The genome of the giant Nomura's jellyfish sheds light on the early evolution of active predation.

BACKGROUND: Unique among cnidarians, jellyfish have remarkable morphological and biochemical innovations that allow them to actively hunt in the water column and were some of the first animals to become free-swimming. The class Scyphozoa, or true jellyfish, are characterized by a predominant medusa life-stage consisting of a bell and venomous tentacles used for hunting and defense, as well as using pulsed jet propulsion for mobility. Here, we present the genome of the giant Nomura's jellyfish (Nemopilema nomurai) to understand the genetic basis of these key innovations. RESULTS: We sequenced the genome and transcriptomes of the bell and tentacles of the giant Nomura's jellyfish as well as transcriptomes across tissues and developmental stages of the Sanderia malayensis jellyfish. Analyses of the Nemopilema and other cnidarian genomes revealed adaptations associated with swimming, marked by codon bias in muscle contraction and expansion of neurotransmitter genes, along with expanded Myosin type II family and venom domains, possibly contributing to jellyfish mobility and active predation. We also identified gene family expansions of Wnt and posterior Hox genes and discovered the important role of retinoic acid signaling in this ancient lineage of metazoans, which together may be related to the unique jellyfish body plan (medusa formation). CONCLUSIONS: Taken together, the Nemopilema jellyfish genome and transcriptomes genetically confirm their unique morphological and physiological traits, which may have contributed to the success of jellyfish as early multi-cellular predators.

CSGM Designer: a platform for designing cross-species intron-spanning genic markers linked with genome information of legumes.

BACKGROUND: Genetic markers are tools that can facilitate molecular breeding, even in species lacking genomic resources. An important class of genetic markers is those based on orthologous genes, because they can guide hypotheses about conserved gene function, a situation that is well documented for a number of agronomic traits. For under-studied species a key bottleneck in gene-based marker development is the need to develop molecular tools (e.g., oligonucleotide primers) that reliably access genes with orthology to the genomes of well-characterized reference species. RESULTS: Here we report an efficient platform for the design of cross-species gene-derived markers in legumes. The automated platform, named CSGM Designer (URL: http://tgil.donga.ac.kr/CSGMdesigner), facilitates rapid and systematic design of cross-species genic markers. The underlying database is composed of genome data from five legume species whose genomes are substantially characterized. Use of CSGM is enhanced by graphical displays of query results, which we describe as "circular viewer" and "search-within-results" functions. CSGM provides a virtual PCR representation (eHT-PCR) that predicts the specificity of each primer pair simultaneously in multiple genomes. CSGM Designer output was experimentally validated for the amplification of orthologous genes using 16 genotypes representing 12 crop and model legume species, distributed among the galegoid and phaseoloid clades. Successful cross-species amplification was obtained for 85.3% of PCR primer combinations. CONCLUSION: CSGM Designer spans the divide between well-characterized crop and model legume species and their less well-characterized relatives. The outcome is PCR primers that target highly conserved genes for polymorphism discovery, enabling functional inferences and ultimately facilitating trait-associated molecular breeding.

Comparison of fermented soybean paste (Doenjang) prepared by different methods based on profiling of volatile compounds.

In this study, 2 different extraction methods, namely solvent-assisted flavor evaporation (SAFE) and solid-phase microextraction (SPME), were employed to investigate the comprehensive volatile profile of Doenjang (one of Korean fermented soybean pastes) efficiently. Quantitatively, major volatiles of Doenjang isolated by SAFE were 3-methylbutanoic acid, butanoic acid, 3-hydroxy-2-methyl-4H-pyran-4-one (maltol), ethyl 2-methylbutanoate, 2-methylpropanoic acid, tetramethylpyrazine, and 4-ethyl-2-methoxyphenol, while ethanol, ethenylbenzene, ethyl benzoate, ethyl linoleate, ethyl acetate, ethyl butanoate, tetramethylpyrazine, and ethyl 2-methylpropanoate extracted by SPME. In addition, volatile profiling that applied principal component analysis to gas chromatography-mass spectrometry datasets allowed Doenjang samples that had been prepared using different traditional and commercial methods to be discriminated, and the volatile compounds that contributed to their discrimination were assigned. The major volatiles that were related to differentiation of traditional and commercial Doenjang samples were 2-pentylfuran, 4-ethylphenol, dihydro-5-methyl-2(3H)-furanone, butanoic acid, pyrazines (for example, 2-ethyl-5-methylpyrazine and 2,3-dimethylpyrazine), esters (for example, ethyl 4-methylpentanoate and diethyl succinate), maltol, dimethyl disulfide, 2- and 3-methylbutanal, hexanal, 4-vinylphenol, and ethanol.

Investigation of the aroma-active compounds formed in the maillard reaction between glutathione and reducing sugars.

Aroma-active compounds formed during the thermal reaction between glutathione (GSH) and reducing sugars were analyzed by gas chromatography-mass spectrometry (GC-MS) and GC-olfactometry (GC-O) with aroma extract dilution analysis (AEDA). Application of AEDA to glutathione Maillard reaction products (GSH MRPs) led to the identification of 19 aroma-active compounds in the thermal reaction of glutathione with glucose or fructose. In addition, the carbohydrate module labeling (CAMOLA) approach was also employed to elucidate the formation pathways for selected target sulfur aroma compounds, such as 5-methylthiophene-2-carbaldehyde and 3-methylthiophene-2-carbaldehyde, which have not been reported previously. The intact carbon skeleton of glucose via 3-deoxyhexosone is incorporated into 5-methylthiophene-2-carbaldehyde with the hydrogen sulfide of GSH. On the other hand, the formation of 3-methylthiophene-2-carbaldehyde may occur via the recombination of a C-4 sugar fragment and mercaptoacetaldehyde.