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Transcriptome Analyses of Two Citrus Cultivars ( Shiranuhi and Huangguogan ) in Seedling Etiolation

View Article: PubMed Central - PubMed

ABSTRACT

Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars—Huangguogan and Shiranuhi, respectively—were investigated. More than 834.16 million clean reads and 125.12 Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30. 124,952 unigenes were finally generated with a mean length of 1,189 bp. 79.15%, 84.35%, 33.62%, 63.12%, 57.67%, 57.99% and 37.06% of these unigenes had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan.

No MeSH data available.


Veen diagram show the number of DEGs between etiolated, multicoloured seedlings of Shiranuhi and Huangguogan.(A) The Venn diagram displays the distribution of up-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G. (B) The Venn diagram displays the distribution of down-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G.
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f2: Veen diagram show the number of DEGs between etiolated, multicoloured seedlings of Shiranuhi and Huangguogan.(A) The Venn diagram displays the distribution of up-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G. (B) The Venn diagram displays the distribution of down-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G.

Mentions: In the process of DEGs screening, we used P-value < 0.00526 and log2FC (fold change) > 1 as the threshold to determine the significance of gene expression difference. FC is the ratio of FPKM between etiolated and green seedlings. DEG profile analysis was used to analyze gene expression in the two stages of Shiranuhi and Huangguogan leaf etiolation. The changes in gene expression between etiolated, multicoloured and green seedlings was analyzed in a Venn diagram (Fig. 2), which illustrated the intersections between the expressed genes detected in the two stages of Shiranuhi and Huangguogan leaf etiolation.


Transcriptome Analyses of Two Citrus Cultivars ( Shiranuhi and Huangguogan ) in Seedling Etiolation
Veen diagram show the number of DEGs between etiolated, multicoloured seedlings of Shiranuhi and Huangguogan.(A) The Venn diagram displays the distribution of up-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G. (B) The Venn diagram displays the distribution of down-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5384249&req=5

f2: Veen diagram show the number of DEGs between etiolated, multicoloured seedlings of Shiranuhi and Huangguogan.(A) The Venn diagram displays the distribution of up-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G. (B) The Venn diagram displays the distribution of down-regulated genes in R_Y vs R_G, R_M vs R_G, Y_Y vs Y_G, and Y_M vs Y_G.
Mentions: In the process of DEGs screening, we used P-value < 0.00526 and log2FC (fold change) > 1 as the threshold to determine the significance of gene expression difference. FC is the ratio of FPKM between etiolated and green seedlings. DEG profile analysis was used to analyze gene expression in the two stages of Shiranuhi and Huangguogan leaf etiolation. The changes in gene expression between etiolated, multicoloured and green seedlings was analyzed in a Venn diagram (Fig. 2), which illustrated the intersections between the expressed genes detected in the two stages of Shiranuhi and Huangguogan leaf etiolation.

View Article: PubMed Central - PubMed

ABSTRACT

Citrus species are among the most important fruit crops. However, gene regulation and signaling pathways related to etiolation in this crop remain unknown. Using Illumina sequencing technology, modification of global gene expression in two hybrid citrus cultivars&mdash;Huangguogan and Shiranuhi, respectively&mdash;were investigated. More than 834.16 million clean reads and 125.12&thinsp;Gb of RNA-seq data were obtained, more than 91.37% reads had a quality score of Q30. 124,952 unigenes were finally generated with a mean length of 1,189&thinsp;bp. 79.15%, 84.35%, 33.62%, 63.12%, 57.67%, 57.99% and 37.06% of these unigenes had been annotated in NR, NT, KO, SwissProt, PFAM, GO and KOG databases, respectively. Further, we identified 604 differentially expressed genes in multicoloured and etiolated seedlings of Shiranuhi, including 180 up-regulated genes and 424 down-regulated genes. While in Huangguogan, we found 1,035 DEGs, 271 of which were increasing and the others were decreasing. 7 DEGs were commonly up-regulated, and 59 DEGs down-regulated in multicoloured and etiolated seedlings of these two cultivars, suggesting that some genes play fundamental roles in two hybrid citrus seedlings during etiolation. Our study is the first to provide the transcriptome sequence resource for seedlings etiolation of Shiranuhi and Huangguogan.

No MeSH data available.