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

Decreased photosynthesis in the erect panicle 3 (ep3) mutant of rice is associated with reduced stomatal conductance and attenuated guard cell development

The ERECT PANICLE 3 gene of rice encodes a peptide that exhibits more than 50% sequence identity with the Arabidopsis F-box protein HAWAIIAN SKIRT (HWS). Ectopic expression of the Os02g15950 coding sequence, driven by the HWS (At3g61950) promoter, rescued the hws-1 flower phenotype in Arabidopsis confirming that EP3 is a functional orthologue of HWS. In addition to displaying an erect inflorescence phenotype, loss-of-function mutants of Os02g15950 exhibited a decrease in leaf photosynthetic capacity and stomatal conductance. Analysis of a range of physiological and anatomical features related to leaf photosynthesis revealed no alteration in Rubisco content and no notable changes in mesophyll size or arrangement. However, both ep3 mutant plants and transgenic lines that have a T-DNA insertion within the Os02g15950 (EP3) gene exhibit smaller stomatal guard cells compared with their wild-type controls. This anatomical characteristic may account for the observed decrease in leaf photosynthesis and provides evidence that EP3 plays a role in regulating stomatal guard cell development

Interaction of Temperature and Light in the Development of Freezing Tolerance in Plants

Abstract Freezing tolerance is the result of a wide range of physical and biochemical processes, such as the induction of antifreeze proteins, changes in membrane composition, the accumulation of osmoprotectants, and changes in the redox status, which allow plants to function at low temperatures. Even in frost-tolerant species, a certain period of growth at low but nonfreezing temperatures, known as frost or cold hardening, is required for the development of a high level of frost hardiness. It has long been known that frost hardening at low temperature under low light intensity is much less effective than under normal light conditions; it has also been shown that elevated light intensity at normal temperatures may partly replace the cold-hardening period. Earlier results indicated that cold acclimation reflects a response to a chloroplastic redox signal while the effects of excitation pressure extend beyond photosynthetic acclimation, influencing plant morphology and the expression of certain nuclear genes involved in cold acclimation. Recent results have shown that not only are parameters closely linked to the photosynthetic electron transport processes affected by light during hardening at low temperature, but light may also have an influence on the expression level of several other cold-related genes; several cold-acclimation processes can function efficiently only in the presence of light. The present review provides an overview of mechanisms that may explain how light improves the freezing tolerance of plants during the cold-hardening period

The Evolutionary Basis of Naturally Diverse Rice Leaves Anatomy

Rice contains genetically and ecologically diverse wild and cultivated species that show a wide variation in plant and leaf architecture. A systematic characterization of leaf anatomy is essential in understanding the dynamics behind such diversity. Therefore, leaf anatomies of 24 Oryza species spanning 11 genetically diverse rice genomes were studied in both lateral and longitudinal directions and possible evolutionary trends were examined. A significant inter-species variation in mesophyll cells, bundle sheath cells, and vein structure was observed, suggesting precise genetic control over these major rice leaf anatomical traits. Cellular dimensions, measured along three growth axes, were further combined proportionately to construct three-dimensional (3D) leaf anatomy models to compare the relative size and orientation of the major cell types present in a fully expanded leaf. A reconstruction of the ancestral leaf state revealed that the following are the major characteristics of recently evolved rice species: fewer veins, larger and laterally elongated mesophyll cells, with an increase in total mesophyll area and in bundle sheath cell number. A huge diversity in leaf anatomy within wild and domesticated rice species has been portrayed in this study, on an evolutionary context, predicting a two-pronged evolutionary pathway leading to the ‘sativa leaf type’ that we see today in domesticated species

Competition between juvenile striped bass and bluefish: resource partitioning and growth rate

ABSTRACT: The potential for competition to influence the population dynamics of bluefish Pomatomus saltatrix and striped bass Morone saxatilis through interactions at the juvenile stage was examined. Habitat and diet utilization were compared between juvenile striped bass and bluefish in 3 New York Bight marine embayments. Juvenile bluefish and striped bass were seldom captured together during the summer and early fall, suggesting low habitat overlap at the scale of a beach seine haul. Diet overlap was also low; age-0 bluefish (spring- and summer-spawned cohorts) had a more piscivorous diet than age-0 and age-1 striped bass. A 60d laboratory growth experiment tested for interference competition between age-0 bluefish (spring-spawned) and age-1 striped bass fed fish prey in mixed- and single-species treatments. In the growth experiment, bluefish grew significantly faster than striped bass; however, within a species, there was no significant difference in growth between the mixed- and single-species treatments. Additionally, long-term field-monitoring data showed that annual estimates of growth rate for bluefish and striped bass were not correlated with annual estimates of their potential competitor’s density. These field and laboratory data provide no evidence for competitive interactions between juvenile striped bass and bluefish

Impact of age-0 bluefish (Pomatomus saltatrix) predation on age-0 fishes in the Hudson River estuary: evidence for density-dependent loss of juvenile striped bass (Morone saxatilis).

Abstract: We measured bluefish (Pomatomus saltatrix) weights, densities, and prey sizes during the summers of 1992 and 1993 and diets over a 4-year period (1990)(1991)(1992)(1993) in the Hudson River estuary. This information was used to estimate the loss of young-of-the-year (YOY) striped bass (Morone saxatilis) resulting from YOY bluefish predation. We then compared this predation mortality with the total loss of striped bass in the system. Data from sampling surveys conducted since the mid-1970's were used to examine relationships between bluefish abundance and striped bass recruitment levels. YOY striped bass, bay anchovy (Anchoa mitchilli), Atlantic silverside (Menidia menidia), and Alosa spp. dominated YOY bluefish diets. There were ontogenetic and interannual differences in YOY bluefish diets. Bluefish avoided striped bass at low densities but selected for them at high densities, suggesting a density-dependent feeding response. In the early summer of 1993, bluefish predation accounted for 50-100% of the total estimated loss of YOY striped bass. A significant negative correlation exists between the relative magnitude of striped bass recruitment and bluefish abundance. We conclude that YOY bluefish are important predators of estuarine fish and can have a substantial impact on their recruitment