MiRNA expression analysis during somatic embryogenesis in Coffea canephora

Plant Cell, Tissue and Organ Culture (PCTOC) - The diploid cotton species G. arboreum offers a better opportunity to elucidate gene structure and function as opposed to the allotetraploid cotton...     

The ankyrin repeat gene family in rice: genome-wide identification,classification and expression profiling

Ankyrin repeat (ANK) containing proteins comprise a large protein family. Although many members of this family have been implicated in plant growth, development and signal transduction, only a few ANK genes have been reported in rice. In this study, we analyzed the structures, phylogenetic relationship, genome localizations and expression profiles of 175 ankyrin repeat genes identified in rice (OsANK). Domain composition analysis suggested OsANK proteins can be classified into ten subfamilies. Chromosomal localizations of OsANK genes indicated nine segmental duplication events involving 17 genes and 65 OsANK genes were involved in tandem duplications. The expression profiles of 158 OsANK genes were analyzed in 24 tissues covering the whole life cycle of two rice genotypes, Minghui 63 and Zhenshan 97. Sixteen genes showed preferential expression in given tissues compared to all the other tissues in Minghui 63 and Zhenshan 97. Nine genes were preferentially expressed in stamen of 1 day before flowering, suggesting that these genes may play important roles in pollination and fertilization. Expression data of OsANK genes were also obtained with tissues of seedlings subjected to three phytohormone (NAA, GA3 and KT) and light/dark treatments. Eighteen genes showed differential expression with at least one phytohormone treatment while under light/dark treatments, 13 OsANK genes showed differential expression. Our data provided a very useful reference for cloning and functional analysis of members of this gene family in rice. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The analysis of differential gene expression in early somatic embryogenesis on Lycium barbarum

Direct exposure of calluses of Lycium barbarum L. to an auxin-free medium can induce somatic embryogenesis. Somatic embryogenesis of Lycium barbarum L. is controlled artificially by regulating 2,4-D concentration. The total RNA that was isolated from calluses, embryonic calluses and early somatic embryos was used for analyzing differential genes expression. We obtained three cDNAs from early somatic embryogenesis which were not found in calluses. The results indicate that these cDNAs were early embryogenesis-specific cDNAs and this gene expression was induced in cultured calluses after a transfer to an auxin- free medium. A cDNA library was constructed using poly(A)⁺-RNA derived from early somatic embryos of Lycium barbarism L. Two full-length cDNAs were isolated from the library by differential screening. Northern blot hybridization analysis indicated that the expression of the full-length cDNA only existed in embryogenic calluses and early somatic embryos of Lycium barbarum L. This revised version was published online in June 2006 with corrections to the Cover Date.     

The thioredoxin gene family in rice: genome-wide identification and expression profiling under different biotic and abiotic treatments

Thioredoxin (TRX) is a multi-functional redox protein. Genome-wide survey and expression profiles of different stresses were observed. Conserved amino acid residues and phylogeny construction using the OsTRX conserved domain sequence suggest that the TRX gene family can be classified broadly into six subfamilies in rice. We compared potential gene birth-and-death events in the OsTRX genes. The Ka/Ks ratio is a measure to explore the mechanism and 3 evolutionary stages of the OsTRX genes divergence after duplication. We used 270 TRX genes from monocots and eudicots for synteny analysis. Furthermore, we investigated expression profiles of this gene family under 5 biotic and 3 abiotic stresses. Several genes were differentially expressed with high levels of expression and exhibited subfunctionalization and neofunctionalization after the duplication event response to different stresses, which provides novel reference for the cloning of the most promising candidate genes from OsTRX gene family for further functional analysis.     

葡萄SAUR基因家族鉴定与生物信息学分析

为了研究葡萄早期应答生长素基因SAUR(Small auxin-up RNA)家族,本研究利用全基因组信息鉴定了葡萄64个SAUR家族成员,并对SAUR家族成员的基因结构、氨基酸特性、染色体定位、基因进化、基因功能以及组织表达进行分析。结果表明,葡萄全基因组上64个SAUR家族成员在19条染色体中的8条染色体上呈现簇状分布,主要分布在3、4号染色体上,其中3号染色体上数量最多为37个;葡萄SAUR家族基因长度较短,有59个基因是无内含子基因;蛋白理化特征分析显示,多数SAUR蛋白呈碱性,结构稳定性较差,蛋白脂溶指数高,呈亲水性;基因功能预测结果表明,葡萄SAUR基因主要担当生长因子、结构蛋白、转录、转录调控以及响应胁迫应答和免疫应答6种功能,其中更多参与生长调节功能;根据系统进化分析将其分为10个分支,另外不同组织表达谱的分析结果表明SAUR基因家族成员具有不同的组织表达模式,对于非生物胁迫具有一定的调节作用。这些信息为葡萄SAUR基因家族功能分析奠定了一定的工作基础。     

基因鉴定集成法:全基因组基因表达研究的新策略

人类基因组包含的核苷酸数目庞大,基因鉴定（识别）的技术策略是基因克隆研究至为重要的基础。在全基因组基因表达分析策略方面,已相继建立了ｍＲＮＡ差异显示、代表性差异分析、抑制性消减杂交、基因表达系列分析和ｃＤＮＡ微阵列等技术。基因鉴定集成法是新近在综合上述技术的优缺点的基础上建立的全基因组分析新策略,具有充分利用生物基因信息数据库进行基因鉴定（识别）,并能提高稀有拷贝基因鉴定效率的优点。本文简要介绍其     

The phenylalanine ammonia-lyase gene family in Salvia miltiorrhiza: genome-wide characterization, molecular cloning and expression analysis

Salvia miltiorrhiza Bunge is a well-known material of traditional Chinese medicine. Hydrophilic phenolic acids, such as rosmarinic acid and salvianolic acid B, are a group of pharmaceutically important compounds in S. miltiorrhiza. The biosynthesis of rosmarinic acid requires the coordination of the phenylpropanoid pathway and the tyrosine-derived pathway. Phenylalanine ammonia-lyase (PAL) is the first key enzyme of the phenylpropanoid pathway. Systematic analysis of the SmPAL gene family has not been carried out. We report here the identification of three SmPALs through searching the recently obtained working draft of the S. miltiorrhiza genome and full-length cDNA cloning. Bioinformatic and phylogenetic analyses showed that SmPAL1 and SmPAL3 clustered in a sub-clade of dicot PALs, whereas SmPAL2 fell into the other one. Some important cis-elements were conserved in three SmPAL promoters, whereas the others were not. SmPAL1 and SmPAL3 were highly expressed in roots and leaves of S. miltiorrhiza, but SmPAL2 were predominately expressed in stems and flowers. It indicates that SmPAL1 and SmPAL3 function redundantly in rosmarinic acid biosynthesis. All SmPALs were induced in roots treated with PEG and MeJA, but the time and degree of responses were different, suggesting the complexity of SmPAL-associated metabolic network in S. miltiorrhiza. This is the first comprehensive study dedicated to SmPAL gene family characterization. The results provide a basis for elucidating the role of SmPAL genes in the biosynthesis of bioactive compounds.     

AtLTP1 luciferase expression during carrot somatic embryogenesis

The carrot (Daucus carota L.) EP2 gene encodes a Lipid Transfer Protein (LTP) which is expressed during protoderm formation in developing embryos. To develop a vital reporter system for gene expression during somatic embryo development a 1.1 kB fragment of the Arabidopsis thaliana LTP1 promoter was fused to the firefly luciferase (LUC) coding sequence. The AtLTP1 luciferase expression pattern in transformed carrot suspension cultures was identical to the expression pattern of the endogenous carrot EP2 gene. Cell tracking experiments revealed that all somatic embryos were derived from AtLTP1 luciferase expressing cell clusters. However, not all cell clusters that expressed the AtLTP1 luciferase reporter gene developed into a somatic embryo, suggesting that initiation of an embryogenic pathway in tissue culture does not always lead to development of a somatic embryo.     

Isolation of the gene encoding Carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis.

The Arabidopsis thaliana LEC1 gene regulates embryo morphology and seed maturation. For a better understanding of its function, we isolated a carrot (Daucus carota L. cv. US-Harumakigosun) counterpart of this gene, C-LEC1, from a cDNA library of carrot somatic embryos, since carrot is a better model plant for preparing large quantities of somatic embryos at the same developmental stage. The predicted amino acid sequence of C-LEC1 is similar to that of LEC1 and contains regions that are conserved in the heme-activated protein 3 (HAP3) subunit of plants, animals and microorganisms. C-LEC1 expression was detected in embryogenic cells, somatic embryos, and developing seeds. In situ hybridization analysis revealed C-LEC1 expression in the peripheral region of the embryos but not in the endosperm. Expression of C-LEC1 driven by Arabidopsis LEC1 promoter was able to complement the defects of the Arabidopsis lec1-1 mutant. These results suggest that C-LEC1 is a functional homolog of Arabidopsis LEC1, an important regulator of zygotic and somatic embryo development.     

The phytocyanin gene family in rice (Oryza sativa L.): genome-wide identification, classification and transcriptional analysis

Background

Phytocyanins (PCs) are plant-specific blue copper proteins involved in electron transport, and a large number of known PCs are considered to be chimeric arabinogalactan proteins (AGPs). To date there has not been a genome-wide overview of the OsPC gene family. Therefore, as the first step and a useful strategy to elucidate the functions of OsPCs, there is an urgent need for a thorough genome-wide analysis of this gene family.

Methodology/Principal Findings

In this study, a total of 62 OsPC genes were identified through a comprehensive bioinformatics analysis of the rice (Oryza sativa L.) genome. Based on phylogeny and motif constitution, the family of OsPCs was classified into three subclasses: uclacyanin-like proteins (OsUCLs), stellacyanin-like proteins (OsSCLs) and early nodulin-like proteins (OsENODLs). Structure and glycosylation prediction indicated that 46 OsPCs were glycosylphosphatigylinositol-anchored proteins and 38 OsPCs were chimeric AGPs. Gene duplication analysis revealed that chromosomal segment and tandem duplications contributed almost equally to the expansion of this gene family, and duplication events were mostly happened in the OsUCL subfamily. The expression profiles of OsPC genes were analyzed at different stages of vegetative and reproductive development and under abiotic stresses. It revealed that a large number of OsPC genes were abundantly expressed in the various stages of development. Moreover, 17 genes were regulated under the treatments of abiotic stresses.

Conclusions/Significance

The genome-wide identification and expression analysis of OsPC genes should facilitate research in this gene family and give new insights toward elucidating their functions in higher plants.     

The effect of genotype and explant age on somatic embryogenesis of coffee

We demonstrate that embryogenic capacity of coffee (Coffea arabica) depends on the genotype, and that it is a character fixed at the early generations F3 or F4. Therefore, the embryogenic capacity F5 lines can be predicted in a breeding program if it is possible to evaluate the F3 of F4 ancestors, or lines with the same parents on those generations.Regeneration via somatic embryogenesis of genotypes from a C. arabica cv. Caturra by Timor Hybrid cross were evaluated, to determine the effect of the pedigree, month of leaf collection, as well as its interaction with the genotype. Large variations in embryogenic capacity among genotypes were detected with rates ranging from 4.8 to 72.7. There was association between embryogenic response of the progenies and the progenitor from which they proceeded. Significant differences were also found in embryogenic responses depending on the month of leaf explant collection, as well as a significant interaction of genotype by planting month.The results are relevant for breeding and tissue culture purposes of coffee because they will allow speed up of the breeding program and save effort by being able to predict embryogenic capacity of a line, based on the response of either its progenitors or the F3 or F4 lines of the same origin. In addition, high embryogenic capacity lines can be considered directly for genetic transformation or for massive multiplication (bioreactors).     

Developmentally regulated expression of the LRRTM gene family during mid-gestation mouse embryogenesis

We have analysed the expression during mid-gestation mouse development of the four member LRRTM gene family which encodes type 1 transmembrane proteins containing 10 extracellular leucine rich repeats and a short intracellular tail. Each family member has a developmentally regulated pattern of expression distinct from all other members. LRRTM1 is expressed in the neural tube, otic vesicle, apical ectodermal ridge, forebrain and midbrain up to a sharp central boundary. LRRTM2 is expressed in a subset of progenitors in the neural tube. LRRTM3 is expressed in a half somite wide stripe in the presomitic mesoderm adjacent to the boundary with the most recently formed somite. Additional expression is seen in the neural tube, forebrain and hindbrain. LRRTM4 is expressed in the limb mesenchyme, neural tube, caudal mesoderm and in three distinct regions of the head. Later expression occurs in a subset of the developing sclerotome. Each family member has a unique expression domain within the neural tube.     

Differential gene expression during somatic embryogenesis in Coffea arabica L., revealed by RT-PCR differential display

Molecular and biochemical studies of somatic embryogenesis may help to shed light on the mechanisms governing this phenomenon. In this article, a differential display analysis approach was employed to investigate the changes taking place during the induction of somatic embryogenesis in leaf explants and suspension cultures of coffee. Cloned fragments show homologies to several proteins reported in databases, but only one has previously been described as regulated during somatic embryogenesis. By a reverse dot blot modification, the expression pattern of such fragments was evaluated.