Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus.

Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (A ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with A , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.

Light conditions can cause quantitative and qualitative changes in anthocyanin. However, little is known about the underlying mechanism of light quality-regulated anthocyanin accumulation in fruits. In this study, light-emitting diodes (LEDs) were applied to explore the effect of red and blue light on strawberry coloration. The results showed contents of total anthocyanins (TA), pelargonidin 3-glucoside (Pg3G) and pelargonidin 3-malonylglucoside (Pg3MG) significantly increased after blue and red light treatment. Pg3G was the major anthocyanin component in strawberry fruits, accounting for more than 80% of TA, whereas Pg3MG accounted for a smaller proportion. Comparative transcriptome analysis was conducted using libraries from the treated strawberries. A total of 1402, 5034, and 3764 differentially-expressed genes (DEGs) were identified in three pairwise comparisons (red light versus white light, RL-VS-WL; blue light versus white light, BL-VS-WL; blue light versus red light, BL-VS-RL), respectively. Photoreceptors and light transduction components remained dynamic to up-regulate the expression of regulatory factors and structural genes related to anthocyanin biosynthesis under red and white light, whereas most genes had low expression levels that were not consistent with the highest total anthocyanin content under blue light. Therefore, the results indicated that light was an essential environmental factor for anthocyanin biosynthesis before the anthocyanin concentration reached saturation in strawberry fruits, and blue light could quickly stimulate the accumulation of anthocyanin in the fruit. In addition, red light might contribute to the synthesis of proanthocyanidins by inducing LAR and ANR.

Anthocyanins are water-soluble pigments in plants. They confer both economical and healthy profits for humans. To gain a deeper insight into the regulation of anthocyanins biosynthesis in octoploid strawberry (Fragaria × ananassa; Fa), a widely-consumed economically important fruit, we performed comparative transcriptomic analysis of red- and white-fleshed strawberry cultivars in two ripening stages. In total, 365,455 non-redundant transcripts were assembled from the RNA sequencing (RNAseq) data. Of this collection, 377 were annotated as putative anthocyanins related transcripts. Differential expression analysis revealed that 57 anthocyanins biosynthesis transcripts were down-regulated, and 89 transcription factors (TFs) were either down- or up- regulated under anthocyanins deficiency. Additionally, amongst the 50,601 putative long non-coding RNAs (lncRNAs) identified here, 68 lncRNAs were differentially expressed and co-expressed with differentially expressed anthocyanins related mRNAs, 2,070 co-expressing lncRNAs-mRNAs pairs were generated. Expression profiles analysis revealed that it was the limited expression of FaF3'H that blocked the cyanidin 3-glucoside accumulation in the two investigated strawberry cultivars. This was further supported by a transient-overexpression experiment with FaMYB10. The down-regulated lncRNAs might participate in anthocyanins regulation by acting as targets for micro RNAs (miRNAs). The level of competitive intensity in miRNA and lncRNA for the same mRNAs target was probably lower in the white-fleshed strawberries, which can release the repression effect of the mRNAs in red-fleshed strawberry as a result. This study for the first time presents lncRNAs related to anthocyanins in strawberries, provides new insights into anthocyanins regulatory network, and also lays the foundation for identifying new anthocyanins regulators in strawberry.

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 Landward seston depletion induced by bivalve filtration in a Dutch coastal bay  Comparable biological and physical impacts on the seston dynamics  A straightforward approach useful for shellfish culture management

Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.

The three‐dimensional unstructured‐grid Finite Volume Coastal Ocean Model (FVCOM) was implemented for Chesapeake Bay and its adjacent coastal ocean to delineate the realistic Chesapeake Bay outflow plume (CBOP) as well as its seasonal and interannual variability. Applying the appropriate horizontal and vertical resolution, the model exhibited relatively high skill in matching the observational water level, temperature, and salinity from 2003 to 2012. The simulated surface plume structure was verified by comparing output to the HF radar current measurements, earlier field observations, and the MODIS and AVHRR satellite imagery. According to the orientation, shape, and size of the CBOP from both model snapshots and satellite images, five types of real‐time plume behavior were detected, which implied strong regulation by wind and river discharge. In addition to the episodic plume modulation, horizontal and vertical structure of the CBOP exhibited variations on seasonal and interannual temporal scales. Seasonally, river discharge with a 1 month lag was primarily responsible for the surface plume area variation, while the plume thickness was mainly correlated to wind magnitude. On the interannual scale, river discharge was the predominant source of variability in both surface plume area and depth; however, the southerly winds also influenced the offshore plume depth. In addition, large‐scale climate variability, such as the North Atlantic Oscillation, could potentially affect the plume signature in the long term by altering wind and upwelling dynamics, underlining the need to understand the impacts of climate change on buoyant plumes, such as the CBOP.