Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

Zambrano, L. Solorzano; Usai, Gabriele; Vangelisti, Alberto; Mascagni, Flavia; Giordani, Tommaso; Bernardi, Rodolfo; Cavallini, Andrea; Gucci, Riccardo; Caruso, Giovanni; D'Onofrio, Claudio; Quartacci, Mike Frank; Picciarelli, Piero; Conti, Bárbara; Lucchi, Andrea; Natali, Lucia

doi:10.1016/j.gdata.2017.07.005

Cited by 12 publications

(4 citation statements)

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“…In recent years, several studies have been carried out on the transcriptomic aspects of fig fruit development and ripening. For example, the predicted transcriptomes of two major cultivars—Dottato and Horaishi—were compared, revealing more than 2000 and 4000 cultivar-specific genes, respectively [16]. Transcriptome comparison has also been applied to elucidate the expression differences of fig biotypes: a comparison between young San Pedro type fig and common fig fruit showed that zeatin biosynthesis and plant hormone signal-transduction pathways are differentially regulated [17], and ethylene synthesis and phytohormone signal transduction were found to be differentially expressed between caprifig and common fig fruit [18].…”

Section: Introductionmentioning

confidence: 99%

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

et al. 2019

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Background Fig fruit are highly perishable at the tree-ripe (TR) stage. Commercial-ripe (CR) fruit, which are harvested before the TR stage for their postharvest transportability and shelf-life advantage, are inferior to TR fruit in size, color and sugar content. The succulent urn-shaped receptacle, serving as the protective structure and edible part of the fruit, determines fruit quality. Quantitative iTRAQ and RNA-Seq were performed to reveal the differential proteomic and transcriptomic traits of the receptacle at the two harvest stages. Results We identified 1226 proteins, of which 84 differentially abundant proteins (DAPs) were recruited by criteria of abundance fold-change (FC) ≥1.3 and p < 0.05 in the TR/CR receptacle proteomic analysis. In addition, 2087 differentially expressed genes (DEGs) were screened by ≥2-fold expression change: 1274 were upregulated and 813 were downregulated in the TR vs. CR transcriptomic analysis. Ficin was the most abundant soluble protein in the fig receptacle. Sucrose synthase, sucrose-phosphate synthase and hexokinase were all actively upregulated at both the protein and transcriptional levels. Endoglucanase, expansin, beta-galactosidase, pectin esterase and aquaporins were upregulated from the CR to TR stage at the protein level. In hormonal synthesis and signaling pathways, high protein and transcriptional levels of aminocyclopropane-1-carboxylate oxidase were identified, together with a few diversely expressed ethylene-response factors, indicating the potential leading role of ethylene in the ripening process of fig receptacle, which has been recently reported as a non-climacteric tissue. Conclusions We present the first delineation of intra- and inter-omic changes in the expression of specific proteins and genes of TR vs. CR fig receptacle, providing valuable candidates for further study of fruit-quality formation control and fig cultivar innovation to accommodate market demand. Electronic supplementary material The online version of this article (10.1186/s12870-019-1742-x) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

et al. 2019

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“…Analysis performed with the Viridiplantae dataset of BUSCO conserved genes found that the assembled transcriptome included 76.6% of complete genes (i.e., single copy and full length) ( Figure S7 ). The assembled transcripts, together with the transcripts from the official annotation and a de novo assembly produced by Solorzano Zambrano ( Solorzano Zambrano et al, 2017 ; Usai et al, 2020 ) were used with the Maker2 pipeline to produce a pre-annotation that was then used to create an Augustus gene model. The model was refined 4 times before the genome annotation was obtained, which contained 35,567 genes.…”

Section: Resultsmentioning

confidence: 99%

“…The assembled transcript and the transcriptome sequences published in Solorzano Zambrano ( Solorzano Zambrano et al, 2017 ) were used with the Maker2 v3.0.0 ( Cantarel et al, 2008 ) pipeline to create a first annotation based only on expressed sequences. The obtained annotation was used to perform a training of an Augustus v3.3 ( Stanke and Morgenstern, 2005 ) model which was then used with Maker2 to perform a new annotation iteration.…”

Section: Methodsmentioning

confidence: 99%

Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy

et al. 2020

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The mechanism behind the bud evolution towards breba or main crop in Ficus carica L. is uncertain. Anatomical and genetic studies may put a light on the possible similarities/ differences between the two types of fruits. For this reason, we collected complimentary data from anatomical, X-ray imaging, and genetic techniques. The RNA seq together with structural genome annotation allowed the prediction of 34,629 known genes and 938 novel protein-coding genes. Transcriptome analysis of genes during bud differentiation revealed differentially expressed genes in two fig varieties (Dottato and Petrelli) and in breba and main crop. We chose Dottato and Petrelli because the first variety does not require pollination to set main crop and the latter does; moreover, Petrelli yields many brebas whereas Dottato few. Of the 1,615 and 1,904 loci expressed in Dottato and Petrelli, specifically in breba or main crop, respectively, only 256 genes appeared to be transcripts in both varieties. The buds of the two fig varieties were observed under optical microscope and using 3D X-ray tomography, highlighting differences mainly related to the stage of development. The X-ray images of buds showed a great structural similarity between breba and main crop during the initial stages of development. Analysis at the microscope indicated that inflorescence differentiation of breba was split in two seasons whereas that of main crop started at the end of winter of season 2 and was completed within 2 to 3 months. The higher expression of floral homeotic protein AGAMOUS in breba with respect to main crop, since this protein is required for normal development of stamens and carpels in the flower, may indicate an original role of these fruits for staminate flowers production for pollination of the main crop, as profichi in the caprifig. Several genes related to auxin (auxin efflux carrier, auxin response factor, auxin binding protein, auxin responsive protein) and to GA synthesis (GA20ox) were highly expressed in brebas with respect to main crop for the development of this parthenocarpic fruit.

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“…Dottato were downloaded from the NCBI database (NCBI, Washington, USA, https://www.ncbi.nlm.nih.gov/sra ) using accession number SRP109082. The construction of libraries was described by Solorzano Zambrano et al [ 91 ]. DNA sequencing was performed with two Illumina sequencers: MiSeq and HiSeq2000, yielding 125 bp reads.…”

Section: Methodsmentioning

confidence: 99%

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

et al. 2021

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Background Long Terminal Repeat retrotransposons (LTR-REs) are repetitive DNA sequences that constitute a large part of the genome. The improvement of sequencing technologies and sequence assembling strategies has achieved genome sequences with much greater reliability than those of the past, especially in relation to repetitive DNA sequences. Results In this study, we analysed the genome of Ficus carica L., obtained using third generation sequencing technologies and recently released, to characterise the complete complement of full-length LTR-REs to study their dynamics during fig genome evolution. A total of 1867 full-length elements were identified. Those belonging to the Gypsy superfamily were the most abundant; among these, the Chromovirus/Tekay lineage was the most represented. For the Copia superfamily, Ale was the most abundant lineage. Measuring the estimated insertion time of each element showed that, on average, Ivana and Chromovirus/Tekay were the youngest lineages of Copia and Gypsy superfamilies, respectively. Most elements were inactive in transcription, both constitutively and in leaves of plants exposed to an abiotic stress, except for some elements, mostly belonging to the Copia/Ale lineage. A relationship between the inactivity of an element and inactivity of genes lying in close proximity to it was established. Conclusions The data reported in this study provide one of the first sets of information on the genomic dynamics related to LTR-REs in a plant species with highly reliable genome sequence. Fig LTR-REs are highly heterogeneous in abundance and estimated insertion time, and only a few elements are transcriptionally active. In general, the data suggested a direct relationship between estimated insertion time and abundance of an element and an inverse relationship between insertion time (or abundance) and transcription, at least for Copia LTR-REs.

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Cultivar-specific transcriptome prediction and annotation in Ficus carica L.

Cited by 12 publications

References 14 publications

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

Proteome and transcriptome analyses reveal key molecular differences between quality parameters of commercial-ripe and tree-ripe fig (Ficus carica L.)

Fruit Development in Ficus carica L.: Morphological and Genetic Approaches to Fig Buds for an Evolution From Monoecy Toward Dioecy

LTR-retrotransposon dynamics in common fig (Ficus carica L.) genome

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