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High-throughput sequencing analysis of common fig (Ficus carica L.) transcriptome during fruit ripening

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Abstract

The Ficus carica L. (Moraceae) tree belongs to one of the largest genera of angiosperms and bears a unique closed inflorescence structure. Ripe fresh figs are highly perishable and require delicate postharvest handling. Studying the pathways that lead to fig ripening may provide additional ways of extending their storage life. We selected four developmental stages of fig fruit for transcriptome sequencing and analysis to identify the major active metabolic pathways and transcription factors during fig fruit ripening. We found 12,751 unigenes, 93 % of which were homologous to at least one nonredundant database sequence, and 46,927 singletons, 39 % with a matching sequence from the nonredundant database. Differential activity related to photosynthesis, anthocyanin and volatile metabolism, cell wall and wax metabolism, cell expansion, transcription, DNA metabolism and organization was traced. In addition, ethylene-synthesis genes were identified. Finally, 516 unigenes encoding transcription factors were found which were active in the regulation of early and late ripening processes. Focusing on eight FcMADS-box transcription factors revealed three genes encoding members of the AGL2 (SEP) subfamily, which is closely associated with ripening regulation. This study provides expressed-gene dataset for multiple developmental stages of fig fruit (F. carica), and analysis directed to ripening metabolism, control, and regulation. It provides a potential platform for further studies of this unique plant family and contributes to ripening process research in nonmodel systems.

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Acknowledgments

The authors wish to thank Dr. Vered Caspi, Inbar Plaschkes, and Guy Rapaport of the Bioinformatics Core Facility, The National Institute for Biotechnology in the Negev, Ben-Gurion University, Beer-Sheva, Israel, for providing us with computer services and support for the annotation analysis. We also thank Dr. Amir Sherman, Dr. Ron Ophir, Dr. Nurit Katzir, and Dr. Shiri Freilich for their helpful advice. This work was supported by a grant from The Ministry of Agriculture, Israel.

Data archiving statement

The sequence data generated in this study have been deposited at NCBI in the Sequence Read Archive (SRA) under the accession numbers SRR1174869- SRR1174872 (sample 1–4, respectively). The Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank under the accession GAYT00000000. The version described in this paper is the first version, GAYT01000000. Sequences of cDNA isolates of Isogroups 1917, 4355, 7031, 10006, 9067, 1334, 5572, and 139 have been deposited at NCBI under the accessions KJ506152- KJ506159 (FcMADS1-8, respectively).

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Authors and Affiliations

  1. Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan, 50250, Israel

    Zohar E. Freiman, Adi Doron-Faigenboim, Rajeswari Dasmohapatra, Zeev Yablovitz & Moshe A. Flaishman

  2. The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 76100, Israel

    Zohar E. Freiman

  3. Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan, 50250, Israel

    Moshe A. Flaishman

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  1. Zohar E. Freiman
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  2. Adi Doron-Faigenboim
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  3. Rajeswari Dasmohapatra
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  4. Zeev Yablovitz
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  5. Moshe A. Flaishman
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Correspondence to Moshe A. Flaishman.

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Communicated by J.L. Wegrzyn

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Freiman, Z.E., Doron-Faigenboim, A., Dasmohapatra, R. et al. High-throughput sequencing analysis of common fig (Ficus carica L.) transcriptome during fruit ripening. Tree Genetics & Genomes 10, 923–935 (2014). https://doi.org/10.1007/s11295-014-0732-2

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