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

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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.


Distribution of KEGG classification of up-regulated DEGs in Shiranuhi and Huangguogan.The P-value was calculated using the Benjamini correction method and Fisher’s exact test (P-value < 0.01). (A) Amino acid metabolism. (B) Carbohydrate metabolism. (C) Energy metabolism. (D) Metabolism of terpenoids and polyketides. (E) Lipid metabolism.
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f4: Distribution of KEGG classification of up-regulated DEGs in Shiranuhi and Huangguogan.The P-value was calculated using the Benjamini correction method and Fisher’s exact test (P-value < 0.01). (A) Amino acid metabolism. (B) Carbohydrate metabolism. (C) Energy metabolism. (D) Metabolism of terpenoids and polyketides. (E) Lipid metabolism.

Mentions: The distribution of top 11 KEGG pathway of up-regulated DEGs showed that in all annotated amino acid metabolism (101 and 165 DEGs in etiolated Shiranuhi and Huangguogan seedlings, respectively) and carbohydrate metabolism (96 and 95 DEGs in etiolated Shiranuhi and Huangguogan seedlings, respectively) have the most hits (Fig. 4). These pathways were mainly over-represented in amino acid metabolism in both R_Y and Y_Y. There were 7 common pathways in both R_Y and Y_Y library, it enriched in amino acid metabolism (KO 00280, KO 00250, KO 00310, KO 00330, KO 00340), carbohydrate metabolism (KO 00053, KO 00500). 32 and 60 up-regulated DEGs were mainly over-represented in valine, leucine and isoleucine degradation (KO 00280) of metabolism in R_Y and Y_Y, respectively (Supplementary Tables S3 and S4).


Transcriptome Analyses of Two Citrus Cultivars ( Shiranuhi and Huangguogan ) in Seedling Etiolation
Distribution of KEGG classification of up-regulated DEGs in Shiranuhi and Huangguogan.The P-value was calculated using the Benjamini correction method and Fisher’s exact test (P-value < 0.01). (A) Amino acid metabolism. (B) Carbohydrate metabolism. (C) Energy metabolism. (D) Metabolism of terpenoids and polyketides. (E) Lipid metabolism.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f4: Distribution of KEGG classification of up-regulated DEGs in Shiranuhi and Huangguogan.The P-value was calculated using the Benjamini correction method and Fisher’s exact test (P-value < 0.01). (A) Amino acid metabolism. (B) Carbohydrate metabolism. (C) Energy metabolism. (D) Metabolism of terpenoids and polyketides. (E) Lipid metabolism.
Mentions: The distribution of top 11 KEGG pathway of up-regulated DEGs showed that in all annotated amino acid metabolism (101 and 165 DEGs in etiolated Shiranuhi and Huangguogan seedlings, respectively) and carbohydrate metabolism (96 and 95 DEGs in etiolated Shiranuhi and Huangguogan seedlings, respectively) have the most hits (Fig. 4). These pathways were mainly over-represented in amino acid metabolism in both R_Y and Y_Y. There were 7 common pathways in both R_Y and Y_Y library, it enriched in amino acid metabolism (KO 00280, KO 00250, KO 00310, KO 00330, KO 00340), carbohydrate metabolism (KO 00053, KO 00500). 32 and 60 up-regulated DEGs were mainly over-represented in valine, leucine and isoleucine degradation (KO 00280) of metabolism in R_Y and Y_Y, respectively (Supplementary Tables S3 and S4).

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.