ORIGINAL PAPER High-throughput sequencing analysis of common fig (Ficus carica L.) transcriptome during fruit ripening Zohar E. Freiman & Adi Doron-Faigenboim & Rajeswari Dasmohapatra & Zeev Yablovitz & Moshe A. Flaishman Received: 6 January 2014 /Revised: 18 March 2014 /Accepted: 28 March 2014 # Springer-Verlag Berlin Heidelberg 2014 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 path- ways 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 identi- fied. 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. Keywords Ethylene . Ficus carica . Fruit development . MADS box . Ripening . Transcriptome Introduction The fig tree, Ficus carica L. (Moraceae), belongs to one of the largest angiosperm genera. The genus is widely cultivated in the tropics and subtropics and exhibits diverse growth habits, including trees, shrubs, hemi-epiphytes, climbers, and creepers (Berg and Corner 2005). Among Ficus species, the fig is the only member suitable for fresh consumption by humans and is believed to be one of the first domesticated plants (Kislev et al. 2006). All Ficus species bear a unique inflorescence structure—the syconium. This closed inflores- cence produces an aggregate fruit, composed of small indi- vidual drupelets which develop from the ovaries following pollination. Female fig syconium development is characterized by a double sigmoid growth curve comprised of three phases (Chessa 1997; Marei and Crane 1971). Phase I is character- ized by a rapid growth in size; during phase II, the fruit remains nearly the same size, color, and firmness. Phase III is the ripening phase and includes exceptionally rapid fruit growth, color change, softening, and alteration of the pulp texture to an edible state (Chessa 1997). The syconium de- velops into a succulent fruit by either pollination occurring at Communicated by J.L. Wegrzyn Electronic supplementary material The online version of this article (doi:10.1007/s11295-014-0732-2) contains supplementary material, which is available to authorized users. Z. E. Freiman : A. Doron-Faigenboim : R. Dasmohapatra : Z. Yablovitz : M. A. Flaishman Institute of Plant Sciences, Agricultural Research Organization, P.O. Box 6, Bet-Dagan 50250, Israel Z. E. Freiman 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 M. A. Flaishman (*) Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, Bet Dagan 50250, Israel e-mail: vhmoshea@agri.gov.il Tree Genetics & Genomes DOI 10.1007/s11295-014-0732-2