How an ancient, salt-tolerant fruit crop, Ficus carica L., copes with salinity: a transcriptome analysis

Abstract

Although Ficus carica L. (fig) is one of the most resistant fruit tree species to salinity, no comprehensive studies are currently available on its molecular responses to salinity. Here we report a transcriptome analysis of F . carica cv. Dottato exposed to 100 mM sodium chloride for 7 weeks, where RNA-seq analysis was performed on leaf samples at 24 and 48 days after the beginning of salinization; a genome-derived fig transcriptome was used as a reference. At day 24, 224 transcripts were significantly up-regulated and 585 were down-regulated, while at day 48, 409 genes were activated and 285 genes were repressed. Relatively small transcriptome changes were observed after 24 days of salt treatment, showing that fig plants initially tolerate salt stress. However, after an early down-regulation of some cell functions, major transcriptome changes were observed after 48 days of salinity. Seven weeks of 100 mM NaCl dramatically changed the repertoire of expressed genes, leading to activation or reactivation of many cell functions. We also identified salt-regulated genes, some of which had not been previously reported to be involved in plant salinity responses. These genes could be potential targets for the selection of favourable genotypes, through breeding or biotechnology, to improve salt tolerance in fig or other crops.

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

“…First, Trinity v2.5.1 (Grabherr et al, 2011) was run with default parameters to obtain a de novo fig transcriptome using already available RNA sequencing (RNA-seq) data (Vangelisti et al, 2019). The Illumina HiSeq 2000 paired-end reads were trimmed with Trimmomatic to remove adapters and low-quality regions (ILLU-MINACLIP:2:30:10 LEADING:20 TRAILING:20 SLIDINGWIN-DOW:4:20 MINLEN:25).…”

“…Fig has valuable nutritional and nutraceutical characteristics (Vinson et al, 2005;Solomon et al, 2006;Veberic et al, 2008) and the ability to adapt to marginal soils and difficult environmental conditions (Vangelisti et al, 2019). However, rapid perishability of its fresh fruits, and deficiencies to its responses to abiotic stresses and new diseases, restricts its world distribution and commercial success.…”

Moderate Salinity Stress Affects Expression of Main Sugar Metabolism and Transport Genes and Soluble Carbohydrate Content in Ripe Fig Fruits (Ficus carica L. cv. Dottato)

“…Ficus carica is well known for its ability to tolerate water deficit and moderate salinity [ 7 , 8 , 9 , 10 ] that makes this species suitable to be cultivated in semi-arid environments where the use of saline or brackish water for irrigation is quite common [ 11 ]. The cultivar ‘Dottato’ is a bifera-type fig that is widely grown in Italy.…”

“…Its ‘brebas’ (the first crop) are harvested between the end of June and the beginning of July, while the syconia fruit of the main crop (‘forniti’) are harvested from early August to late September [ 5 ]. This cultivar showed moderate resilience to salinity [ 8 , 10 ].…”

Short Time-Series Expression Transcriptome Data Reveal the Gene Expression Patterns of Dairy Cow Mammary Gland as Milk Yield Decreased Process

“…A p -value ≤ 0.05 is considered statistically significant, both past and present [ 7 , 44 , 45 , 46 , 47 , 48 , 49 ]. Recently years some studies identified statistical significances using FDR [ 50 , 51 , 52 ]. In the coming years, FDR will increasingly be applied to assess the significances of data.…”