We identified a cis-prenyltransferase gene, neryl diphosphate synthase 1 (NDPS1), that is expressed in cultivated tomato (Solanum lycopersicum) cultivar M82 type VI glandular trichomes and encodes an enzyme that catalyzes the formation of neryl diphosphate from isopentenyl diphosphate and dimethylallyl diphosphate. mRNA for a terpene synthase gene, phellandrene synthase 1 (PHS1), was also identified in these glands. It encodes an enzyme that uses neryl diphosphate to produce ␤-phellandrene as the major product as well as a variety of other monoterpenes. The profile of monoterpenes produced by PHS1 is identical with the monoterpenes found in type VI glands. PHS1 and NDPS1 map to chromosome 8, and the presence of a segment of chromosome 8 derived from Solanum pennellii LA0716 causes conversion from the M82 gland monoterpene pattern to that characteristic of LA0716 plants. The data indicate that, contrary to the textbook view of geranyl diphosphate as the ''universal'' substrate of monoterpene synthases, in tomato glands neryl diphosphate serves as a precursor for the synthesis of monoterpenes.plant biochemistry ͉ terpene synthases ͉ cis-prenyltransferases ͉ biochemical diversity ͉ specialized metabolism

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.com/dib-lab/khmer/.

Glandular secreting trichomes on the surface of tomato plants and many of its relatives in the Solanaceae produce a mixture of O-acyl sugars that contribute to insect resistance. The majority of acyl sucroses produced by the cultivated tomato (Solanum lycopersicum) contain three or four short chain aliphatic acyl esters, and tetra-acyl sucroses have an acetyl group as one of the acyl chains. We previously reported overlapping S. lycopersicum × Solanum pennellii introgression lines (ILs) that fail to accumulate high levels of acetylated tetra-acyl sucroses. A survey of the annotated genes in this region of cultivated tomato chromosome 1 revealed three candidate acyltransferases that were tested for function using virus-induced gene silencing. A member of the BAHD family of acyltransferases (Solyc01g105580, SlAT2) was shown to encode an acetyl-CoA-dependent acyltransferase enzyme capable of acyl sucrose acetylation in vitro. RNAi suppression of SlAT2 in transgenic S. lycopersicum cv. M82 resulted in reduced acyl sugar acetylation, whereas expression of the functional S. lycopersicum allele of SlAT2 in the triacyl sucrose producing IL1-3 restored the ability of the IL to synthesize acetylated tetra-acyl sugars. Transgenic plants with the SlAT2 promoter driving GFP expression showed fluorescence in tips cells of long, slender trichomes that is consistent with acyl sugar acetylation occurring in these cells.

Glandular secreting trichomes of cultivated tomato (Solanum lycopersicum) and close relatives produce a variety of structurally diverse volatile and non-volatile specialized (‘secondary’) metabolites, including terpenes, flavonoids and acyl sugars. A genetic screen is described here to profile leaf trichome and surface metabolite extracts of nearly isogenic chromosomal substitution lines covering the tomato genome. These lines contain specific regions of the Solanum pennellii LA0716 genome in an otherwise ‘wild-type’ M82 tomato genetic background. Regions that have an impact on the total amount of extractable mono- and sesquiterpenes (IL2-2) or only sesquiterpenes (IL10-3) or specifically influence accumulation of the monoterpene α-thujene (IL1-3 and IL1-4) were identified using GC-MS. A rapid LC-TOF-MS method was developed and used to identify changes in non-volatile metabolites through non-targeted analysis. Metabolite profiles generated using this approach led to the discovery of introgression lines producing different acyl chain substitutions on acyl sugar metabolites (IL1-3/1-4 and IL8-1/8-1-1), as well as two regions that influence the quantity of acyl sugars (IL5-3 and IL11-3). Chromosomal region 1-1/1-1-3 was found to influence the types of glycoalkaloids that are detected in leaf surface extracts. These results show that direct chemical screening is a powerful way to characterize genetic diversity in trichome specialized metabolism.

As more digital resources are produced by the research community, it is becoming increasingly important to harmonize and organize them for synergistic utilization. The findable, accessible, interoperable, and reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge. The FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual and automated FAIR assessments. FAIR assessments are visualized as an insignia that can be embedded within digital-resources-hosting websites. Using FAIRshake, a variety of biomedical digital resources were manually and automatically evaluated for their level of FAIRness.