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De novo sequencing and comparative analysis of expressed sequence tags from gynodioecious fig (Ficus carica L.) fruits: caprifig and common fig

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An Erratum to this article was published on 20 November 2015

Abstract

We conducted an exhaustive study of gene expression in fig fruits to identify the gene complexes responsible for fundamental fruit physiology and phenotypic differences between ecotypes. We performed high-throughput pyrosequencing on cDNA libraries constructed from caprifig and common fig fruits and compared their transcriptomes by analyzing the expressed sequence tags obtained. We collected a total of 290,594 expressed sequence tag reads from the two fruit types and assembled them into 71,455 unigenes (19,166 contigs and 52,289 singletons). We identified many metabolic genes, including those encoding proteins in the ethylene, glucose, and anthocyanin synthesis pathways that are involved in fruit maturation. This set also contained unigenes with unidentified functions. We observed no significant differences between the fruit types with respect to Gene Ontology term representation. By reverse transcription polymerase chain reaction, however, we detected several polymorphisms at the level of individual genes. Inter-type variations with respect to the expression level or transcription product size were observed in B- and C-class MADS-box gene homologs and chalcone synthase homologs, which are believed to be involved in sexuality and parthenocarpy, respectively. Expression polymorphisms were also observed for other genes, including a gibberellin-regulated protein gene. Our data and results contribute to genetic research on fig fruits and will aid in the understanding of fruit physiology and mechanisms of phenotypic differentiation.

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Acknowledgment

The authors would like to thank Edanz (http://www.edanzediting.co.jp/) for English language support.

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Authors and Affiliations

  1. Fukuoka Agricultural Research Center, 587 Yoshiki, Chikushino, Fukuoka, 818-8549, Japan

    Hidetoshi Ikegami, Chiharu Hirata & Keita Hirashima

  2. Faculty of Agriculture, Ehime University, Matsuyama, 790-8566, Japan

    Tsuyoshi Habu

  3. Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan

    Kazuki Mori, Kousuke Tashiro & Satoru Kuhara

  4. Fukuoka Control Station for Pests, 423 Yoshiki, Chikushino, Fukuoka, 818-0004, Japan

    Hitoshi Nogata

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  1. Hidetoshi Ikegami
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Correspondence to Hidetoshi Ikegami.

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Communicated by J. Wegrzyn

Data archiving statement

The sequence data generated in this study have been deposited at DDBJ in the Sequence Read Archive (DRA) and Transcriptome Shotgun Assembly (TSA) database under the accession number DRA000630 and FX376975-FX394131, respectively.

An erratum to this article is available at http://dx.doi.org/10.1007/s11295-015-0958-7.

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Ikegami, H., Habu, T., Mori, K. et al. De novo sequencing and comparative analysis of expressed sequence tags from gynodioecious fig (Ficus carica L.) fruits: caprifig and common fig. Tree Genetics & Genomes 9, 1075–1088 (2013). https://doi.org/10.1007/s11295-013-0622-z

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