BackgroundCelery is an increasing popular vegetable species, but limited transcriptome and genomic data hinder the research to it. In addition, a lack of celery molecular markers limits the process of molecular genetic breeding. High-throughput transcriptome sequencing is an efficient method to generate a large transcriptome sequence dataset for gene discovery, molecular marker development and marker-assisted selection breeding.Principal FindingsCelery transcriptomes from four tissues were sequenced using Illumina paired-end sequencing technology. De novo assembling was performed to generate a collection of 42,280 unigenes (average length of 502.6 bp) that represent the first transcriptome of the species. 78.43% and 48.93% of the unigenes had significant similarity with proteins in the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr) and Swiss-Prot database respectively, and 10,473 (24.77%) unigenes were assigned to Clusters of Orthologous Groups (COG). 21,126 (49.97%) unigenes harboring Interpro domains were annotated, in which 15,409 (36.45%) were assigned to Gene Ontology(GO) categories. Additionally, 7,478 unigenes were mapped onto 228 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Large numbers of simple sequence repeats (SSRs) were indentified, and then the rate of successful amplication and polymorphism were investigated among 31 celery accessions.ConclusionsThis study demonstrates the feasibility of generating a large scale of sequence information by Illumina paired-end sequencing and efficient assembling. Our results provide a valuable resource for celery research. The developed molecular markers are the foundation of further genetic linkage analysis and gene localization, and they will be essential to accelerate the process of breeding.

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BackgroundThe use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility.ResultsWe generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.ConclusionsOur study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

There is growing evidence to suggest that epigenetic tags, especially DNA methylation, are critical regulators of fruit ripening. To examine whether this is the case in sweet pepper (Capsicum annuum) we conducted experiments at the transcriptional, epigenetic, and physiological levels. McrBC PCR, bisulfite sequencing, and real-time PCR demonstrated that DNA hypomethylation occurred in the upstream region of the transcription start site of some genes related to pepper ripening at the turning stage, which may be attributed to up-regulation of CaDML2-like and down-regulation of CaMET1-like1, CaMET1-like2, CaCMT2-like, and CaCMT4-like. Silencing of CaMET1-like1 by virus-induced gene silencing led to DNA hypomethylation, increased content of soluble solids, and accumulation of carotenoids in the fruit, which was accompanied by changes in expression of genes involved in capsanthin/capsorubin biosynthesis, cell wall degradation, and phytohormone metabolism and signaling. Endogenous ABA increased during fruit ripening, whereas endogenous IAA showed an opposite trend. No ethylene signal was detected during ripening. DNA hypomethylation repressed the expression of auxin and gibberellin biosynthesis genes as well as cytokinin degradation genes, but induced the expression of ABA biosynthesis genes. In mature-green pericarp, exogenous ABA induced expression of CaDML2-like but repressed that of CaCMT4-like. IAA treatment promoted the transcription of CaMET1-like1 and CaCMT3-like. Ethephon significantly up-regulated the expression of CaDML2-like. Treatment with GA3 and 6-BA showed indistinct effects on DNA methylation at the transcriptional level. On the basis of the results, a model is proposed that suggests a high likelihood of a role for DNA methylation in the regulation of ripening in the non-climacteric pepper fruit.

Bacterial soft rot of banana was first noticed in 2009 in Guangzhou city, China. The disease also was observed on various banana cultivars of different genotypes in several other cities. Symptoms of the disease included leaf wilting, collapse of pseudostems, and unusual odor. Five isolated strains that fulfilled Koch's postulates were used for biochemical testing. The five strains were most similar to Dickeya dadantii or D. zeae, but were much less similar to D. paradisiaca when using several phenotype characteristics. Sequence analysis of 16S rDNA, dnaX, gryB, and recA of a reference strain revealed a similarity of 99% with the sequences of D. zeae, rather than D. paradisiaca. Phylogenic analysis of concatenated sequences of dnaX, gryB, and recA indicated that the banana strain constituted a distinguishable clade with several D. zeae strains involving rice pathogens D. zeae EC1 and ZJU1202 from Guangdong province, but the banana pathogen had several characteristics that distinguished it from the rice pathogens. Therefore, the banana pathogen was determined to be D. zeae. This is the first report of banana soft rot caused by D. zeae in China; however, the pathogen can infect other important crops.

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Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion–deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.

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