Correction: Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus.
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ABSTRACT:
SUBMITTER: Chen J
PROVIDER: S-EPMC4461166 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Correction: Transcriptome Analysis Comparison of Lipid Biosynthesis in the Leaves and Developing Seeds of Brassica napus.
Chen Jie J Tan Ren-Ke RK Guo Xiao-Juan XJ Fu Zheng-Li ZL Wang Zheng Z Zhang Zhi-Yan ZY Tan Xiao-Li XL
PloS one 20150609 6
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Project description:Brassica napus seed is a lipid storage organ containing approximately 40% oil, while its leaves contain many kinds of lipids for many biological roles, but the overall amounts are less than in seeds. Thus, lipid biosynthesis in the developing seeds and the leaves is strictly regulated which results the final difference of lipids. However, there are few reports about the molecular mechanism controlling the difference in lipid biosynthesis between developing seeds and leaves. In this study, we tried to uncover this mechanism by analyzing the transcriptome data for lipid biosynthesis. The transcriptome data were de novo assembled and a total of 47,216 unigenes were obtained, which had an N50 length and median of 1271 and 755 bp, respectively. Among these unigenes, 36,368 (about 77.02%) were annotated and there were 109 up-regulated unigenes and 72 down-regulated unigenes in the developing seeds lipid synthetic pathway after comparing with leaves. In the oleic acid pathway, 23 unigenes were up-regulated and four unigenes were down-regulated. During triacylglycerol (TAG) synthesis, the key unigenes were all up-regulated, such as phosphatidate phosphatase and diacylglycerol O-acyltransferase. During palmitic acid, palmitoleic acid, stearic acid, linoleic acid and linolenic acid synthesis in leaves, the unigenes were nearly all up-regulated, which indicated that the biosynthesis of these particular fatty acids were more important in leaves. In the developing seeds, almost all the unigenes in the ABI3VP1, RKD, CPP, E2F-DP, GRF, JUMONJI, MYB-related, PHD and REM transcript factor families were up-regulated, which helped us to discern the regulation mechanism underlying lipid biosynthesis. The differential up/down-regulation of the genes and TFs involved in lipid biosynthesis in developing seeds and leaves provided direct evidence that allowed us to map the network that regulates lipid biosynthesis, and the identification of new TFs that are up-regulated in developing seeds will help us to further elucidate the lipids biosynthesis pathway in developing seeds and leaves.
| S-EPMC4429122 | biostudies-literature
Project description:Gene expression profiles during seed development and fatty acid (FA) metabolism, as well as the relevant regulation, of Brassica napus were studied through multiple high-throughput genomic approaches. Serial Analysis of Gene Expression (SAGE) using seed materials obtained a total of 68,718 tags, of which 23,897 were unique and 503 tags were functionally identified, and revealed the transcriptome of approximately 35,000 transcripts in B. napus developing seeds. Further, ~22,000 independent ESTs were obtained by large-scale sequencing using immature embryos at different stages, and 8343 uni-ESTs and 3355 full-length cDNAs were identified respectively, resulting in the systemic identification of B. napus FA biosynthesis-related genes. Gene expression profiles were further studied employing cDNA chip hybridization to reveal the global regulatory network of FA metabolism in developing seeds. Together with the analysis on FA amounts and composition, it was shown that 17-21 days after pollination (DAP) was a crucial stage for transition of seed to sink tissue. High expressions of FA biosynthesis-related genes and transition of FA components are mainly at stages 21 DAP or 21-25 DAP respectively. In addition, compared to Arabidopsis, more critical roles of starch metabolism are detected for B. napus seed FA metabolism and storage components accumulation. Crucial effects of starch metabolism, carbon flux, oxidative pentose phosphate pathway (OPPP), photosynthesis, and other regulators in FA metabolism were discussed. Keywords: Brassica napus, immature seed, SAGE, EST, cDNA microarray
2008-02-26 | GSE7204 | GEO
Project description: Not available
| S-BSST1715 | biostudies-other
Project description:With dwindling available agricultural land, concurrent with increased demand for oil, there is much current interest in raising oil crop productivity. We have been addressing this issue by studying the regulation of oil accumulation in oilseed rape (Brassica napus L). As part of this research we have carried out a detailed lipidomic analysis of developing seeds. The molecular species distribution in individual lipid classes revealed quite distinct patterns and showed where metabolic connections were important. As the seeds developed, the molecular species distributions changed, especially in the period of early (20days after flowering, DAF) to mid phase (27DAF) of oil accumulation. The patterns of molecular species of diacylglycerol, phosphatidylcholine and acyl-CoAs were used to predict the possible relative contributions of diacylglycerol acyltransferase (DGAT) and phospholipid:diacylglycerol acyltransferase to triacylglycerol production. Our calculations suggest that DGAT may hold a more important role in influencing the molecular composition of TAG. Enzyme selectivity had an important influence on the final molecular species patterns. Our data contribute significantly to our understanding of lipid accumulation in the world's third most important oil crop.
| S-EPMC5791847 | biostudies-literature
Project description:BackgroundThe upgrading of rapeseed cultivars has resulted in a substantial improvement in yield and quality in China over the past 30 years. With the selective pressure against fatty acid composition and oil content, high erucic acid- and low oil-content cultivars have been replaced by low erucic acid- and high oil-content cultivars. The high erucic acid cultivar Zhongyou 821 and its descendent, low erucic acid cultivar Zhongshuang 9, are representatives of two generations of the most outstanding Chinese rapeseed cultivars (B. napus) developed the past 2 decades. This paper compares the transcriptional profiles of Zhongshuang 9 and Zhongyou 821 for 32 genes that are principally involved in lipid biosynthesis during seed development in order to elucidate how the transcriptional profiles of these genes responded to quality improvement over the past 20 years.ResultsComparison of the cultivar Zhongyou 821 with its descendent, Zhongshuang 9, shows that the transcriptional levels of seven of the 32 genes were upregulated by 30% to 109%, including FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC. Of the 32 genes, 10 (KAS3, beta-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, alpha-CT and SUC1) were downregulated by at least 20% and most by 50%. The Napin gene alone accounted for over 75% of total transcription from all 32 genes assessed in both cultivars. Most of the genes showed significant correlation with fatty acid accumulation, but the correlation in ZS9 was significantly different from that in ZY821. Higher KCR2 activity is associated with higher C16:0, C18:0, and C18:2 in both cultivars, lower C22:1 and total fatty acid content in ZY821, and lower 18:1 in ZS9.ConclusionThis paper illustrates the response of the transcription levels of 32 genes to breeding in developing rapeseed seeds. Both cultivars showed similar transcription profiles, with the Napin gene predominantly transcribed. Selective pressure for zero erucic acid, low glucosinolate, high oleic acid and high oil content, as well as high yield, resulted in higher FAD3, ACCase, FAE1, GKTP, Caleosin, GAPDH, and PEPC expression levels and lower KAS3, beta-CT, BcRK6, P450, FatA, Oleosin, FAD6, FatB, alpha-CT and SUC1 expression levels. It also resulted in altered relationships between these genes during storage accumulation in seed development.
| S-EPMC2697984 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2014-08-01 | GSE38020 | GEO
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.
| S-EPMC6524335 | biostudies-literature
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.
| S-EPMC6524335 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-08-01 | E-GEOD-38020 | biostudies-arrayexpress
Project description:Seed development has a critical role during the spermatophyte life cycle. In Brassica napus, a major oil crop, fatty acids are synthesized and stored in specific tissues during embryogenesis, and understanding the molecular mechanism underlying fatty acid biosynthesis during seed development is an important research goal. In this study, we constructed three small RNA libraries from early seeds at 14, 21, and 28 days after flowering (DAF) and used high-throughput sequencing to examine microRNA (miRNA) expression. A total of 85 known miRNAs from 30 families and 1160 novel miRNAs were identified, of which 24, including 5 known and 19 novel miRNAs, were found to be involved in fatty acid biosynthesis.bna-miR156b, bna-miR156c, bna-miR156g, novel_mir_1706, novel_mir_1407, novel_mir_173, and novel_mir_104 were significantly down-regulated at 21 DAF and 28 DAF, whereas bna-miR159, novel_mir_1081, novel_mir_19 and novel_mir_555 were significantly up-regulated. In addition, we found that some miRNAs regulate functional genes that are directly involved in fatty acid biosynthesis and that other miRNAs regulate the process of fatty acid biosynthesis by acting on a large number of transcription factors. The miRNAs and their corresponding predicted targets were partially validated by quantitative RT-PCR. Our data suggest that diverse and complex miRNAs are involved in the seed development process and that miRNAs play important roles in fatty acid biosynthesis during seed development.
| S-EPMC5075540 | biostudies-literature