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Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L.).

Liu C, Ma N, Wang PY, Fu N, Shen HL - PLoS ONE (2013)

Bottom Line: Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively.Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

View Article: PubMed Central - PubMed

Affiliation: China Agricultural University, Beijing, China.

ABSTRACT

Background: The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility.

Results: We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.

Conclusions: Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

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Gene Ontology classification of assembled unigenes.
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pone-0065209-g003: Gene Ontology classification of assembled unigenes.

Mentions: A total of 9,896 unigenes were assigned to 58 functional groups using GO assignment (Figure 3). In each of the three main categories (cellular component, molecular function and biological progress) of the GO classification, the dominant terms were “cell”, “binding” and “cellular process”, respectively. “Intracellular”, “catalytic activity” and “metabolic process” were also well represented. However, few genes were assigned to the terms “proteinaceous extracellular matrix & cell surface”, “translation regulator activity” and “extracellular structure organization”.


Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L.).

Liu C, Ma N, Wang PY, Fu N, Shen HL - PLoS ONE (2013)

Gene Ontology classification of assembled unigenes.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672106&req=5

pone-0065209-g003: Gene Ontology classification of assembled unigenes.
Mentions: A total of 9,896 unigenes were assigned to 58 functional groups using GO assignment (Figure 3). In each of the three main categories (cellular component, molecular function and biological progress) of the GO classification, the dominant terms were “cell”, “binding” and “cellular process”, respectively. “Intracellular”, “catalytic activity” and “metabolic process” were also well represented. However, few genes were assigned to the terms “proteinaceous extracellular matrix & cell surface”, “translation regulator activity” and “extracellular structure organization”.

Bottom Line: Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively.Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

View Article: PubMed Central - PubMed

Affiliation: China Agricultural University, Beijing, China.

ABSTRACT

Background: The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility.

Results: We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen.

Conclusions: Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations.

Show MeSH
Related in: MedlinePlus