Dataset Information

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed.

ABSTRACT: Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.

SUBMITTER: Lin A

PROVIDER: S-EPMC7465011 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature

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Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed.

Lin Ai A Ma Jinqi J Xu Fei F Xu Wen W Jiang Huanhuan H Zhang Haoran H Qu Cunmin C Wei Lijuan L Li Jiana J

Plants (Basel, Switzerland) 20200731 8

Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus ...[more]

PMID: 32752101

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Project description:BackgroundBrassica napus is of substantial economic value for vegetable oil, biofuel, and animal fodder production. The breeding of yellow-seeded B. napus to improve seed quality with higher oil content, improved oil and meal quality with fewer antinutrients merits attention. Screening the genes related to this phenotype is valuable for future rapeseed breeding.ResultsA total of 85,407 genes, including 4317 novel genes, were identified in the developing seeds of yellow- and black-seeded B. napus, and yellow rapeseed was shown to be an introgression line between black-seeded B. napus and yellow-seeded Sinapis alba. A total of 15,251 differentially expressed genes (DEGs) were identified among all the libraries, and 563 and 397 common DEGs were identified throughout black and yellow seed development, including 80 upregulated and 151 downregulated genes related to seed development and fatty acid accumulation. In addition, 11 up-DEGs and 31 down-DEGs were identified in all developmental stages of yellow rapeseed compared with black seed. Enrichment analysis revealed that many DEGs were involved in biosynthetic processes, pigment metabolism, and oxidation-reduction processes, such as flavonoid and phenylpropanoid biosynthesis, phenylalanine metabolism, flavone and flavonol biosynthesis, and fatty acid biosynthesis and metabolism. We found that more than 77 DEGs were related to flavonoid and lignin biosynthesis, including 4CL, C4H, and PAL, which participated in phenylalanine metabolism, and BAN, CHI/TT5, DFR, F3H, FLS, LDOX, PAP, CHS/TT4, TT5, bHLH/TT8, WD40, MYB, TCP, and CYP, which were involved in flavonoid biosynthesis. Most of these DEGs were downregulated in yellow rapeseed and were consistent with the decreased flavonoid and lignin contents. Both up- and down-DEGs related to fatty acid biosynthesis and metabolism were also analyzed, which could help to explain the improved oil content of yellow rapeseed.ConclusionThis research provided comprehensive transcriptome data for yellow-seeded B. napus with a unique genetic background, and all the DEGs in comparison with the black-seeded counterpart could help to explain seed quality differences, such as lower pigmentation and lignin contents, and higher oil content.

Project description:Alzheimer's disease is characterized by neuritic plaques, the main protein components of which are β-amyloid (Aβ) peptides deposited as β-sheet-rich amyloid fibrils. Cerebral Amyloid Angiopathy (CAA) consists of cerebrovascular deposits of Aβ peptides; it usually accompanies Alzheimer's disease, though it sometimes occurs in the absence of neuritic plaques, as AD also occurs without accompanying CAA. Although neuritic plaques and vascular deposits have similar protein compositions, one of the characteristic features of amyloids is polymorphism, i.e., the ability of a single pure peptide to adopt multiple conformations in fibrils, depending on fibrillization conditions. For this reason, we asked whether the Aβ fibrils in neuritic plaques differed structurally from those in cerebral blood vessels. To address this question, we used seeding techniques, starting with amyloid-enriched material from either brain parenchyma or cerebral blood vessels (using meninges as the source). These amyloid-enriched preparations were then added to fresh, disaggregated solutions of Aβ to make replicate fibrils, as described elsewhere. Such fibrils were then studied by solid-state NMR, fiber X-ray diffraction, and other biophysical techniques. We observed chemical shift differences between parenchymal vs. vascular-seeded replicate fibrils in select sites (in particular, Ala2, Phe4, Val12, and Gln15 side chains) in two-dimensional 13C-13C correlation solid-state NMR spectra, strongly indicating structural differences at these sites. X-ray diffraction studies also indicated that vascular-seeded fibrils displayed greater order than parenchyma-seeded fibrils in the "side-chain dimension" (~ 10 Å reflection), though the "hydrogen-bond dimensions" (~ 5 Å reflection) were alike. These results indicate that the different nucleation conditions at two sites in the brain, parenchyma and blood vessels, affect the fibril products that get formed at each site, possibly leading to distinct pathophysiological outcomes.

Dataset Information

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed.

Publications

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed.

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