[Show abstract][Hide abstract] ABSTRACT: Pleurochrysis is a coccolithophorid genus, which belongs to the Coccolithales in the Haptophyta. The genus has been used extensively for
biological research, together with Emiliania in the Isochrysidales, to understand distinctive features between the two coccolithophorid-including orders. However, molecular
biological research on Pleurochrysis such as elucidation of the molecular mechanism behind coccolith formation has not made great progress at least in part because
of lack of comprehensive gene information. To provide such information to the research community, we built an open web database,
the Pleurochrysome (http://bioinf.mind.meiji.ac.jp/phapt/), which currently stores 9,023 unique gene sequences (designated as UNIGENEs) assembled from expressed sequence tag sequences
of P. haptonemofera as core information. The UNIGENEs were annotated with gene sequences sharing significant homology, conserved domains, Gene
Ontology, KEGG Orthology, predicted subcellular localization, open reading frames and orthologous relationship with genes
of 10 other algal species, a cyanobacterium and the yeast Saccharomyces cerevisiae. This sequence and annotation information can be easily accessed via several search functions. Besides fundamental functions
such as BLAST and keyword searches, this database also offers search functions to explore orthologous genes in the 12 organisms
and to seek novel genes. The Pleurochrysome will promote molecular biological and phylogenetic research on coccolithophorids
and other haptophytes by helping scientists mine data from the primary transcriptome of P. haptonemofera.
Preview · Article · Jan 2016 · Plant and Cell Physiology
[Show abstract][Hide abstract] ABSTRACT: LjABCG1, a full-size ABCG subfamily of ATP-binding cassette proteins of a model legume, Lotus japonicus, was reported as a gene highly expressed during the early stages of nodulation, but have not been characterized in detail. In this study we showed that the induction of LjABCG1 expression was remarkable by methyl jasmonate treatment, and reporter gene experiments indicated that LjABCG1 was strongly expressed in the nodule parenchyma and cell layers adjacent to the root vascular tissue toward the nodule. LjABCG1 was suggested to be localized at the plasma membrane based on the fractionation of microsomal membranes as well as separation via aqueous two-phase partitioning. The physiological functions of LjABCG1 in symbiosis and pathogenesis were analyzed in homologous and heterologous systems. LjABCG1 knock-down L. japonicus plants did not show clear phenotypic differences in nodule formation, and not in defense against Pseudomonas syringae, either. In contrast, when LjABCG1 was expressed in the Arabidopsis pdr8-1 mutant, the penetration frequency of Phytophthora infestans, a potato late blight pathogen, was significantly reduced in LjABCG1/pdr8-1 than in pdr8-1 plants. This finding indicated that LjABCG1, at least partially, complemented the phenotype of pdr8 in Arabidopsis, suggesting the multiple roles of this protein in plant-microbe interactions.
[Show abstract][Hide abstract] ABSTRACT: We release a high-resolution map of genomic transformation-competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library, which consists of more than ten thousand TAC clones harboring large genomic DNA fragments extending over the whole genome of Arabidopsis. Here, we determined 13,577 end sequences from 6,987 Arabidopsis TAC clones and mapped 5,937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large-scale data set of TAC clones with high-resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready-to-go transformable genomic DNA clones corresponding to certain loci on the Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants, and DNA transformation for heterologous gene expression. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
No preview · Article · Jul 2015 · The Plant Journal
[Show abstract][Hide abstract] ABSTRACT: In Batesian mimicry, animals avoid predation by resembling distasteful models. In the swallowtail butterfly Papilio polytes, only mimetic-form females resemble the unpalatable butterfly Pachliopta aristolochiae. A recent report showed that a single gene, doublesex (dsx), controls this mimicry; however, the detailed molecular mechanisms remain unclear. Here we determined two whole-genome sequences of P. polytes and a related species, Papilio xuthus, identifying a single ∼130-kb autosomal inversion, including dsx, between mimetic (H-type) and non-mimetic (h-type) chromosomes in P. polytes. This inversion is associated with the mimicry-related locus H, as identified by linkage mapping. Knockdown experiments demonstrated that female-specific dsx isoforms expressed from the inverted H allele (dsx(H)) induce mimetic coloration patterns and simultaneously repress non-mimetic patterns. In contrast, dsx(h) does not alter mimetic patterns. We propose that dsx(H) switches the coloration of predetermined wing patterns and that female-limited polymorphism is tightly maintained by chromosomal inversion.
[Show abstract][Hide abstract] ABSTRACT: In leguminous root nodules, rhizobia differentiate into morphology specific to symbiosis, called bacteroids. As bacteroids are surrounded with peribacteroid membranes filled with peribacteroid solution (PBS), it is considered that PBS contains substances inducing differentiation of rhizobia into bacteroids. In this study, genome-wide expression profiles of Bradyrhizobium japonicum cells cultured in PBS purified from root nodule of soybean (Glycine max L.) were compared with those of bacteroids using macroarray. PBS treatment preferentially induced regions in a large symbiosis island including various symbiosis relevant genes such as nod, fix, nol and noe, in which 75% of regions were commonly induced in bacteroids, while general repressions outside of the symbiosis island seen in bacteroids were not observed in PBS treated cells. The present results suggest that PBS contained some, but not all, substances inducing expression of the genes which are involved in differentiation into bacteroids.
No preview · Article · Jan 2015 · Soil Science and Plant Nutrition
[Show abstract][Hide abstract] ABSTRACT: Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South
America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic
nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds
termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated
to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant
along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer
eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant
scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two
species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic
architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.
Preview · Article · Sep 2014 · DNA research: an international journal for rapid publication of reports on genes and genomes
[Show abstract][Hide abstract] ABSTRACT: To develop a high density linkage map in faba bean, a total of 1,363 FBES ( Faba bean
expressed sequence tag [EST] derived s
imple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs
developed in this study. A total of 109 plants of a ‘Nubaria 2’
‘Misr 3’ F
mapping population were used for
map construction. Because the parents were not pure homozygous lines, the 109 F
plants were divided into
three subpopulations according to the original F
plants. Linkage groups (LGs) generated in each subpopula
tion were integrated by commonly mapped markers. The integrated ‘Nubaria 2’
‘Misr 3’ map consisted of
six LGs, representing a total length of 684.7
cM, with 552 loci. Of the mapped loci, 47% were generated from
multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group re
vealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes,
. In a polymorphic analysis with ten Egyptian faba bean varieties,
78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense
map developed in this study is expected to accelerate marker assisted breeding in faba bean
[Show abstract][Hide abstract] ABSTRACT: In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.
[Show abstract][Hide abstract] ABSTRACT: The nuclear export of proteins is regulated largely through the exportin/CRM1 pathway, which involves the specific recognition of leucine-rich nuclear export signals (NESs) in the cargo proteins, and modulates nuclear-cytoplasmic protein shuttling by antagonizing the nuclear import activity mediated by importins and the nuclear import signal (NLS). Although the prediction of NESs can help to define proteins that undergo regulated nuclear export, current methods of predicting NESs, including computational tools and consensus-sequence-based searches, have limited accuracy, especially in terms of their specificity. We found that each residue within an NES largely contributes independently and additively to the entire nuclear export activity. We created activity-based profiles of all classes of NESs with a comprehensive mutational analysis in mammalian cells. The profiles highlight a number of specific activity-affecting residues not only at the conserved hydrophobic positions but also in the linker and flanking regions. We then developed a computational tool, NESmapper, to predict NESs by using profiles that had been further optimized by training and combining the amino acid properties of the NES-flanking regions. This tool successfully reduced the considerable number of false positives, and the overall prediction accuracy was higher than that of other methods, including NESsential and Wregex. This profile-based prediction strategy is a reliable way to identify functional protein motifs. NESmapper is available at http://sourceforge.net/projects/nesmapper.
[Show abstract][Hide abstract] ABSTRACT: In this study, the genes expressed in response to low pH stress were identified in the unicellular cyanobacterium Synechocystis sp. PCC 6803 using DNA microarrays. The expression of slr0967 and sll0939 constantly increased throughout 4-h acid stress conditions. Overexpression of these two genes under the control of the trc promoter induced the cells to become tolerant to acid stress. The Δslr0967 and Δsll0939 mutant cells exhibited sensitivity to osmotic and salt stress, whereas the trc mutants of these genes exhibited tolerance to these types of stress. Microarray analysis of the Δslr0967 mutant under acid stress conditions showed that expression of the high light-inducible protein ssr2595 (HliB) and the two-component response regulator slr1214 (rre15) were out of regulation due to gene inactivation, whereas they were upregulated by acid stress in the wild-type cells. Microarray analysis and real-time quantitative reverse transcription-polymerase chain reaction analysis showed that the expression of sll0939 was significantly repressed in the slr0967 deletion mutant. These results suggest that sll0939 is directly involved in the low pH tolerance of Synechocystis sp. PCC 6803 and that slr0967 may be essential for the induction of acid stress-responsive genes.
No preview · Article · Aug 2014 · Plant Physiology and Biochemistry
[Show abstract][Hide abstract] ABSTRACT: Genetic transformation systems using reporter genes in whole plants have a wide variety of applications for molecular biological study including the visualization of expression patterns of particular genes and intracellular biological phenomena as well as the identification of novel genes. In this study, we assessed co-expression of each three codon-optimized reporter genes and a selectable marker in the nuclear transformation system of whole Pyropia yezoensis, a red marine alga. With the use of an endogenous promoter, both the codon-optimized hygromycin resistance gene and ß-glucuronidase gene (PyGUS) were co-expressed in P. yezoensis cells. A high level of GUS activity was observed in 60 % of the individuals in hygromycin-resistant lines. A histochemical GUS assay revealed that the PyGUS reporter gene was stably introduced and expressed throughout the algae's life cycle. In addition, two live cell reporters, humanized cyan fluorescent protein from Anemonia majano and luciferase from Gaussia princeps, were successfully expressed in whole P. yezoensis. The development of this transformation system involving three types of reporter genes provides opportunities for monitoring temporal changes in gene expression and for genetic screening in red marine algae.
No preview · Article · Aug 2014 · Journal of Applied Phycology
[Show abstract][Hide abstract] ABSTRACT: Using a whole-genome-sequencing approach to explore germplasm resources can serve as an important strategy for crop improvement, especially in investigating wild accessions that may contain useful genetic resources that have been lost during the domestication process. Here we sequence and assemble a draft genome of wild soybean and construct a recombinant inbred population for genotyping-by-sequencing and phenotypic analyses to identify multiple QTLs relevant to traits of interest in agriculture. We use a combination of de novo sequencing data from this work and our previous germplasm re-sequencing data to identify a novel ion transporter gene, GmCHX1, and relate its sequence alterations to salt tolerance. Rapid gain-of-function tests show the protective effects of GmCHX1 towards salt stress. This combination of whole-genome de novo sequencing, high-density-marker QTL mapping by re-sequencing and functional analyses can serve as an effective strategy to unveil novel genomic information in wild soybean to facilitate crop improvement.
[Show abstract][Hide abstract] ABSTRACT: Single or double flower type is one of the most important breeding targets in carnation (Dianthus caryophyllus L.). We mapped the D
85 locus, which controls flower type, to LG 85P_15–2 using a simple sequence repeat (SSR)-based genetic linkage map constructed using 91 F2 progeny derived from a cross between line 85–11 (double flower) and ‘Pretty Favvare’ (single flower). A positional comparison using SSR markers as anchor loci revealed that the map positions of the D
85 locus corresponded to the single locus controlling the single flower type derived from wild D. capitatus ssp. andrzejowskianus. We identified four co-segregating SSR markers on the D
85 locus. Verification of the SSR markers in commercial cultivars revealed that two of the four SSR markers (CES0212 and CES1982) were tightly linked to the D
85 locus, and amplified a 176-bp and 269-bp allele, respectively, which were common and unique to double flower cultivars. The map positions of the D
85 locus and the tightly linked SSR markers will be useful for determining the genetic basis of flower type and for marker-assisted breeding of carnations.