to exogenous application of ABA and GA hormones showed that the majority of the members display stress-induced expression patterns. Taken together, our results provide valuable reference for further functional analysis of the SRO gene family in maize, especially in abiotic stress responses.     

Genomic location and expression analysis of expansin gene family reveals the evolutionary and functional significance in <Emphasis Type="Italic">Triticum aestivum</Emphasis>

The plant-specific expansin proteins constitute an ancient and major gene family known to have roles in regulating diverse biological processes in plants. Although the functions of many expansin genes have been identified in wheat and other species, little is known about the evolution and genomic locations of the expansin genes in wheat (Triticum aestivum). In this study, a total of 87 expansin genes were identified in the wheat genome, including 52 EXPAs, 42 EXPBs and 4 EXLAs. The EXLB gene was not found in the wheat genome. Phylogenetic tree and comparative analysis revealed amplification of the EXPBs in rice, maize and wheat. The predicted wheat expansins were distributed across 14 of 21 chromosomes with different densities, 3 tightly co-located clusters and 15 paralogous pairs, indicating that tandem duplication and segmental duplication events also played roles in the evolution of expansins in wheat. In addition, the gene structures and conserved protein domains of wheat expansins suggest high levels of conservation within the phylogenetic subgroups. Analysis of a published microarray database showed that most wheat expansin genes exhibit different expression levels in different tissues and developmental stages. To our knowledge, this is the first report of a genome-wide analysis of the wheat expansin gene family, which should provide valuable information for further elucidating the classification and putative functions of the entire gene family.     

Genome-wide identification and resistance expression analysis of the <Emphasis Type="Italic">NBS</Emphasis> gene family in <Emphasis Type="Italic">Triticum urartu</Emphasis>

As the largest class of resistant genes, the nucleotide binding site (NBS) has been studied extensively at a genome-wide level in rice, sorghum, maize, barley and hexaploid wheat. However, no such comprehensive analysis has been conducted of the NBS gene family in Triticum urartu, the donor of the A genome to the common wheat. Using a bioinformatics method, 463 NBS genes were isolated from the whole genome of T. urartu, of which 461 had location information. The expansion pattern and evolution of the 461 NBS candidate proteins were analyzed, and 118 of them were duplicated. By calculating the lengths of the copies, it was inferred that the NBS resistance gene family of T. urartu has experienced at least two duplication events. Expression analysis based on RNA-seq data found that 6 genes were differentially expressed among Tu38, Tu138 and Tu158 in response to Blumeria graminis f.sp.tritici (Bgt). Following Bgt infection, the expression levels of these genes were up-regulated. These results provide critical references for further identification and analysis of NBS family genes with important functions.     

Expression analysis of genes encoding double B-box zinc finger proteins in maize

The B-box proteins play key roles in plant development. The double B-box (DBB) family is one of the subfamily of the B-box family, with two B-box domains and without a CCT domain. In this study, 12 maize double B-box genes (ZmDBBs) were identified through a genome-wide survey. Phylogenetic analysis of DBB proteins from maize, rice, Sorghum bicolor, Arabidopsis, and poplar classified them into five major clades. Gene duplication analysis indicated that segmental duplications made a large contribution to the expansion of ZmDBBs. Furthermore, a large number of cis-acting regulatory elements related to plant development, response to light and phytohormone were identified in the promoter regions of the ZmDBB genes. The expression patterns of the ZmDBB genes in various tissues and different developmental stages demonstrated that ZmDBBs might play essential roles in plant development, and some ZmDBB genes might have unique function in specific developmental stages. In addition, several ZmDBB genes showed diurnal expression pattern. The expression levels of some ZmDBB genes changed significantly under light/dark treatment conditions and phytohormone treatments, implying that they might participate in light signaling pathway and hormone signaling. Our results will provide new information to better understand the complexity of the DBB gene family in maize.     

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.     

Late Embryogenesis Abundant (<Emphasis Type="Italic">LEA</Emphasis>) Gene Family in Maize: Identification,Evolution, and Expression Profiles

Late embryogenesis abundant (LEA) proteins are identified as a large and highly diverse group of polypeptides accumulating in response to cellular dehydration in many organisms. However, there are only very limited reports of this protein family in maize until this study. In the present paper, we identified 32 LEA genes in maize. A total of 83 LEA proteins including 51 members in Arabidopsis and 32 putative members in maize were classified into nine groups. Gene organization and motif compositions of the LEA members are highly conserved in each of the groups, indicative of their functional conservation. The predicted ZmLEA genes were non-random distributed across chromosomes, and transposition event and segmental duplication contributed to the expansion of the LEA gene family in maize. Some abiotic stress-responsive cis-elements were also found in the promoters of ZmLEA genes. Microarray expression analyses revealed different accumulation patterns of ZmLEA family members. Moreover, some members of ZmLEAs were regulated under IAA and some abiotic stresses. This study will provide comprehensive information for maize LEA gene family and may pave the way for deciphering their functions in further studies.     

Genome-wide analysis and expression profiling of the phospholipase D gene family in Gossypium arboreum

The plant phospholipase D(PLD)plays versatile functions in multiple aspects of plant growth,development,and stress responses.However,until now,our knowledge concerning the PLD gene family members and their expression patterns in cotton has been limited.In this study,we performed for the first time the genome-wide analysis and expression profiling of PLD gene family in Gossypium arboretum,and finally,a total of 19 non-redundant PLD genes(GaPLDs)were identified.Based on the phylogenetic analysis,they were divided into six well-supported clades(α,β/γ,δ,ε,ζ and φ).Most of the GaPLD genes within the same clade showed the similar exon-intron organization and highly conserved motif structures.Additionally,the chromosomal distribution pattern revealed that GaPLD genes were unevenly distributed across 10 of the 13 cotton chromosomes.Segmental duplication is the major contributor to the expansion of Ga PLD gene family and estimated to have occurred from19.61 to 20.44 million years ago when a recent large-scale genome duplication occurred in cotton.Moreover,the expression profiling provides the functional divergence of GaPLD genes in cotton and provides some new light on the molecular mechanisms of GaPLDα1 and GaPLDδ2 in fiber development.     

Genome-wide bioinformatics analysis of Dof transcription factor gene family of chickpea and its comparative phylogenetic assessment with Arabidopsis and rice

The genome mining of chickpea (Cicer arietinum L.) revealed a total of 37 putative Dof genes using NCBI BLAST search against the genome with a highly conserved Dof domain. The translated Dof proteins possessed 150–493 amino acid residues with molecular weight ranging from 16.9 to 54.4 kD and pI varied from 4.98 to 9.64 as revealed by ExPASy server ProtParam. The exon–intron organization showed predominance of intronless Dof genes in chickpea. The predicted Dof genes were distributed among the eight chromosomes with a maximum of 9 Dof genes present on chromosome 7 and a single Dof gene was found on chromosome 8.The predominance of segmental gene duplication as compared to tandem duplication was observed which might be the prime cause of Dof gene family expansion in chickpea. The cis-regulatory element analysis revealed the presence of light-responsive, hormone-responsive, endosperm-specific, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analyses of Dof genes of chickpea with Arabidopsis, rice, soybean and pigeonpea revealed several orthologs and paralogs assisting in understanding the putative functions of CaDof genes. The functional divergence and site-specific selective pressures of chickpea Dof genes have been investigated. The bioinformatics-based genome-wide assessment of Dof gene family of chickpea attempted in the present study could be a significant step for deciphering novel Dof genes based on genome-wide expression profiling.