Cinvestav  The Chili Database  Computational Biology Lab

Objective

This page gives access to the data presented in the research paper

"Dynamics of the chili pepper transcriptome during fruit development"
Luis A Martínez-López (1,2), Neftalí Ochoa-Alejo (2,3) and Octavio Martínez (1)*

* Corresponding author:    Octavio Martínez (also maintainer of this site)

Author Affiliations
1 Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO),
Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav),
36821 Irapuato, Guanajuato, México

2 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

3 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

BMC Genomics 2014, 15:143  doi:10.1186/1471-2164-15-143

Summary of the experiment

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.

chili fruits at different development stage

What can I do in this page?

You can make queries to our database, to obtain information about the sequences
(transcripts), their identification, annotation, expression levels etc.

You are free to explore the database in any form that you want. We hope that you find
interesting facts. If you use the information in your research, please cite the source
(the URL of this page), and the paper above.

You can also perform a BLAST analysis of your own sequences of nucleotides to the database (click HERE).

Mantainer: Octavio Martínez

Tables in the database

What follows is a partial list of the tables in the database (the ones that you
can access at this moment). The link in the name of the table will take you to
a technical description of the corresponding table. With this you can know which
variables are in the table and design queries for the database.

Table
Brief description
seq
Sequences (transcripts) assembled from the experiment
seq_ident
Identification of sequences (source and description)
info_seq
Information about sequences (length and % of GC)
expression
Expression level per gene and library
expressTPMround Expression level in Transcripts Per Million (rounded) per gene and treatment
annotBPexpress Annotation by Biological Process (BP) from Gene Ontology
annotCCexpress Annotation by Cellular Component (CC) from Gene Ontology
annotMFexpress Annotation by Molecular Function (MF) from Gene Ontology
annotKegPathExpress Annotation by KEG metabolic pathway
DisDE
Summary of statistical results from the analysis
discoveries
Summary of gene expression discoveries
desc_tables Description of the tables in the chili database

QUERIES

(using the database)

Acknowledgements

This research was funded by grants to NO-A Conacyt project 177063, OM Conacyt project 165778,
LAM-L Conacyt scholarship 262926. We thank Alejandra Aguilar-Barragán for her technical help in
NO-A’s lab, Fernando Hernández Godínez for technical help in OM lab and the
Data Intensive Academic Grid (DIAG) for computing facilities used in the transcriptome assembly.
We also acknowledge Araceli Fenández Cortés by the development of the php programs used to query
the database.