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Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type.

Xu Q, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X - BMC Genomics (2010)

Bottom Line: Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT).Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange.This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China. xuqiang@mail.hzau.edu.cn

ABSTRACT

Background: Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far.

Results: We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT.

Conclusion: This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.

Show MeSH
Expression confirmation of citrus miRNAs derived from high throughput sequencing. (A). novel miRNAs expression detected by stem-loop qRT-PCR; (B) differentially expressed known miRNAss expression detected by stem-loop qRT-PCR; (C) electrophoresis of the stem-loop PCR products. Each primer has been used for the PCR amplifications on two samples, mutant and wild type.
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Figure 4: Expression confirmation of citrus miRNAs derived from high throughput sequencing. (A). novel miRNAs expression detected by stem-loop qRT-PCR; (B) differentially expressed known miRNAss expression detected by stem-loop qRT-PCR; (C) electrophoresis of the stem-loop PCR products. Each primer has been used for the PCR amplifications on two samples, mutant and wild type.

Mentions: To confirm the expression of the novel miRNAs, we analyzed the expression of all the 12 novel miRNAs using stem-loop qRT-PCR. All the genes could be detected by qRT-PCR (Figure 4A). Of the 12 novel miRNAs, 8 genes showed similar expression pattern to that revealed from sequencing data of the sRNA libraries. The electrophoresis of the qRT-PCR products confirmed the size and expression of these novel miRNAs (Figure 4C). Moreover, we analyzed the expression of three miRNA*s (csi-novel-03, -05, -06); and results showed that two miRNA*s had different expression pattern from those of corresponding mature miRNAs (Figure 4A).


Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type.

Xu Q, Liu Y, Zhu A, Wu X, Ye J, Yu K, Guo W, Deng X - BMC Genomics (2010)

Expression confirmation of citrus miRNAs derived from high throughput sequencing. (A). novel miRNAs expression detected by stem-loop qRT-PCR; (B) differentially expressed known miRNAss expression detected by stem-loop qRT-PCR; (C) electrophoresis of the stem-loop PCR products. Each primer has been used for the PCR amplifications on two samples, mutant and wild type.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2864249&req=5

Figure 4: Expression confirmation of citrus miRNAs derived from high throughput sequencing. (A). novel miRNAs expression detected by stem-loop qRT-PCR; (B) differentially expressed known miRNAss expression detected by stem-loop qRT-PCR; (C) electrophoresis of the stem-loop PCR products. Each primer has been used for the PCR amplifications on two samples, mutant and wild type.
Mentions: To confirm the expression of the novel miRNAs, we analyzed the expression of all the 12 novel miRNAs using stem-loop qRT-PCR. All the genes could be detected by qRT-PCR (Figure 4A). Of the 12 novel miRNAs, 8 genes showed similar expression pattern to that revealed from sequencing data of the sRNA libraries. The electrophoresis of the qRT-PCR products confirmed the size and expression of these novel miRNAs (Figure 4C). Moreover, we analyzed the expression of three miRNA*s (csi-novel-03, -05, -06); and results showed that two miRNA*s had different expression pattern from those of corresponding mature miRNAs (Figure 4A).

Bottom Line: Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT).Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange.This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China. xuqiang@mail.hzau.edu.cn

ABSTRACT

Background: Red-flesh fruit is absent from common sweet orange varieties, but is more preferred by consumers due to its visual attraction and nutritional properties. Our previous researches on a spontaneous red-flesh mutant revealed that the trait is caused by lycopene accumulation and is regulated by both transcriptional and post-transcriptional mechanisms. However, the knowledge on post-transcriptional regulation of lycopene accumulation in fruits is rather limited so far.

Results: We used Illumina sequencing method to identify and quantitatively profile small RNAs on the red-flesh sweet orange mutant and its wild type. We identified 85 known miRNAs belonging to 48 families from sweet orange. Comparative profiling revealed that 51 known miRNAs exhibited significant expression differences between mutant (MT) and wild type (WT). We also identified 12 novel miRNAs by the presence of mature miRNAs and corresponding miRNA*s in the sRNA libraries. Comparative analysis showed that 9 novel miRNAs are differentially expressed between WT and MT. Target predictions of the 60 differential miRNAs resulted 418 target genes in sweet orange. GO and KEGG annotation revealed that high ranked miRNA-target genes are those implicated in transcription regulation, protein modification and photosynthesis. The expression profiles of target genes involved in carotenogenesis and photosynthesis were further confirmed to be complementary to the profiles of corresponding miRNAs in WT and MT.

Conclusion: This study comparatively characterized the miRNAomes between the red-flesh mutant and the wild type, the results lay a foundation for unraveling the miRNA-mediated molecular processes that regulate lycopene accumulation in the sweet orange red-flesh mutant.

Show MeSH