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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.


Functional classification of up-regulated DEGs in R_Y and Y_Y.Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs. Oxidoreductase activity, et al. is the short for oxidoreductase activity, acting on single donors with incorporation of molecular oxygen.
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f3: Functional classification of up-regulated DEGs in R_Y and Y_Y.Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs. Oxidoreductase activity, et al. is the short for oxidoreductase activity, acting on single donors with incorporation of molecular oxygen.

Mentions: To further highlight the distinct biological function, Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs of R_Y and Y_Y libraries. Functional classification of up-regulated DEGs in R_Y and Y_Y are displayed in Fig. 3. The results showed that in both libraries, genes involved in gene ontology biological process (GO-BP), such as inositol catabolic process (GO: 0019310), alcohol catabolic process (GO: 0046164), polyol catabolic process (GO: 0046174), organic hydroxy compound catabolic process (GO: 1901616), cellular carbohydrate metabolic process (GO: 0044262), and trehalose biosynthetic process (GO: 0005992). Genes involved in gene ontology cellular component (GO-CC), such as voltage-gated sodium channel complex (GO: 0001518), sodium channel complex (GO: 0034706), type III protein secretion system complex (GO: 0030257), and anchored component of plasma membrane (GO: 0046658). Genes involved in gene ontology molecular function (GO-MF), such as oxidoreductase activity (GO: 0016491), oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO: 0016701), inositol oxygenase activity (GO: 0050113), acyl-CoA dehydrogenase activity (GO: 0003995), catalytic activity (GO: 0003824), and voltage-gated sodium channel activity (GO: 0005248). Therefore, our analysis is focused on these aspects. In these groups, the number of up-regulated genes in Y_Y was higher than R_Y. In R_Y and Y_Y, 1105 (37.95%) and 1329 (31.46%) DEGs were clustered in “not assigned” of gene ontology (GO), respectively. Some of these gene may be novel genes involving in etiolation response that have never been reported.


Transcriptome Analyses of Two Citrus Cultivars ( Shiranuhi and Huangguogan ) in Seedling Etiolation
Functional classification of up-regulated DEGs in R_Y and Y_Y.Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs. Oxidoreductase activity, et al. is the short for oxidoreductase activity, acting on single donors with incorporation of molecular oxygen.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: Functional classification of up-regulated DEGs in R_Y and Y_Y.Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs. Oxidoreductase activity, et al. is the short for oxidoreductase activity, acting on single donors with incorporation of molecular oxygen.
Mentions: To further highlight the distinct biological function, Gene ontology biological process (GO-BP), gene ontology cellular component (GO-CC), and gene ontology molecular function (GO-MF) categories enriched in the up-regulated DEGs of R_Y and Y_Y libraries. Functional classification of up-regulated DEGs in R_Y and Y_Y are displayed in Fig. 3. The results showed that in both libraries, genes involved in gene ontology biological process (GO-BP), such as inositol catabolic process (GO: 0019310), alcohol catabolic process (GO: 0046164), polyol catabolic process (GO: 0046174), organic hydroxy compound catabolic process (GO: 1901616), cellular carbohydrate metabolic process (GO: 0044262), and trehalose biosynthetic process (GO: 0005992). Genes involved in gene ontology cellular component (GO-CC), such as voltage-gated sodium channel complex (GO: 0001518), sodium channel complex (GO: 0034706), type III protein secretion system complex (GO: 0030257), and anchored component of plasma membrane (GO: 0046658). Genes involved in gene ontology molecular function (GO-MF), such as oxidoreductase activity (GO: 0016491), oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO: 0016701), inositol oxygenase activity (GO: 0050113), acyl-CoA dehydrogenase activity (GO: 0003995), catalytic activity (GO: 0003824), and voltage-gated sodium channel activity (GO: 0005248). Therefore, our analysis is focused on these aspects. In these groups, the number of up-regulated genes in Y_Y was higher than R_Y. In R_Y and Y_Y, 1105 (37.95%) and 1329 (31.46%) DEGs were clustered in “not assigned” of gene ontology (GO), respectively. Some of these gene may be novel genes involving in etiolation response that have never been reported.

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.