Identification of rice TUBBY-like genes and their evolution

The identification of TUBBY-like genes in organisms ranging from single-celled to multicellular eukaryotes has allowed the phylogenetic history of this gene family to be traced back to the early evolutionary stages of eukaryote development. Rice TUBBY-like genes were located on chromosomes 1, 2, 3, 4, 5, 7, 8, 11 and 12 without any obvious clustering. On a genomic scale, it was revealed that the rice TUBBY-like gene family probably evolved mainly through segmental duplication produced by polyploidy. The altered selective constraints (or site-specific rate changes), related to functional divergence during protein evolution between plant and animal TUBBY-like genes, were statistically significant. Based on posterior probability analysis, five amino acid sites (103, 312, 315, 317 and 319) are thought to be responsible for functional divergence.     

Identification and expression analysis of hypoxia stress inducible CCCH-type zinc finger protein genes in rice

Flooding is one of the threatening abiotic stresses in recent global warming. In order to understand flooding-caused low oxygen stress response at molecular level, microarray-linked isolation of the hypoxia inducible genes were conducted. Seventeen genes that were up-regulated by the factor of more than 3 fold, were confirmed as hypoxia inducible. Among them, a CCCH-type zinc finger protein gene, OsCCCH-Zn-1, was further characterized due to its novelty as a hypoxia-inducible zinc finger gene as well as its significant induction by hypoxia stress. OsCCCH-Zn-1 was also up-regulated by submergence, ABA and drought stresses. In the normal growth condition, OsCCCH-Zn-1 was expressed in the flag leaf sheath, highest internode and developing seeds. In rice, at least 12 CCCH-type zinc finger protein genes were retrieved by in silico analysis. Among these, we found that the zinc finger genes OsCCCH-Zn-1, -2, -6 were induced by hypoxia stress.     

Genome-wide identification and expression analysis of rice cell cycle genes

Cyclins, cyclin-dependent kinases, and a number of other proteins control the progression of plant cell cycle. Although extensive studies have revealed the roles of some cell cycle regulators and the underlying mechanisms in Arabidopsis, relatively a small number of cell cycle regulators were functionally analyzed in rice. In this study, we describe 41 regulators in the rice genome. Our results indicate that the rice genome contains a less number of the core cell cycle regulators than the Arabidopsis one does, although the rice genome is much larger than the Arabidopsis one. Eight groups of CDKs similar to those in Arabidopsis were identified in the rice genome through phylogenetic analysis, and the corresponding members in the different groups include E2F, CKI, Rb, CKS and Wee. The structures of the core cell regulators were relatively conserved between the rice and Arabidopsis genomes. Furthermore, the expression of the majority of the core cell cycle genes was spatially regulated, and the most closely related ones showed very similar patterns of expression, suggesting functional redundancy and conservation between the highly similar core cell cycle genes in rice and Arabidopsis. Following auxin or cytokinin treatment, the expression of the core cell cycle genes was either upregulated or downregulated, suggesting that auxin and/or cytokinin may directly regulate the expression of the core cell cycle genes. Our results provide basic information to understand the mechanism of cell cycle regulation and the functions of the rice cell cycle genes. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Jing Guo and Jian Song have contributed equally.     

Effect of hydropriming on germination and aquaporin gene expression in rice

Plant Growth Regulation - Water uptake, modulated by aquaporins, is closely correlated with germination. This study aimed to evaluate the roles of aquaporins during germination by comparing the...     

丽蝇蛹集金小蜂几丁质酶基因鉴定与表达分析

几丁质酶是降解几丁质的糖苷水解酶,参与昆虫蜕皮、器官发育、免疫等重要生理过程。目前,寄生蜂等膜翅目昆虫中几丁质酶的鉴定以及功能研究仍较少。本研究基于生物信息学分析,在丽蝇蛹集金小蜂Nasonia vitripennis基因组中鉴定到14个几丁质酶基因,氨基酸个数介于312~2 682之间。系统进化分析表明丽蝇蛹集金小蜂几丁质酶分为9个亚家族,其中Group Ⅳ、Ⅶ亚家族可能通过基因串联复制而发生基因家族扩增。qRT-PCR分析结果表明几丁质酶基因的表达具有多样性,其中NvCht1、NvCht5、NvCht6、NvCht7 4个基因在1.5 d幼虫表达量最高,NvCht3在5 d幼虫表达量最高,NvCht8在幼虫期高表达。此外,幼虫组织中的表达分析结果表明NvCht4、NvCht5、NvCht10、NvCht12在表皮中高表达,NvCht7、NvCht8、NvCht13在肠道中高表达,NvCht9在脂肪体和表皮中高表达,NvCht11在唾液腺中高表达。本研究为寄生蜂几丁质酶的进化分析以及功能研究提供理论基础。     

Identification and expression analysis of mical family genes in zebrafish

Mical(molecule interacting with CasL)represent a conserved family of cytosolic multidomain proteins that has been shown to be associated with a variety of cellular processes,including axon guidance,cell movement,cell-cell junction formation,vesicle trafficking and cancer cell metastasis.However,the expression and function of these genes during embryonic development have not been comprehensively characterized,especially in vertebrate species,although some limited in vivo studies have been carried out in neural and musculature systems of Drosophila and in neural systems of vertebrates.So far,no mica/family homologs have been reported in zebrafish,an ideal vertebrate model for the study of developmental processes.Here we report eight homologs of m/ca/family genes in zebrafish and their expression profiles during embryonic development.Consistent with the findings in Drosophila and mammals,most zebrafish mical family genes display expression in neural and musculature systems.In addition,five mica/homologs are detected in heart,and one,micall2a,in blood vessels.Our data established an important basis for further functional studies of mica/family genes in zebrafish,and suggest a possible role for mica/genes in cardiovascular development.     

Identification and functional analysis of light-responsive unique genes and gene family members in rice

Functional redundancy limits detailed analysis of genes in many organisms. Here, we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants. Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue, we identified 365 genes that showed significant 8-fold or greater induction in the light relative to dark conditions. We then screened collections of rice T-DNA insertional mutants to identify rice lines with mutations in the strongly light-induced genes. From this analysis, we identified 74 different lines comprising two independent mutant lines for each of 37 light-induced genes. This list was further refined by mining gene expression data to exclude genes that had potential functional redundancy due to co-expressed family members (12 genes) and genes that had inconsistent light responses across other publicly available microarray datasets (five genes). We next characterized the phenotypes of rice lines carrying mutations in ten of the remaining candidate genes and then carried out co-expression analysis associated with these genes. This analysis effectively provided candidate functions for two genes of previously unknown function and for one gene not directly linked to the tested biochemical pathways. These data demonstrate the efficiency of combining gene family-based expression profiles with analyses of insertional mutants to identify novel genes and their functions, even among members of multi-gene families.     

Identification of rice genes induced in a rice blast-resistant mutant

To clarify mechanisms of rice blast resistance in rice plants we used suppression subtractive hybridization (SSH) to isolate genes induced upon rice blast inoculation in a rice blast-resistant mutant. A total of 26 rice cDNAs were isolated and found to have elevated expression upon rice blast infection in a rice blast-resistant derivative, SHM-11, of the rice cultivar, Sanghaehyanghyella. Sequencing of the cDNAs revealed that many of the proteins they encoded had been previously described as involved in plant responses against pathogen attack. Two interesting groups of the defense-related proteins consisted of three different PR5 homologues and four different protease inhibitors, all highly expressed in the rice blast mutant. Genes encoding proteins involved in signal transduction and regulation were also identified, including translation initiation factor eIF5A, C2 domain DNA binding protein, putative rice EDS and putative receptor like kinase. Most of the identified cDNAs were highly expressed 24 h after blast inoculation. Our results suggest that a pathway regulating defense gene expression may be altered in the mutant, resulting in early induction of the defense genes upon fungal infection.     

Identification,characterization and expression analysis of lineage-specific genes within Triticeae

Lineage-specific genes (LSGs) are a set of genes in a given taxon without significant sequence similarity to genes and intergenic sequences of other taxa and are functional. The tribe Triticeae mainly includes species of different ploidy levels, such as staple food crops wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.). This study is aimed at mining and characterizing the Triticeae-specific genes (TSGs) using expressed sequence data of wheat. A total of 3812 TSGs was identified and they were generally characterized by smaller size, fewer exons, shorter open reading frames and lower expression levels. Most TSGs were expressed with tissue preference and many of them were predominantly expressed in reproduction related tissues, especially in young stamen. Nearly one third of the TSGs were stress-responsive and inducible under abiotic and/or biotic stresses. A co-expression-based annotation supported the relevance of some TSGs with reproduction and stress responses, indicating their potential economic importance.     

Identification and expression analysis of genes associated with bovine blastocyst formation

Background  

Normal preimplantation embryo development encompasses a series of events including first cleavage division, activation of the embryonic genome, compaction and blastocyst formation.     

Identification of the Weevil immune genes and their expression in the bacteriome tissue

Background  

Persistent infections with mutualistic intracellular bacteria (endosymbionts) are well represented in insects and are considered to be a driving force in evolution. However, while pathogenic relationships have been well studied over the last decades very little is known about the recognition of the endosymbionts by the host immune system and the mechanism that limits their infection to the bacteria-bearing host tissue (the bacteriome).