A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms

Background: Summer squash (Cucurbita pepo: Cucurbitaceae) are a popular horticultural crop for which there is insufficient genomic and transcriptomic information. Gene expression atlases are crucial for the identification of genes expressed in different tissues at various plant developmental stages. Here, we present the first comprehensive gene expression atlas for a summer squash cultivar, including transcripts obtained from seeds, shoots, leaf stem, young and developed leaves, male and female flowers, fruits of seven developmental stages, as well as primary and lateral roots. Results: In total, 27,868 genes and 2352 novel transcripts were annotated from these 16 tissues, with over 18,000 genes common to all tissue groups. Of these, 3812 were identified as housekeeping genes, half of which assigned to known gene ontologies. Flowers, seeds, and young fruits had the largest number of specific genes, whilst intermediate-age fruits the fewest. There also were genes that were differentially expressed in the various tissues, the male flower being the tissue with the most differentially expressed genes in pair-wise comparisons with the remaining tissues, and the leaf stem the least. The largest expression change during fruit development was early on, from female flower to fruit two days after pollination. A weighted correlation network analysis performed on the global gene expression dataset assigned 25,413 genes to 24 coexpression groups, and some of these groups exhibited strong tissue specificity. Conclusions: These findings enrich our understanding about the transcriptomic events associated with summer squash development and ripening. This comprehensive gene expression atlas is expected not only to provide a global view of gene expression patterns in all major tissues in C. pepo but to also serve as a valuable resource for functional genomics and gene discovery in Cucurbitaceae

Cloning and primary structure of the chiA gene from Aeromonas caviae.

The chiA gene from Aeromonas caviae encodes an extracellular chitinase, 865 amino acids long, that shows a high degree of similarity to chitinase A of Serratia marcescens. Expression in Escherichia coli yielded an enzymatically active protein from which a leader sequence was removed, presumably during transport of the enzyme across the cell membrane

Analysis of the Ac promoter: structure and regulation.

The Ac-encoded transposase, a factor that is essential for the mobility of the Ac element, is expressed under the control of a promoter that lacks a conventional TATA box. The regulation of this promoter is poorly understood. We have analyzed Ac promoter structure and activity, both in vitro and in vivo, using transgenic tobacco plants and cell suspensions. A deletion analysis of the Ac 5' region showed that the minimal promoter is located within 70 bp of the major transcription initiation site (at position 334). The minimal promoter includes the sequence TAAGAAATA at position 294 303, i.e., about 30 nucleotides upstream from the transcription start site. This sequence binds specifically to the TATA-binding protein (TBP), suggesting that it is functional as a TATA box. The regulation of the Ac promoter was studied throughout plant development. Levels of Ac mRNA were low in all tissues studied, with higher expression being observed in dividing cells. In order to test whether Ac promoter is regulated during the cell cycle, a tobacco cell suspension transformed with Ac, was grown synchronously. No differences were found in Ac mRNA levels between cells in S, G2, M, or G1 phases; however, expression was lower in the stationary phase. We conclude that Ac promoter is not cell-cycle regulated but is expressed at a higher level in dividing cells. The possible relationship between promoter features and the regulation of Ac element transposition is discussed

Introduced Tuber aestivum spreading spontaneously in Israel

A T. melanosporum plantation was established during 1994-95 in Kibbutz Bar´am in the Upper Galilee, Israel. In 1998, only approximately 70% of the trees maintained the inoculated mycorrhiza. A number of trees died; thus, several tree species were initially introduced. These included both European and local oak species, as well as hazelnuts. In 1999, seedlings were introduced into the plantation to fill the gaps between trees. These included, inadvertently, plants inoculated with T. aestivum. In July 2009, fruiting bodies of T. aestivum were collected from the plantation. In 2010, a manual search was conducted and a total of 2.2 kg of fruiting bodies of T. aestivum (a calculated yield of approximately 6.0 kg/acre) were obtained. No fruiting bodies were collected in 2011. In 2012, truffles were found in the original plantation and in a grove within a research farm approximately 3.5 km away. The latter appeared to be of the same origin as the originally introduced T. aestivum. The environmental conditions in the Upper Galilee, although unsuitable for T. melanosporum, are highly suitable for the more robust T. aestivum, which thrives on local oak species