Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics

<p>Abstract</p> <p>Background</p> <p>The Solanaceae family includes several economically important vegetable crops. The tomato (<it>Solanum lycopersicum</it>) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance.</p> <p>Results</p> <p>To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%.</p> <p>Conclusion</p> <p>The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom <url>http://www.pgb.kazusa.or.jp/kaftom/</url> via the website of the National Bioresource Project Tomato <url>http://tomato.nbrp.jp</url>.</p

ペピーノ（Solanum muricatum Aiton）ヲ ダイギ ニ モチイタ トマト ノ アオガレビョウ オヨビ トマトイチョウビョウ ノ ハツビョウ ヨクセイ コウカ

ペピーノを台木に用いたトマトの青枯病および萎凋病に対する発病抑制効果を検討した。青枯病Ⅰ～Ⅴ群菌にそれぞれ属する15菌株を接種したところ，ペピーノ‘ゴールドNo.1’およびペピーノ台接ぎ木トマト（‘大型福寿’/‘ゴールドNo.1’）では，外部病徴および導管褐変は認められなかった。トマト萎凋病レース1，2および3の菌株を接種したところ，ペピーノ‘ゴールドNo.1’およびペピーノ台接ぎ木トマト（‘大型福寿’/‘ゴールドNo.1’）では，外部病徴および導管褐変は認められなかった。以上，ペピーノ‘ゴールドNo.1’をトマトの台木として用いることで，青枯病およびトマト萎凋病に対する発病抑制効果が期待できる。Bacterial wilt caused by Ralstonia solanacearum and fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici induce damage during the production of tomato. In this study, we investigated the control effect of these diseases by using pepino (Solanum muricatum Aiton) as a rootstock. In inoculation test of R. solanacearum of bacterial groupⅠ-Ⅴ and F. oxysporum f. sp. lycopersici races 1-3, own-rooted tomato ‘Ogata-fukuju’ was highly susceptible to all of the strains, whereas own-rooted pepino ‘Gold No.1’ and tomato ‘Ogatafukuju’ grafted on pepino ‘Gold No.1’ were completely resistant to all of the strains. Our results indicate that pepino ‘Gold No.1’ is resistant to the R. solanacearum bacterial groups and F. oxysporum f. sp. lycopersici races 1-3, and application of pepino as a rootstock can be an effective method for control of bacterial wilt and wilt diseases

Resistant and Susceptible Responses in Tomato to Cyst Nematode are Differentially Regulated by Salicylic Acid

To understand the machinery underlying a tomato cultivar harboring the Hero A gene against cyst nematode using microarrays, we first analyzed tomato gene expression in response to potato cyst nematode (PCN; Globodera rostochiensis) during the early incompatible and compatible interactions at 3 and 7 days postinoculation (dpi). Transcript levels of the phenylalanine ammonia lyase (PAL) and Myb-related genes were upregulated at 3 dpi in the incompatible interaction. Transcription of the genes encoding pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) was also upregulated at 3dpi in the incompatible interaction. On the other hand, the four genes (PAL, Myb, PDC and ADH) were downregulated in the compatible interaction at 3 dpi. When the expression levels of several pathogenesis-related (PR) protein genes in tomato roots were compared between the incompatible and compatible interactions, the SA-dependent PR genes were found to be induced in the incompatible interaction at 3 dpi. The PR-1(P4) transcript increased to an exceptionally high level at 3 dpi in the cyst nematode-infected resistant plants compared to the uninoculated controls. The free SA levels were elevated to similar levels in both incompatible and compatible interactions. We then confirmed that PR-1(P4) was not significantly induced in the NahG tomato harboring the Hero A gene, compared with the resistant cultivar. We thus found that PR-1(P4) was a hallmark for the cultivar resistance conferred by Hero A against PCN and that nematode parasitism resulted in the inhibition of the SA signaling pathway in the susceptible cultivars

PCR-based analysis of disease in tomato singly or mixed inoculated with Fusarium oxysporum f. sp. lycopersici races 1 and 2

The pathogenic response of two tomato cultivars to races of Fusarium oxysporum f. sp.. lycopersici (cv. Momotaro, insensitive to race 1 of the pathogen, and cv. Ponderosa sensitive to race 1), was studied in greenhouse and laboratory experiments by inoculating the cultivars singly with race 1 or race 2, and in mixed inoculation with the two races of the pathogen. A pre-symptom PCR assay two weeks after inoculation showed that a fragment of the intergenic spacer region (IGS) of ribosomal DNA was amplifi ed by DNA templates from leaf samples of cv. Momotaro tomato plants inoculated with only race 2, or with race 1+2, but in the cv. Ponderosa the fragment was amplifi ed only in plants inoculated with race 1+2. Race-specifi c analysis using the sp13 and sp23 primers confi rmed that the amplifi ed fragment was from race 2 in cv. Momotaro and from races 1+2 in cv. Ponderosa. Later wilt symptoms mirrored the pre-symptom and post-symptom molecular analytical results: cv. Momotaro plants inoculated with only race 1 remained symptomless, while the ‘Momotaro’ plants inoculated with both races (1+2) did not manifest more severe wilt symptoms than plants inoculated with race 2 alone; cv. Ponderosa plants that were mixed-inoculated with race 1+2 manifested more severe symptoms, and at an earlier date than plants inoculated with only race 2. Growth parameters such as number of leaves and plant height showed the race 1+2 infected cv. Ponderosa were significantly retarded in growth, suggesting that significant synergism between the fungal races in tomato pathosystem can occur only when the host cultivar is sensitive to both races. An additional important finding is that pre-symptom leaf sampling of apparently healthy plants is useful in PCR diagnostic analysis to predict impending fusarial wilt outbreaks in tomato especially in infested soil

Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species

Sexual reproduction in heterothallic ascomycete fungi is controlled by a single mating-type locus called MAT1 with two alternate alleles or idiomorphs, MAT1-1 and MAT1-2 . These alleles lack sequence similarity and encode different transcriptional regulators. A large number of phytopathogenic fungi including Alternaria spp. are considered asexual, yet still carry expressed MAT1 genes. The molecular evolution of Alternaria MAT1 was explored using nucleotide diversity, nonsynonymous vs. synonymous substitution ( dn/ds ) ratios and codon usage statistics. Likelihood ratio tests of site-branch models failed to detect positive selection on MAT1-1-1 or MAT1-2-1 . Codon-site models demonstrated that both MAT1-1-1 and MAT1-2-1 are under purifying selection and significant differences in codon usage were observed between MAT1-1-1 and MAT1-2-1 . Mean GC content at the third position (GC3) and effective codon usage (ENC) were significantly different between MAT1-1-1 and MAT1-2-1 with values of 0.57 and 48 for MAT1-1-1 and 0.62 and 46 for MAT1-2-1 , respectively. In contrast, codon usage of Pleospora spp. (anamorph Stemphylium ), a closely related Dothideomycete genus, was not significantly different between MAT1-1-1 and MAT1-2-1 . The purifying selection and biased codon usage detected at the MAT1 locus in Alternaria spp. suggest a recent sexual past, cryptic sexual present and/or that MAT1 plays important cellular role(s) in addition to mating

Discovery, Genomic Sequence Characterization and Phylogenetic Analysis of Novel RNA Viruses in the Turfgrass Pathogenic Colletotrichum spp. in Japan

Turfgrass used in various areas of the golf course has been found to present anthracnose disease, which is caused by Colletotrichum spp. To obtain potential biological agents, we identified four novel RNA viruses and obtained full-length viral genomes from turfgrass pathogenic Colletotrichum spp. in Japan. We characterized two novel dsRNA partitiviruses: Colletotrichum associated partitivirus 1 (CaPV1) and Colletotrichum associated partitivirus 2 (CaPV2), as well as two negative single-stranded (ss) RNA viruses: Colletotrichum associated negative-stranded RNA virus 1 (CaNSRV1) and Colletotrichum associated negative-stranded RNA virus 2 (CaNSRV2). Using specific RT-PCR assays, we confirmed the presence of CaPV1, CaPV2 and CaNSRV1 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-264, as well as CaNSRV2 in dsRNAs from original and sub-isolates of Colletotrichum sp. MBCT-288. This is the first time mycoviruses have been discovered in turfgrass pathogenic Colletotrichum spp. in Japan. CaPV1 and CaPV2 are new members of the newly proposed genus &ldquo;Zetapartitivirus&rdquo; and genus Alphapartitivirus, respectively, in the family Partitiviridae, according to genomic characterization and phylogenetic analysis. Negative sense ssRNA viruses CaNSRV1 and CaNSRV2, on the other hand, are new members of the family Phenuiviridae and the proposed family &ldquo;Mycoaspirividae&rdquo;, respectively. These findings reveal previously unknown RNA virus diversity and evolution in turfgrass pathogenic Colletotrichum spp