Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed
Abstract
:1. Introduction
2. Results
2.1. Putative Transcript Assembly
2.2. Analysis of the AS Landscape in Yellow- and Black-Seeded B. napus
2.3. Differential AS gene
2.4. Identification of Modules Associated with Seed Color by Construction of Weighted Gene Co-Expression Network and Correlation between Each Module
3. Discussion
4. Materials and Methods
4.1. Downloading of RNA-Seq Data
4.2. Analysis of Processed RNA-Seq Data and AS Landscape
4.3. Construction of Weighted Gene Co-Expression Networks and Analysis of Overlapping Differentially Spliced Genes
4.4. Analysis of Overlapping Differentially Spliced Genes
4.5. Functional Enrichment Analysis of Genes in Every Module
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Gene | Homologous Genes | Annotated | Module | Stage |
---|---|---|---|---|
BnaA03g60670D | AT1G61720 | BANYULS (BAN) | black | 28 d |
BnaC09g50050D | AT5G05270 | Chalcone-flavanone isomerase family protein (CHI) | black | 28 d |
BnaC09g17150D | AT5G42800 | dihydroflavonol 4-reductase (DFR) | dark grey | 28 d, 35 d, 42 d |
BnaA08g23220D | AT1G17260 | autoinhibited H(+)-ATPase isoform 10 (AHA10) | black | 14 d, 21 d, 28 d, 42 d |
BnaC08g17280D | AT1G17260 | autoinhibited H(+)-ATPase isoform 10 (AHA10) | black | 21 d, 28 d |
BnaAnng39120D | AT4G09960 | SEEDSTICK (STK) | not included | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaCnng46740D | AT4G09960 | SEEDSTICK (STK) | dark red | 42 d |
BnaC08g21130D | AT3G49430 | SER/ARG-rich protein 34A (SRp34a) | not included | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaC01g26160D | AT3G49430 | SER/ARG-rich protein 34A (SRp34a) | not included | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaA06g15930D | AT3G49430 | SER/ARG-rich protein 34A (SRp34a) | turquoise | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaA09g34840D | AT3G55120 | TRANSPARENT TESTA 5 (TT5) | black | 28 d, 42 d |
BnaC08g26020D | AT3G55120 | TRANSPARENT TESTA 5 (TT5) | black | 28 d, 35 d, 42 d |
BnaC09g24870D | AT4G09820 | TRANSPARENT TESTA 8 (TT8) | black | 21 d, 28 d, 35 d, 42 d |
BnaC06g17050D | AT3G59030 | TRANSPARENT TESTA 12 (TT12) | black | 21 d, 28 d, 35 d, 42 d |
BnaA07g18120D | AT3G59030 | TRANSPARENT TESTA 12 (TT12) | black | 42 d |
BnaAnng08030D | AT5G48100 | TRANSPARENT TESTA 10 (TT10) | not included | 21 d, 28 d, 35 d, 42 d |
BnaA06g30430D | AT5G48100 | TRANSPARENT TESTA 10 (TT10) | blue | 21 d, 28 d, 35 d, 42 d |
BnaC02g38340D | AT5G48100 | TRANSPARENT TESTA 10 (TT10) | turquoise | 28 d, 35 d, 42 d |
BnaAnng30140D | AT5G23260 | TRANSPARENT TESTA16 (TT16) | turquoise | 14 d |
BnaC09g04950D | AT5G23260 | TRANSPARENT TESTA16 (TT16) | turquoise | 42 d |
BnaC04g41260D | AT5G03495 | RNA-binding family protein | not included | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaC07g01360D | AT5G03495 | RNA-binding family protein | turquoise | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaC03g02460D | AT5G03480 | RNA-binding family protein | turquoise | 14 d, 21 d, 28 d, 35 d, 42 d |
BnaAnng15850D | AT5G03480 | RNA-binding family protein | blue | 14 d, 21 d, 28 d, 35 d, 42 d |
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Lin, A.; Ma, J.; Xu, F.; Xu, W.; Jiang, H.; Zhang, H.; Qu, C.; Wei, L.; Li, J. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. Plants 2020, 9, 977. https://doi.org/10.3390/plants9080977
Lin A, Ma J, Xu F, Xu W, Jiang H, Zhang H, Qu C, Wei L, Li J. Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed. Plants. 2020; 9(8):977. https://doi.org/10.3390/plants9080977
Chicago/Turabian StyleLin, Ai, Jinqi Ma, Fei Xu, Wen Xu, Huanhuan Jiang, Haoran Zhang, Cunmin Qu, Lijuan Wei, and Jiana Li. 2020. "Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed" Plants 9, no. 8: 977. https://doi.org/10.3390/plants9080977