Correction to: Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

After publication of the original article [1] the authors noted that the following errors had occurred.

Generation of expressed sequence tags for discovery of genes responsible for floral traits of Chrysanthemum morifolium by next-generation sequencing technology.

BACKGROUND: Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits. RESULTS: To obtain useful information about molecular bases for floral traits of chrysanthemums, we read expressed sequence tags (ESTs) of chrysanthemums by high-throughput sequencing using the 454 pyrosequencing technology. We constructed normalized cDNA libraries, consisting of full-length, 3'-UTR, and 5'-UTR cDNAs derived from various tissues of chrysanthemums. These libraries produced a total number of 3,772,677 high-quality reads, which were assembled into 213,204 contigs. By comparing the data obtained with those of full genome-sequenced species, we confirmed that our chrysanthemum contig set contained the majority of all expressed genes, which was sufficient for further molecular analysis in chrysanthemums. CONCLUSION: We confirmed that our chrysanthemum EST set (contigs) contained a number of contigs that encoded transcription factors and enzymes involved in pigment and aroma compound metabolism that was comparable to that of other species. This information can serve as an informative resource for identifying genes involved in various biological processes in chrysanthemums. Moreover, the findings of our study will contribute to a better understanding of the floral characteristics of chrysanthemums including the myriad cultivars at the molecular level.

Rice ubiquitin ligase EL5 prevents root meristematic cell death under high nitrogen conditions and interacts with a cytosolic GAPDH.

Root formation in rice transformants overexpressing mutated EL5 (mEL5) was severely inhibited because of meristematic cell death. Cell death was caused by nitrogen sources, particularly nitrate forms, in the culture medium. Nitrite treatment increased the cytokinin contents in roots, but mEL5 contained more cytokinins than non-transformants. Transcriptome profiling showed overlaps between nitrite-responsive genes in non-transformants and genes with altered expression in untreated mEL5. These results indicate that impairment of EL5 function activates nitrogen signaling despite the absence of a nitrogen source. Physical interaction between the EL5 C-terminal region and a cytosolic glyceraldehyde-3-phosphate dehydrogenase, OsGapC2, was demonstrated in vitro and in vivo. Elucidation of the role of glyceraldehyde-3-phosphate dehydrogenase in oxidative cell death in plants is expected in future.

Sequence analysis of the genome of carnation (Dianthus caryophyllus L.).

The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. 'Francesco' was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568,887,315 bp, consisting of 45,088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16,644 bp and 60,737 bp, respectively, and the longest scaffold was 1,287,144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼ 98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp.

Enhancement of MAMP signaling by chimeric receptors improves disease resistance in plants.

Plants activate defense responses through the recognition of microbe-associated molecular patterns (MAMPs). Recently, several pattern-recognition receptors (PRRs) have been identified in plants, paving the way for manipulating MAMP signaling. CEBiP is a receptor for the chitin elicitor (CE) identified in the rice plasma membrane and XA21 is a member of the receptor-like protein kinase (RLK) family that confers disease resistance to rice bacterial leaf blight expressing the sulfated protein Ax21. To improve resistance to rice blast, the most serious fungal disease of rice, we aimed to create a defense system that combines high affinity of CEBiP for CE and the ability of XA21 to confer disease resistance. Cultured rice cells expressing the chimeric receptor CRXA, which consists of CEBiP and the intracellular region of XA21, induced cell death accompanied by an increased production of reactive oxygen and nitrogen species after exposure to CE. Rice plants expressing the chimeric receptor exhibited more resistance to rice blast. Engineering PRRs may be a new strategy in molecular breeding for achieving disease resistance.

Perception of the chitin oligosaccharides contributes to disease resistance to blast fungus Magnaporthe oryzae in rice.

Chitin is a component of fungal cell walls, and its fragments act as elicitors in many plants. The plasma membrane glycoprotein CEBiP, which possesses LysM domains, is a receptor for the chitin elicitor (CE) in rice. Here, we report that the perception of CE by CEBiP contributes to disease resistance against the rice blast fungus, Magnaporthe oryzae, and that enhanced responses to CE by engineering CEBiP increase disease tolerance. Knockdown of CEBiP expression allowed increased spread of the infection hyphae. To enhance defense responses to CE, we constructed chimeric genes composed of CEBiP and Xa21, which mediate resistance to rice bacterial leaf blight. The expression of either CRXa1 or CRXa3, each of which contains the whole extracellular portion of CEBiP, the whole intracellular domain of XA21, and the transmembrane domain from either CEBiP or XA21, induced cell death accompanied by an increased production of reactive oxygen and nitrogen species after treatment with CE. Rice plants expressing the chimeric receptor exhibited necrotic lesions in response to CE and became more resistant to M. oryzae. Deletion of the first LysM domain in CRXA1 abolished these cellular responses. These results suggest that CEs are produced and recognized through the LysM domain of CEBiP during the interaction between rice and M. oryzae and imply that engineering pattern recognition receptors represents a new strategy for crop protection against fungal diseases.

Direct fungicidal activities of C6-aldehydes are important constituents for defense responses in Arabidopsis against Botrytis cinerea.

C6-aldehydes, such as (Z)-3-hexenal, (E)-2-hexenal, and n-hexanal, are volatile compounds formed by hydroperoxide lyase (HPL) and found in most terrestrial plants. They are fungicidal and bactericidal compounds, and are also signaling compounds to induce defense responses in plants. Transgenic plants having overexpressed or suppressed HPL activity (SH or ASH, respectively) showed lower or higher susceptibility against a necrotrophic fungal pathogen, Botrytis cinerea. In this study, we examined whether the modulated susceptibility was accountable to the direct fungicidal activity or to the signaling potency of C6-aldehydes. When wild-type Arabidopsis leaves were inoculated with B. cinerea, HPL expression was upregulated, and concomitantly, the amounts of C6-aldehydes increased. Higher amounts of C6-aldehydes found in inoculated SH plants inhibited growth of B. cinerea in vitro, while lower amounts found in ASH plants caused no inhibitory effect on the fungi. Thus, it was suggested that direct fungicidal activity of C6-aldehydes accounted for the modulated susceptibility. With SH plants higher amounts of camalexin could be found, but with the ASH plants no difference from wild-type plants could be found. Surplus amounts of C6-aldehydes could induce formation of camalexin as signaling compounds; however, this was not the case with wild-type and ASH plants. Accordingly, it could be assumed that direct fungicidal activity of C6-aldehydes were prominently responsible to the defense against B. cinerea but their signaling roles could be little responsible if any.

Changing green leaf volatile biosynthesis in plants: an approach for improving plant resistance against both herbivores and pathogens.

Green leaf volatiles (GLVs) are commonly emitted by green plants, and their production is drastically enhanced when they are under biotic stress. To clarify the ecological function of naturally emitted GLVs, we studied the response of Arabidopsis, whose GLV biosynthesis had been modified, when subjected to herbivory or a pathogenic infection. There was a significant increase in GLV production after herbivory by cabbage white butterfly larvae and pathogen (gray mold) infection in hydroperoxide lyase (HPL) sense Arabidopsis compared with WT controls. The HPL sense modification resulted in the plant being more attractive to the parasitic wasp Cotesia glomerata, leading to higher mortality of the herbivores. The HPL sense modification also resulted in greater inhibition of growth of the fungus. By contrast, HPL antisense Arabidopsis produced fewer GLVs, attracted fewer parasitoids, and was more susceptible to the pathogens than the WT control. These data show that (i) one of the ecological functions of GLV biosynthesis related to resistance against both herbivores and pathogens, and (ii) the genetic modification of GLV biosynthesis could be a unique approach for improving plant resistance against such biotic stresses.

Analysis of defensive responses activated by volatile allo-ocimene treatment in Arabidopsis thaliana.

Since volatile allo-ocimene enhances resistance of Arabidopsis thaliana against Botrytis cinerea, we attempted to dissect the factors involved in this induced resistance. The penetration of B. cinerea hyphae into Arabidopsis epidermis and the growth of hyphae after penetration were suppressed on allo-ocimene-treated leaves. allo-Ocimene also induced lignification on cell walls and veins of the leaves. The treatment induced accumulation of antifungal substances including the Arabidopsis phytoalexin, camalexin. Induction of lignification and accumulation of camalexin elicited by B. cinerea infection on Arabidopsis leaves after treating with allo-ocimene was faster and more intense than that observed with the leaves that had not been treated with this volatile. This suggested that allo-ocimene could prime defensive responses in Arabidopsis. allo-Ocimene enhanced resistance against B. cinerea in an ethylene resistant mutant (etr1-1), a jasmonic acid resistant mutant (jar1-1) and a salicylic acid resistant mutant (npr1-1). Thus, it is suggested that a signaling pathway independent for ETR1, JAR1 and NPR1 was operative to induce the resistance. The series of responses observed after allo-ocimene-treatment was mostly similar to that observed after C6-aldehyde-treatment. The effect of C6-aldehyde-treatment has been largely accounted to the chemical reactivities of the compounds; however, from this result it can be suggested that resistance responses of Arabidopsis could be induced by the volatiles mostly independent on their reactivities and that a common signaling pathway unaffected by the reactivities of compound was activated by the volatiles.

Role of the lipoxygenase/lyase pathway of host-food plants in the host searching behavior of two parasitoid species, Cotesia glomerata and Cotesia plutellae.

To elucidate the role of the plant lipoxygenase (LOX)/lyase pathway for host search behavior of two parasitic wasps attacking herbivorous larvae, an Arabidopsis mutant (all84) was isolated with a mutation somewhere in the LOX/lyase pathway. Detached leaves of the mutant were shown to release less (Z)-3-hexenal, a first green leaf volatile (GLV) product of the LOX/lyase pathway. The braconid larval parasitoids studied, Cotesia glomerata and Cotesia plutella, differ in their ability to discriminate among plant volatiles induced by feeding of lepidopteran hosts and nonhosts: C. plutella only responds to plant volatiles induced by hosts (Plutella larvae), whereas the response by the more generalist C. glomerata is not host specific. The Arabidopsis mutant all84 infested by Pieris larvae was less attractive to C. glomerata than Arabidopsis wild type (wt) infested by the host larvae. C. glomerata was attracted by two of the GLV biosynthesized through the LOX/lyase pathway, (E)-2-hexenal and (Z)-3-hexenyl acetate. However, attraction of C. plutellae to volatiles from Plutella-infested all84 plants did not differ from attraction to host-infested wt Arabidopsis. Both wasp species were arrested to the respective host-infested edge of the wt leaf by showing characteristic antennal searching behavior on the edge. In C. glomerata, the duration of this searching behavior at the infested leaf edge was significantly shorter on all84 plants than on wt plants. By contrast, the duration of the searching behavior of C. plutellae on the host-infested leaf edge of all84 was not significantly different from that on the wt leaf. These data suggest that the LOX/lyase pathway is directly involved in the production of attractants and arrestants important for host search behavior of the more generalist C. glomerata, but not for the specialist C. plutellae.

Biosynthesis of fatty acid derived aldehydes is induced upon mechanical wounding and its products show fungicidal activities in cucumber.

Fatty acid 9/13-hydroperoxide lyase (9/13-HPL) in cucumber is an enzyme that can cleave either 9- or 13-hydroperoxides of polyunsaturated fatty acids to form C9- or C6-aldehydes, respectively, as products. In order to reveal the physiological function of 9/13-HPL, its expression profiles were analyzed, and it was found that 9/13-HPL expression was developmentally regulated and high in the hypocotyls, female flowers and mature fruits. However, its transcript as well as its activity was only induced by mechanical wounding in mature leaves. To analyze the biosynthesis of HPL-derived aldehydes in more detail we isolated and characterized the yet missing 9-lipoxygenase (LOX) that is mainly expressed in hypocotyls, cotyledons and flowers and that may provide HPL with fatty acid 9-hydroperoxides as substrates. As in the case with C6-aldehydes in most plant species, C9-aldehydes were also formed rapidly after disruption of the tissues. C9-aldehydes had fungicidal activities against fungal pathogens, Botrytis cinerea and Fusarium oxysporum. Because the concentration needed to cause toxic effect on the pathogens was almost equivalent to that found in disrupted tissues, the C9-aldehydes thus formed could be helpful to sterilize the wounds since they are less volatile in comparison to C6-aldehydes.

ETR1-, JAR1- and PAD2-dependent signaling pathways are involved in C6-aldehyde-induced defense responses of Arabidopsis.

C6-aldehydes [(E)-2-hexenal and (Z)-3-hexenal] induce expression of defense genes, accumulation of antifungal substances, and resistance against Botrytis cinerea with Arabidopsis. In order to elucidate the signaling pathway mediating the defense responses induced by C6-aldehydes in Arabidopsis, we compared the responses of Arabidopsis mutants deficient in the signaling pathways; i.e., etr1-1 (ethylene resistant), jar1-1 (jasmonate resistant), npr1-1 (salicylic acid insensitive), or pad2-1 (phytoalexin-deficient) with those of wild type (WT) plants. Induction of some, but not all of the defense genes in response to C6-aldehydes was significantly repressed in jar1-1, etr1-1, and pad2-1, but not at all in npr1-1. C6-aldehyde-treatment enhanced accumulation of camalexin with WT and npr1-1, but only partially with etr1-1 and jar1-1. pad2-1 showed little accumulation of camalexin. npr1-1 accumulated the antifungal substances as WT did, however, etr1-1, jar1-1 and pad2-1 exhibited only partial accumulation. The treatment enhanced resistance of etr1-1, jar1-1 and npr1-1 against B. cinerea, but failed to enhance the resistance of pad2-1. Taken together, it was suggested that ETR1-, JAR1-, and PAD2-dependent signaling pathways were simultaneously activated by C6-aldehyde-treatment. Among these, PAD2-dependent signaling appeared to be most important. In contrast, involvement of NPR1-dependent signaling was minimal.

Volatile C6-aldehydes and Allo-ocimene activate defense genes and induce resistance against Botrytis cinerea in Arabidopsis thaliana.

Green leafy volatiles or isoprenoids are produced after mechanical wounding or pathogen/herbivore attacks in higher plants. We monitored expression profiles of the genes involved in defense responses upon exposing Arabidopsis thaliana to the volatiles. Among the genes investigated, those known to be induced by mechanical wounding and/or jasmonate application, such as chalcone synthase (CHS), caffeic acid-O-methyltransferase (COMT), diacylglycerol kinase1 (DGK1), glutathione-S-transferase1 (GST1) and lipoxygenase2 (LOX2), were shown to be induced with (E)-2-hexenal, (Z)-3-hexenal, (Z)-3-hexenol or allo-ocimene (2,6-dimethyl-2,4,6-octatriene). A salicylic acid-responsive gene, pathogenesis-related protein2 (PR2), was not induced by the volatiles. Detailed analyses of the expression profiles showed that the manner of induction varied depending on either the gene monitored or the volatile used. A chemically inert compound, (Z)-3-hexenol, was also potent, which suggested that chemical reactivity was not the sole requisite for the inducing activity. With a jasmonate-insensitive mutant (jar1), the induction by the volatiles was mostly suppressed, however, that of LOX2 was unaltered. An ethylene-insensitive mutant (etr1) showed responses almost identical to the wild type, with minor exceptions. From these observations, it was suggested that both the jasmonate-dependent and -independent pathways were operative upon perception of the volatiles, while the ETR1-dependent pathway was not directly involved. When Botrytis cinerea was inoculated after the volatile treatment, retardation of disease development could be seen. It appears that volatile treatment could make the plants more resistant against the fungal disease.