Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
Visualitza/Obre
Autor/a
Clepet, Christian
Joobeur, Tarek
Zheng, Yi
Jublot, Delphine
Huang, Mingyun
Truniger, Veronica
Boualem, Adnane
Hernandez-Gonzalez, Maria Elena
Portnoy, Vitaly
Mascarell-Creus, Albert
Caño-Delgado, Ana I.
Katzir, Nurit
Bendahmane, Abdelhafid
Giovannoni, James J.
Aranda, Miguel A.
Fei, Zhangjun
Data de publicació
2011-05-20ISSN
1471-2164
Resum
Background: Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae
family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as
a model system for sex determination and vascular biology studies. However, genomic resources currently available
for melon are limited.
Result: We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves,
roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from fulllength enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in
public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their
sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and
mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes
revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had
homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and
monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae
family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which
provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified
4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST
collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length
enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that
sizes of melon 5’ and 3’ UTRs were similar to those of tomato, but longer than many other dicot plants. Codon
usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.
Conclusion: The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is
expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be
useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related
species, comparative genomic studies and for gaining insights into gene expression patterns.
Tipus de document
Article
Versió del document
Versió publicada
Llengua
English
Matèries (CDU)
575 - Genètica general. Citogenètica general. Immunogenètica. Evolució. Filogènia
Pàgines
12
Publicat per
BMC
Publicat a
BMC Genomics
Citació
Clepet, Christian, Tarek Joobeur, Yi Zheng, Delphine Jublot, Mingyun Huang, Veronica Truniger, Adnane Boualem, et al. 2011. “Analysis of Expressed Sequence Tags Generated From Full-length Enriched cDNA Libraries of Melon.” BMC Genomics 12 (1): 252. doi:10.1186/1471-2164-12-252
Programa
Genòmica i Biotecnologia
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