Genome-wide Analysis of Glucose-6-phosphate Dehydrogenase(G6PDH) and Its Evolution in Eucalyptus grandsis

[Objective] The aim of this study was to perform genome-wide analysis of glucose-6-phosphate dehydrogenase（G6PDH） and reveal its evolution in Eucalyptus grandsis.[Method] The gene character,protein sequence and phylogenetic tree of G6PDH gene were analyzed by BLAST and other bioinformatics software within Eucalyptus grandsis whole genome database.[Result] Six G6PDH genes,including one cytomic type and five plastids,were detected in the E.grandsis genome.All the G6PDHs have conserved motifs of motif 1,motif 2,motif 3,motif 7,motif 9 and motif 11.Furthermore,promoter sequences of all E.grandsis G6PDH contain TATA box,enhancer,light-responsive,hormone-responsive and stress-responsive regulatory elements.[Conclusion] This study provided reference for the further revealing molecular function of E.grandsis G6PDH gene family

Identification and Comparative Analysis of DGAT1 Genes among Cotton and Other Model Plants

Diacylglycerol acyltransferase （DGAT） is the key enzyme that catalyzes the triacylglycerol biosynthesis. The comparative analysis was performed on the DGAT1 genes of cotton and other model plants. Sequence analysis showed that most of the DGAT1 genes,with high variation of intron length and high conservation of intron phrase,from the cotton and other model plants had 16 exons. Additionally, 7 conserved motifs were present in these DGAT1 proteins. The core motifs were overlapped with the functional domain of DGAT1 protein. Phylogenetic analysis demonstrated that gene tree was highly consistent to species tree,suggesting that the evolutionary history of species was revealed by gene tree. There was single copy of DGAT1 gene in cotton,but at least two duplicated DGAT1 genes were iden- tified in rice,maize,poplar and moss genomes. The selective pressure analysis showed that the PtDGATla/PtDGATlb was under positive selection,but other four pairs of homologous genes were under negative selection. 17 positively selected sites were identified at subgroup level （P〉0.05）,suggesting these subgroups under relaxed functional constraint. The findings provide a basis for further studying func- tion and evolution of DGAT1 genes in cotton and other model plants.

Functional structure analysis and genome‑wide identification of CNX gene family in cotton

Background:Under abiotic stress conditions,cotton growth is inhibited and yield losses are severe.Identification of calnexin family members and function analysis under abiotic stress laid the foundation for the screening of stressrelated candidate genes.Results:A total of 60 CNX family members have been identified in Gossypium hirsutum,G.barbadense,G.arboreum,and G.raimondii,and they were divided into two categories:CNX and CRT genes.Through the construction of a phylogenetic tree,they were subdivided into three classes.Further analysis of chromosome localization,conserved promoters,gene structure and selection under pressure showed that the family members were highly conserved in the evolution process.Analysis of cis-acting elements in the promoter regions showed that CNX family genes contain regulatory elements for growth and development,anaerobic,drought,defense and stress response,and plant hormones.Using RNA-seq data to study the expression pattern of GhCNX genes under cold,hot,salt stress and Polyethylene glycol,it was observed that the gene expression levels changed by different degrees under different stress conditions,indicating that GhCNX members were involved in the regulation of multiple biological stresses.Conclusion:This study provides an insight into the members of cotton CNX genes.The results of this study suggested that CNX family members play a role in defense against adversity and provide a foundation for the discovery of stress-related genes.

The discovery of archaea origin phosphomannomutase in algae based on the algal transcriptome

Phosphomannomutase （PMM;EC 5.4.2.8） is an enzyme that catalyzes the interconversion reaction between mannose-6-phosphate and mannose-1-phosphate. However, its systematic molecular and functional in-vestigations in algae have not hitherto been reported. In this work, with the accomplishment of the 1 000 Plant Project （OneKP） in which more than 218 species of Chromista, including 19 marine phaeophytes, 22 marine rhodophytes, 171 chlorophytes, 5 cryptophytes, 4 haptophytes, and 5 glaucophytes were sequenced, we used a gene analysis method to analyze the PMM gene sequences in algae and confirm the existence of the PMM gene in the transcriptomic sequencing data of Rhodophyta and Ochrophyta. Our results showed that only one type of PMM with four conserved motifs exists in Chromista which is similar to human PMM. Moreover, the phylogenetic tree revealed that algae PMM possibly originated from archaea.

Computational identification and systematic classification of novel GRAS genes in Isatis indigotica

Isatis indigotica Fort., belonging to Cruciferae, is one of the most commonly used plants in traditional Chinese medicine. The accumulation of the effective components of I. indigotica is related with its growth conditions. The GRAS genes are members of a multigene family of transcriptional regulators that play a crucial role in plant growth. Although the activities of many GRAS genes have long been recognized, only in recent years were some of them identified and functionally characterized in detail. In the present study, 41 GRAS genes were identified from 1. indigotica through bioinformatics methods for the first time. They were classified into ten groups according to the classification of Arabidopsis and rice. The characterization, gene structure, conserved motifs, disordered N-terminal domains, and phylogenetic reconstruction of these GRASs were analyzed. Forty-three orthologous gene pairs were shared by I. indigotica and Arabidopsis, and interaction networks of these orthologous genes were constructed. Furthermore, gene expression patterns were investigated by analysis in methyl jasmonate （MeJA）-treated I. indigotica hairy roots based on RNA-seq data. In conclusion, this comprehensive analysis would provide rich resources for further studies of GRAS protein functions in this plant.