Cotton Science

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Comparison of the transcriptomes between pink flower buds and yellow flower buds in upland cotton

Liu Linqiang, Han Xiao, Yang Lan, Yan Qingdi, Hu Wei, Jin Yuying, Yu Jie, Yang Zhaoen, Li Fuguang

Cotton Science, 2023, 35(4): 259-273. DOI: 10.11963/cs20200102

代谢通路 Pathway ID	通路名称 Name of pathway	DEG数量 DEG number	P值 P value
ko00195	光合作用 Photosynthesis	32	4.88×10^-12
ko00196	光合作用-触角蛋白 Photosynthesis - antenna proteins	15	2.77×10^-10
ko00860	卟啉与叶绿素代谢 Porphyrin and chlorophyll metabolism	11	13.65×10^-3
ko00053	抗坏血酸和醛酸代谢 Ascorbate and aldarate metabolism	12	1.97×10^-3
ko00500	淀粉和蔗糖代谢 Starch and sucrose metabolism	33	7.31×10^-3
ko00730	硫胺素代谢 Thiamine metabolism	5	1.09×10^-2
ko03410	碱基切除修复 Base excision repair	10	1.28×10^-2
ko04075	激素信号转导 Plant hormone signal transduction	45	1.96×10^-2
ko00920	硫代谢 Sulfur metabolism	7	3.98×10^-2
ko00052	半乳糖代谢 Galactose metabolism	12	4.37×10^-2
ko03430	错配修复 Mismatch repair	7	4.39×10^-2
ko00904	二萜类生物合成 Diterpenoid biosynthesis	6	4.43×10^-2
ko00910	氮代谢 Nitrogen metabolism	7	4.60×10^-2

Table 6 Metabolic pathways of down-regulated DEG

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Fig. 1 Flowers and buds at different development stages of CCRI 24 and Zhongyihong A: Flowers and buds at different development stages of CCRI 24 (upper panel) and Zhongyihong (bottorn panel); B: Flowers of CCRI 24 (right) and Zhongyihong (left), photos were taken at the flowering day; C: The color of petals at different development stages of CCRI 24 (upper panel) and Zhongyihong (bottorn panel).
Table 1 Primers used in this study
Table 2 Anthocyanin content in buds at B1 and A9 stages of CCRI 24 and Zhongyihong
Table 3 Basic information for transcriptome sequencing data
Fig. 2 Correlation analysis between different samples based on gene expression levels 1, 2, and 3 followed W-B1, W-A9, P-B1 and P-A9 indicate three replicates. r is the correlation coefficient.
Fig. 3 Comparison of gene expression profiles between qRT-PCR and RNA-Seq Black bars represent gene expression level detected by qRT-PCR, and gray bars represent TPM of genes by RNA-seq.
Table 4 Numbers of DEG between different sample group
Fig. 4 Venn analysis of DEG in buds of CCRI 24 and Zhongyihong at different developmental stages
Fig. 5 The expression profiles of Gh_A07G083500 and Gh_A07G079800 Statistical analyses have been the Student’s test. ** and **** indicate significance at the 0.01 and 0.000 1 probability level, respectively.
Fig. 6 GO enrichment analysis of DEG A: GO enrichment analysis of up-regulated DEG, B: GO enrichment analysis of down-regulated DEG.
Table 5 Metabolic pathways of up-regulated PEG
Fig. 7 Gene expression level involved in the biosynthesis, modification and transport pathway of anthocyanin
Fig. 8 The regulation and transport model of anthocyanin in pink flower The dotted line indicates the genes not enriched in this pathway in this study.

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