Dynamics of the chili pepper transcriptome during fruit development

BMC Genomics

Octavio Martínez²  Neftalí Ochoa-Alejo¹  Luis A Martínez-López³ 

[1] Departamento de Biotecnología y Bioquímica, Unidad de Biotecnología e Ingeniería Genética, Centro de Investigacíon y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-Unidad Irapuato), 36821 Irapuato, Guanajuato, México;Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), 36821 Irapuato, Guanajuato, México;Departamento de Ingeniería Genética de Plantas, Unidad de Biotecnología e Ingeniería Genética, Centro de Investigacíon y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav-Unidad Irapuato), 36821 Irapuato, Guanajuato, México

关键词: Illumina MiSeq;    Pathway analysis;    High-throughput sequencing;    RNA-Seq;    Gene expression;    Fruit ripening;    Fruit development;    Transcriptome;    Chili pepper;    Capsicum;   

Others  :  1217853
DOI  :  10.1186/1471-2164-15-143

 received in 2013-10-18, accepted in 2014-02-18,  发布年份 2014

【 摘 要 】

Background

The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening.

Results

RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; ‘Tampiqueño 74’) collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40–60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR.

Conclusions

In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled.

【 授权许可】

   
2014 Martínez-López et al.; licensee BioMed Central Ltd.

【 图 表 】

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