Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

Abstract Background Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study.Results White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis. Conclusion This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.

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Transcriptome Sequencing and Biochemical Analysis of Perianths and Coronas Reveal Flower Color Formation in Narcissus pseudonarcissus

International Journal of Molecular Sciences ◽

10.3390/ijms19124006 ◽

2018 ◽

Vol 19 (12) ◽

pp. 4006 ◽

Cited By ~ 1

Author(s):

Xi Li ◽

Dongqin Tang ◽

Hui Du ◽

Yimin Shi

Keyword(s):

Flower Color ◽

Carotenoid Biosynthesis ◽

Carotenoid Content ◽

Rna Seq ◽

Color Formation ◽

Light Yellow ◽

Color Fading ◽

Narcissus Pseudonarcissus ◽

Bulbous Plant ◽

Β Carotene

Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars (‘Slim Whitman’ and ‘Pinza’) with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N. pseudonarcissus. The results showed that the content of carotenoids in the corona was higher than that in the perianth in both cultivars. Accordingly, phytoene synthase (PSY) transcripts have a higher abundance in the coronas than that in perianths. While the expression levels of carotenoid biosynthetic genes, like GGPPS, PSY, and LCY-e, were not significantly different between two cultivars. In contrast, the carotenoid degradation gene NpCCD4 was highly expressed in white-perianth cultivars, but was hardly detected in yellow-perianth cultivars. Silencing of NpCCD4 resulted in a significant increase in carotenoid accumulation, especially in all-trans-β-carotene. Therefore, we presume that NpCCD4 is a crucial factor that causes the low carotenoid content and color fading phenomenon of ‘Slim Whitman’ by mediating carotenoid turnover. Our findings provide mass RNA-seq data and new insights into carotenoid metabolism in N. pseudonarcissus.

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Tissue-Specific Expression Pattern in Ancherythroculter nigrocauda, a Sexually Size Dimorphic Fish

Frontiers in Genetics ◽

10.3389/fgene.2021.777581 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yanhong Sun ◽

Huijie Wei ◽

Jian Chen ◽

Pei Li ◽

Qing Yang ◽

...

Keyword(s):

Body Weight ◽

Economic Value ◽

Rna Seq ◽

Specific Expression ◽

Phenotypic Differences ◽

Pathway Enrichment ◽

Network Analyses ◽

Ppar Signaling ◽

Hormone Biosynthesis ◽

Specific Expression Pattern

Certain members of the Actinopterygii class are known to exhibit sexual dimorphism (SD) that results in major phenotypic differences between male and female fishes of a species. One of the most common differences between the two sexes is in body weight, a factor with a high economic value in aquaculture. In this study, we used RNA sequencing (RNA-seq) to study the liver and brain transcriptomes of Ancherythroculter nigrocauda, a fish exhibiting SD. Females attain about fourfold body weight of males at sexual maturity. Sample clustering showed that both sexes were grouped well with their sex phenotypes. In addition, 2,395 and 457 differentially expressed genes (DEGs) were identified in the liver and brain tissues, respectively. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses predicted the association of PPAR signaling, cytochrome P450, and steroid hormone biosynthesis to the differences in sexual size. In addition, weighted gene co-expression network analyses (WGCNA) were conducted, and the green module was identified to be significantly correlated with sexual size dimorphism (SSD). Altogether, these results improve our understanding of the molecular mechanism underlying SSD in A. nigrocauda.

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Comparison of differential expression genes in ovaries and testes of Pearlscale angelfish Centropyge vrolikii based on RNA-Seq analysis

Fish Physiology and Biochemistry ◽

10.1007/s10695-021-00977-y ◽

2021 ◽

Vol 47 (5) ◽

pp. 1565-1583

Author(s):

Zhaowei Zhong ◽

Lulu Ao ◽

Yilei Wang ◽

Shuhong Wang ◽

Liping Zhao ◽

...

Keyword(s):

Differential Expression ◽

Rna Seq ◽

Differential Expression Genes

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Important Roles of Key Genes and Transcription Factors in Flower Color Differences of Nicotiana alata

Genes ◽

10.3390/genes12121976 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1976

Author(s):

Yalin Zheng ◽

Yudong Chen ◽

Zhiguo Liu ◽

Hui Wu ◽

Fangchan Jiao ◽

...

Keyword(s):

Differential Expression ◽

Anthocyanin Biosynthesis ◽

Chlorophyll Biosynthesis ◽

Enrichment Analysis ◽

Flower Color ◽

Nicotiana Alata ◽

Biosynthesis Pathway ◽

Color Differences ◽

Differential Expression Genes ◽

Horticultural Plant

Nicotiana alata is an ornamental horticultural plant with a variety of flower colors and a long flowering period. The genes in four different colored N. alata (white, purple, red, and lemon green) were analyzed to explain the differences in flower color using transcriptomes. A total of 32 differential expression genes in the chlorophyll biosynthesis pathway and 41 in the anthocyanin biosynthesis pathway were identified. The enrichment analysis showed that the chlorophyll biosynthesis pathway and anthocyanin biosynthesis pathway play critical roles in the color differences of N. alata. The HEMA of the chlorophyll biosynthesis pathway was up-regulated in lemon green flowers. Compared with white flowers, in the red and purple flowers, F3H, F3′5′H and DFR were significantly up-regulated, while FLS was significantly down-regulated. Seventeen differential expression genes homologous to transcription factor coding genes were obtained, and the homologues of HY5, MYB12, AN1 and AN4 were also involved in flower color differences. The discovery of these candidate genes related to flower color differences is significant for further research on the flower colors formation mechanism and color improvements of N. alata.

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Identification of differential expression genes related to anthocyanin biosynthesis in carmine radish (Raphanus sativus L.) fleshy roots using comparative RNA-Seq method

PLoS ONE ◽

10.1371/journal.pone.0231729 ◽

2020 ◽

Vol 15 (4) ◽

pp. e0231729

Author(s):

Jian Gao ◽

Wen-Bo Li ◽

Hong-Fang Liu ◽

Fa-Bo Chen

Keyword(s):

Differential Expression ◽

Raphanus Sativus ◽

Anthocyanin Biosynthesis ◽

Rna Seq ◽

Differential Expression Genes ◽

Raphanus Sativus L

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Screening effective differential expression genes for hepatic carcinoma with metastasis in the peripheral blood mononuclear cells by RNA-seq

Oncotarget ◽

10.18632/oncotarget.15855 ◽

2017 ◽

Vol 8 (17) ◽

pp. 27976-27989 ◽

Cited By ~ 2

Author(s):

Yanting Shen ◽

Lu Bu ◽

Rui Li ◽

Zhenzhu Chen ◽

Fei Tian ◽

...

Keyword(s):

Differential Expression ◽

Peripheral Blood Mononuclear Cells ◽

Peripheral Blood ◽

Mononuclear Cells ◽

Rna Seq ◽

Hepatic Carcinoma ◽

Peripheral Blood Mononuclear ◽

Differential Expression Genes ◽

Blood Mononuclear Cells

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Identifying differential expression genes and single nucleotide variations using RNA-seq in metastatic melanoma

Genetics and Molecular Research ◽

10.4238/2014.october.7.10 ◽

2014 ◽

Vol 13 (4) ◽

pp. 8153-8162 ◽

Cited By ~ 3

Author(s):

D. Liu ◽

Z.G. Zhao ◽

Z.L. Jiao ◽

H.J. Li

Keyword(s):

Metastatic Melanoma ◽

Differential Expression ◽

Rna Seq ◽

Single Nucleotide ◽

Differential Expression Genes ◽

Single Nucleotide Variations

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Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)

10.21203/rs.2.18759/v1 ◽

2019 ◽

Author(s):

Xiujuan Zhang ◽

Jiabin Zhou ◽

Linmiao Li ◽

Wenzhong Huang ◽

Hafiz Ishfaq Ahmad ◽

...

Keyword(s):

Differential Expression ◽

Average Length ◽

Full Length ◽

Rna Seq ◽

Genetic Characteristics ◽

Kegg Pathways ◽

Amur Sturgeon ◽

Differential Expression Genes ◽

Transcription Data ◽

Development And Evolution

Abstract Background Sturgeons (Acipenseriformes) are polyploid chondrostean fish that constitute an important model species for studying development and evolution in vertebrates. To better understand the mechanisms of reproduction regulation in sturgeon, this study combined PacBio isoform sequencing (Iso-Seq) with Illumina short-read RNA-seq methods to discover full-length genes involved in early gametogenesis of the Amur sturgeon, Acipenser schrenckii .Results A total of 50.04 G subread bases were generated from two SMRT cells, and herein 164,618 nonredundant full-length transcripts (unigenes) were produced with an average length of 2,782 bp from gonad tissues (three testes and four ovaries) from seven 3-year-old A. schrenckii individuals. The number of ovary-specific expressed unigenes was greater than those of testis (19,716 vs. 3,028), and functional assignment indicated that 6 of 14 annotated KEGG pathways were directly ovary-related and had abundant transcripts and differential expression genes. Importantly, 60 early gametogenesis-related genes (involving 755 unigenes) were successfully identified, and exactly 50 percent (30/60) of those showed differential expression in testes and ovaries. The Amh and Gsdf with testis-biased expression, and Foxl2 and Cyp19a with ovary-biased expression strongly suggested the important regulatory roles in spermatogenesis and oogenesis of A. schrenckii , respectively. We also found the four novel Sox9 transcript variants, which increase the numbers of regulatory genes and imply function complexity of early gametogenesis. Finally, a total of 236,672 AS events (involving 36,522 unigenes) were detected, and 10,556 putative long noncoding RNAs (lncRNAs) and 4,339 predicted transcript factors (TFs) were also respectively identified, which all significantly associated with the early gametogenesis of A. schrenckii .Conclusions Overall, our results provide new genetic resources of full-length transcription data and information as a genomic-level reference for sturgeon. Crucially, we explored the comprehensive genetic characteristics that differ between the testes and ovaries of A. schrenckii in the early gametogenesis stage. These provide candidate genes and theoretical basis for further the mechanisms of reproduction regulation of sturgeon.

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