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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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Related in: MedlinePlus

KOG functional classifications of the Capsicum annuum L. anther transcriptome.
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pone-0065209-g002: KOG functional classifications of the Capsicum annuum L. anther transcriptome.

Mentions: Out of 85,144 assembled unigenes, 35,393 unigenes were classified into 25 KOG categories (Figure 2), among which “Signal transduction mechanisms” represented the largest group (4,656, 13.16%), followed by “General function prediction only” (4,176, 11.80%), “Function unknown” (3,157, 8.92%) and “Posttranslational modification, protein turnover, chaperones” (2,917, 8.24%). “Nuclear structure” (234, 0.66%), “Extracellular structures” (182, 0.51%) and “Cell motility” (46, 0.13%) were the smallest groups.


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)

KOG functional classifications of the Capsicum annuum L. anther transcriptome.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0065209-g002: KOG functional classifications of the Capsicum annuum L. anther transcriptome.
Mentions: Out of 85,144 assembled unigenes, 35,393 unigenes were classified into 25 KOG categories (Figure 2), among which “Signal transduction mechanisms” represented the largest group (4,656, 13.16%), followed by “General function prediction only” (4,176, 11.80%), “Function unknown” (3,157, 8.92%) and “Posttranslational modification, protein turnover, chaperones” (2,917, 8.24%). “Nuclear structure” (234, 0.66%), “Extracellular structures” (182, 0.51%) and “Cell motility” (46, 0.13%) were the smallest groups.

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