BackgroundThe usual analysis of RNA sequencing (RNA-seq) reads is based on an existing reference genome and annotated gene models. However, when a reference for the sequenced species is not available, alternatives include using a reference genome from a related species or reconstructing transcript sequences with de novo assembly. In addition, researchers are faced with many options for RNA-seq data processing and limited information on how their decisions will impact the final outcome. Using both a diploid and polyploid species with a distant reference genome, we have tested the influence of different tools at various steps of a typical RNA-seq analysis workflow on the recovery of useful processed data available for downstream analysis.FindingsAt the preprocessing step, we found error correction has a strong influence on de novo assembly but not on mapping results. After trimming, a greater percentage of reads could be used in downstream analysis by selecting gentle quality trimming performed with Skewer instead of strict quality trimming with Trimmomatic. This availability of reads correlated with size, quality, and completeness of de novo assemblies and with number of mapped reads. When selecting a reference genome from a related species to map reads, outcome was significantly improved when using mapping software tolerant of greater sequence divergence, such as Stampy or GSNAP.ConclusionsThe selection of bioinformatic software tools for RNA-seq data analysis can maximize quality parameters on de novo assemblies and availability of reads in downstream analysis.

Southern highbush blueberry cultivation has expanded into non-traditional growing areas worldwide due to elite cultivars and improved horticultural practices. This article presents a comprehensive review of current production systems—alternatives to traditional open field production—such as production in protected environments, high-density plantings, evergreen production, and container-based production. We discuss the advantages and disadvantages of each system and compare their differences to open field production. In addition, we provide potential solutions for some of the disadvantages. We also highlight some of the gaps existing between academic studies and production in industry, providing a guide for future academic research. All these alternative systems have shown the potential to produce high yields with high-quality berries. Alternative systems, compared to field production, require higher establishment investments and thus create an entry barrier for new producers. Nevertheless, with their advantages, alternative productions have the potential to be profitable.

Vaccinium arboreum (VA) is a wild blueberry species that exhibits wider soil pH tolerance and greater ability for iron and nitrate uptake than cultivated Vaccinium species, including southern highbush blueberry (SHB, V. corymbosum interspecific hybrids). The ability of VA and SHB to respond to iron deficiency by rhizosphere acidification was investigated. Rooted cuttings of the VA genotype FL09-502 and SHB ‘Emerald’ were transplanted to a hydroponic system filled with complete nutrient solution. After 14 days of acclimation at 45 µm iron, plants were transferred to unbuffered nutrient solutions containing 90 or 10 µm iron. ‘Emerald’ and FL09-502 plants grown in 10 µm iron exhibited less iron uptake and lower chlorophyll, total iron, and active iron contents than plants grown in 90 µm iron. Generally, there were no species-level differences in iron or nitrate uptake. Neither FL09-502 nor ‘Emerald’ acidified the rhizosphere in either the nutrient solution or in a gel-based assay, regardless of external iron concentration. A screen of 18 additional genotypes of VA and SHB confirmed that this response is absent in these taxa. Thus, rhizosphere acidification is not part of the iron deficiency response of SHB and VA. In addition, the ability to acidify the soil is not likely to be responsible for the wider soil pH tolerance of VA.

BackgroundBlueberries are one of the few horticultural crops adapted to grow in acidic soils. Neutral to basic soil pH is detrimental to all commonly cultivated blueberry species, including Vaccinium corymbosum (VC). In contrast, the wild species V. arboreum (VA) is able to tolerate a wider range of soil pH. To assess the molecular mechanisms involved in near neutral pH stress response, plants from pH-sensitive VC (tetraploid) and pH-tolerant VA (diploid) were grown at near neutral pH 6.5 and at the preferred pH of 4.5.ResultsTranscriptome sequencing of root RNA was performed for 4 biological replications per species x pH level interaction, for a total of 16 samples. Reads were mapped to the reference genome from diploid V. corymbosum, transforming ~55% of the reads to gene counts. A quasi-likelihood F test identified differential expression due to pH stress in 337 and 4867 genes in VA and VC, respectively. Both species shared regulation of genes involved in nutrient homeostasis and cell wall metabolism. VA and VC exhibited differential regulation of signaling pathways related to abiotic/biotic stress, cellulose and lignin biosynthesis, and nutrient uptake.ConclusionsThe specific responses in VA likely facilitate tolerance to higher soil pH. In contrast, response in VC, despite affecting a greater number of genes, is not effective overcoming the stress induced by pH. Further inspection of those genes with differential expression that are specific in VA may provide insight on the mechanisms towards tolerance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3967-0) contains supplementary material, which is available to authorized users.

Blueberry (Vacciniumcorymbosum interspecific hybrids) production in soilless substrates is becoming increasingly popular. Soilless substrates have low pH buffering capacity. Blueberry plants preferentially take up ammonium, which acidifies the rhizosphere. Consequently, soilless substrates where blueberry plants are grown exhibit a tendency to get acidified over time. Agricultural lime (CaCO3) is commonly used to raise soil and substrate pH in other crops, but it is rarely used in blueberry cultivation. We hypothesized that substrate amendment with low rates of agricultural lime increases substrate pH buffering capacity and provides nutritional cations that can benefit blueberry plants. We tested this hypothesis in a greenhouse experiment with ‘Emerald’ southern highbush blueberry plants grown in rhizoboxes filled with a 3:1 mix of coconut coir and perlite. We found that substrate amendment with CaCO3 did not cause high pH stress. This amendment maintained substrate pH between 5.5 and 6.5 and provided Ca and Mg for plant uptake. When blueberry plants were grown in CaCO3-amended substrate and fertigated with low pH nutrient solution (pH 4.5), they exhibited greater biomass accumulation than plants grown in unamended substrates. These results suggest that low rates of CaCO3 could be useful for blueberry cultivation in soilless substrates.