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Gene expression profiles responses to aphid feeding in chrysanthemum (Chrysanthemum morifolium).

Xia X, Shao Y, Jiang J, Ren L, Chen F, Fang W, Guan Z, Chen S - BMC Genomics (2014)

Bottom Line: Approximately 76.35% of the clean reads were mapped to a reference gene database including all known chrysanthemum unigene sequences. 1,157, 527 and 340 differentially expressed genes (DEGs) were identified in the comparison of CK-VS-Y, CK-VS-Z and Z-VS-Y, respectively.These DEGs were involved in phytohormone signaling, cell wall biosynthesis, photosynthesis, reactive oxygen species (ROS) pathway and transcription factor regulatory networks, and so on.There are various forms of crosstalk between different pathways those genes belonging to, which would allow plants to fine-tune its defense responses.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, No,1 Weigang, Nanjing 210095, China. chensm@njau.edu.cn.

ABSTRACT

Background: Chrysanthemum is an important ornamental plant all over the world. It is easily attacked by aphid, Macrosiphoniella sanbourni. The molecular mechanisms of plant defense responses to aphid are only partially understood. Here, we investigate the gene expression changes in response to aphid feeding in chrysanthemum leaf by RNA-Seq technology.

Results: Three libraries were generated from pooled leaf tissues of Chrysanthemum morifolium 'nannongxunzhang' that were collected at different time points with (Y) or without (CK) aphid infestations and mock puncture treatment (Z), and sequenced using an Illumina HiSeqTM 2000 platform. A total of 7,363,292, 7,215,860 and 7,319,841 clean reads were obtained in library CK, Y and Z, respectively. The proportion of clean reads was >97.29% in each library. Approximately 76.35% of the clean reads were mapped to a reference gene database including all known chrysanthemum unigene sequences. 1,157, 527 and 340 differentially expressed genes (DEGs) were identified in the comparison of CK-VS-Y, CK-VS-Z and Z-VS-Y, respectively. These DEGs were involved in phytohormone signaling, cell wall biosynthesis, photosynthesis, reactive oxygen species (ROS) pathway and transcription factor regulatory networks, and so on.

Conclusions: Changes in gene expression induced by aphid feeding are shown to be multifaceted. There are various forms of crosstalk between different pathways those genes belonging to, which would allow plants to fine-tune its defense responses.

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Related in: MedlinePlus

Distribution of gene coverage in each library (CK, Y and Z). CK: control; Y: aphid infestation treatment; Z: mock puncture treatment. The term ā€œgene coverageā€ reflects the proportion of the full gene sequence represented by RNA-Seq reads.
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Fig2: Distribution of gene coverage in each library (CK, Y and Z). CK: control; Y: aphid infestation treatment; Z: mock puncture treatment. The term ā€œgene coverageā€ reflects the proportion of the full gene sequence represented by RNA-Seq reads.

Mentions: A reference gene database including all known Chrysanthemum morifolium unigene sequences was applied to map the clean reads. According to the chosen criteria, an average of 76.35% of the clean reads were mapped (TableĀ 1), which consisted of perfect match andā€‰<ā€‰=2Ā bp mismatch. Regarding each library, the scales of clean reads uniquely mapped to the database were 50.84%, 50.34% and 50.54%, respectively. There were still approximately 23.65% of clean reads that cannot be mapped, mainly due to the restriction of the reference gene database of chrysanthemum. The number of genes identified increased with the number of reads until above 6,000,000, implying saturation of sequencing (FigureĀ 1). The unigene coverage analysed as a means of evaluating the quality of the RNA-Seq data was mostly >50% (FigureĀ 2).Figure 1


Gene expression profiles responses to aphid feeding in chrysanthemum (Chrysanthemum morifolium).

Xia X, Shao Y, Jiang J, Ren L, Chen F, Fang W, Guan Z, Chen S - BMC Genomics (2014)

Distribution of gene coverage in each library (CK, Y and Z). CK: control; Y: aphid infestation treatment; Z: mock puncture treatment. The term ā€œgene coverageā€ reflects the proportion of the full gene sequence represented by RNA-Seq reads.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4265409&req=5

Fig2: Distribution of gene coverage in each library (CK, Y and Z). CK: control; Y: aphid infestation treatment; Z: mock puncture treatment. The term ā€œgene coverageā€ reflects the proportion of the full gene sequence represented by RNA-Seq reads.
Mentions: A reference gene database including all known Chrysanthemum morifolium unigene sequences was applied to map the clean reads. According to the chosen criteria, an average of 76.35% of the clean reads were mapped (TableĀ 1), which consisted of perfect match andā€‰<ā€‰=2Ā bp mismatch. Regarding each library, the scales of clean reads uniquely mapped to the database were 50.84%, 50.34% and 50.54%, respectively. There were still approximately 23.65% of clean reads that cannot be mapped, mainly due to the restriction of the reference gene database of chrysanthemum. The number of genes identified increased with the number of reads until above 6,000,000, implying saturation of sequencing (FigureĀ 1). The unigene coverage analysed as a means of evaluating the quality of the RNA-Seq data was mostly >50% (FigureĀ 2).Figure 1

Bottom Line: Approximately 76.35% of the clean reads were mapped to a reference gene database including all known chrysanthemum unigene sequences. 1,157, 527 and 340 differentially expressed genes (DEGs) were identified in the comparison of CK-VS-Y, CK-VS-Z and Z-VS-Y, respectively.These DEGs were involved in phytohormone signaling, cell wall biosynthesis, photosynthesis, reactive oxygen species (ROS) pathway and transcription factor regulatory networks, and so on.There are various forms of crosstalk between different pathways those genes belonging to, which would allow plants to fine-tune its defense responses.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, No,1 Weigang, Nanjing 210095, China. chensm@njau.edu.cn.

ABSTRACT

Background: Chrysanthemum is an important ornamental plant all over the world. It is easily attacked by aphid, Macrosiphoniella sanbourni. The molecular mechanisms of plant defense responses to aphid are only partially understood. Here, we investigate the gene expression changes in response to aphid feeding in chrysanthemum leaf by RNA-Seq technology.

Results: Three libraries were generated from pooled leaf tissues of Chrysanthemum morifolium 'nannongxunzhang' that were collected at different time points with (Y) or without (CK) aphid infestations and mock puncture treatment (Z), and sequenced using an Illumina HiSeqTM 2000 platform. A total of 7,363,292, 7,215,860 and 7,319,841 clean reads were obtained in library CK, Y and Z, respectively. The proportion of clean reads was >97.29% in each library. Approximately 76.35% of the clean reads were mapped to a reference gene database including all known chrysanthemum unigene sequences. 1,157, 527 and 340 differentially expressed genes (DEGs) were identified in the comparison of CK-VS-Y, CK-VS-Z and Z-VS-Y, respectively. These DEGs were involved in phytohormone signaling, cell wall biosynthesis, photosynthesis, reactive oxygen species (ROS) pathway and transcription factor regulatory networks, and so on.

Conclusions: Changes in gene expression induced by aphid feeding are shown to be multifaceted. There are various forms of crosstalk between different pathways those genes belonging to, which would allow plants to fine-tune its defense responses.

Show MeSH
Related in: MedlinePlus