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

Advancing understanding of Ficus carica: a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights

Ficus carica L. (dioecious), the most significant commercial species in the genus Ficus, which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive F. carica genome currently. The contig N50 of the Orphan fig was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that F. carica diverged from Ficus microcarpa ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of F. carica, chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the F. carica as a new species. And the selections of F. carica for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the F. carica has the FhAG2 gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type F. carica to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of CHS among different varieties of F. carica. The CHS playing an important role in the anthocyanin metabolism pathway of F. carica. Moreover, the CHS gene of F. carica has a different evolutionary trend compared to other Ficus species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich F. carica genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of Ficus.

The Effects of Irrigation Water Salinity on the Synthesis of Photosynthetic Pigments, Gas Exchange, and Photochemical Efficiency of Sour Passion Fruit Genotypes

The objective of this study was to evaluate the synthesis of photosynthetic pigments, gas exchange, and photochemical efficiency of sour passion fruit genotypes irrigated with saline water under the conditions of the semi-arid region of Paraíba state, Brazil. The experiment was conducted at the experimental farm in São Domingos, PB. A randomized block design was adopted, in a 5 × 3 factorial scheme, with five levels of electrical conductivity of irrigation water-ECw (0.3, 1.1, 1.9, 2.7, and 3.5 dS m-1)-and three genotypes of sour passion fruit (Gigante Amarelo-'BRS GA1'; Sol do Cerrado-'BRS SC1'; and Catarina-'SCS 437'. The increase in the electrical conductivity of irrigation water negatively affected most of the physiological characteristics of the sour passion fruit at 154 days after transplanting. Significant differences were observed between sour passion fruit genotypes when its tolerance was subjected to the salinity of irrigation water. There was an increase in the percentage of damage to the cell membrane with the increase in the electrical conductivity of irrigation water, with maximum values of 70.63, 60.86, and 80.35% for the genotypes 'BRS GA1', 'BRS SC1', and SCS 437', respectively, when irrigated with water of 3.5 dS m-1. The genotype 'BRS Sol do Cerrado' showed an increase in the synthesis of photosynthetic pigments when irrigated with water of 3.5 dS m-1, with maximum values estimated at 1439.23 μg mL-1 (Chl a); 290.96 μg mL-1 (Chl b); 1730.19 μg mL-1 (Chl t); and 365.84 μg mL-1 (carotenoids). An increase in photosynthetic efficiency parameters (F0, Fm, and Fv) of the genotype 'BRS Gigante Amarelo' was observed when cultivated with water with high electrical conductivity (3.5 dS m-1).

Foliar Applications of Salicylic Acid on Boosting Salt Stress Tolerance in Sour Passion Fruit in Two Cropping Cycles

Brazil stands out as the largest producer of sour passion fruit; however, the water available for irrigation is mostly saline, which can limit its cultivation. This study was carried out with the objective of evaluating the effects of salicylic acid in the induction of tolerance in sour passion fruit to salt stress. The assay was conducted in a protected environment, using a completely randomized design in a split-plot scheme, with the levels of electrical conductivity of the irrigation water (0.8, 1.6, 2.4, 3.2, and 4.0 dS m-1) considering the plots and concentrations of salicylic acid (0, 1.2, 2.4, and 3.6 mM) the subplots, with three replications. The physiological indices, production components, and postharvest quality of sour passion fruit were negatively affected by the increase in the electrical conductivity of irrigation water, and the effects of salt stress were intensified in the second cycle. In the first cycle, the foliar application of salicylic acid at concentrations between 1.0 and 1.4 mM partially reduced the harmful effects of salt stress on the relative water content of leaves, electrolyte leakage, gas exchange, and synthesis of photosynthetic pigments, in addition to promoting an increase in the yield and quality parameters of sour passion fruit.

Genome-wide in silico identification of glutathione S-transferase (GST) gene family members in fig (Ficus carica L.) and expression characteristics during fruit color development

Glutathione S-transferase (GSTs), a large and diverse group of multi-functional enzymes (EC 2.5.1.18), are associated with cellular detoxification, various biotic and abiotic stress responses, as well as secondary metabolites transportation. Here, 53 members of the FcGST gene family were screened from the genome database of fig (Ficus carica), which were further classified into five subfamilies, and the tau and phi were the major subfamilies. These genes were unevenly distributed over all the 13 chromosomes, and 12 tandem and one segmental duplication may contribute to this family expansion. Syntenic analysis revealed that FcGST shared closer genetic evolutionary origin relationship with species from the Ficus genus of the Moraceae family, such as F. microcarpa and F. hispida. The FcGST members of the same subfamily shared similar gene structure and motif distribution. The α helices were the chief structure element in predicted secondary and tertiary structure of FcGSTs proteins. GO and KEGG indicated that FcGSTs play multiple roles in glutathione metabolism and stress reactions as well as flavonoid metabolism. Predictive promoter analysis indicated that FcGSTs gene may be responsive to light, hormone, stress stimulation, development signaling, and regulated by MYB or WRKY. RNA-seq analysis showed that several FcGSTs that mainly expressed in the female flower tissue and peel during 'Purple-Peel' fig fruit development. Compared with 'Green Peel', FcGSTF1, and FcGSTU5/6/7 exhibited high expression abundance in the mature fruit purple peel. Additionally, results of phylogenetic sequences analysis, multiple sequences alignment, and anthocyanin content together showed that the expression changes of FcGSTF1, and FcGSTU5/6/7 may play crucial roles in fruit peel color alteration during fruit ripening. Our study provides a comprehensive overview of the GST gene family in fig, thus facilitating the further clarification of the molecular function and breeding utilization.

Cations and Phenolic Compounds Concentrations in Fruits of Fig Plants Exposed to Moderate Levels of Salinity

Fig trees are often grown in areas affected by salinity problems. We investigated changes in the concentrations of 15 phenolic compounds and mineral elements (Mg, Ca, K, Zn, Cu, Mn, Mo, Fe, Na) in fruits of fig plants (Ficus carica L. cv. Dottato) subjected to irrigation with saline water (100 mM of NaCl) for 28 days. We used UHPLC-MS/MS techniques to determine chlorogenic acid, tiliroside, catechin, epicatechin (ECTC), p-coumaric acid, trans-ferulic acid, phloridzin, phloretine, quercetagetin 7-O-glucoside, rutin, quercetin 3-O-glucoside, kaempferol 3-O-rutinoside, kaempferol 7-O-glucoside, kaempferol 3-O-glucoside, and quercetin. There was a steep gradient of Na⁺ concentrations between the root and the canopy of salinized plants, but leaf Na⁺ was similar in control and salt-treated plants. Quercetin, ECTC, and chlorogenic acid were the most abundant phenolic compounds in fig fruits. Salinity increased total phenols by 5.6%, but this increase was significant only for ECTC. Salt stress significantly increased Zn and Mg concentration in the fruit. Leaf levels of K, Mg, Ca, and Mn were similar in control and salinized plants. Moderate salt stress appears to improve fig fruit quality because of its positive effect on nutrients and antioxidant compounds such as epicatechin.

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)

Fig trees (Ficus carica L.) are commonly grown in the Mediterranean area, where salinity is an increasing problem in coastal areas. Young, fruiting plants of cv. Dottato were subjected to moderate salt stress (100 mM NaCl added to irrigation water) for 48 days before fruit sampling. To clarify the effect of salinity stress, we investigated changes in the transcription of the main sugar metabolism-related genes involved in the synthesis, accumulation and transport of soluble carbohydrates in ripe fruits by quantitative real-time PCR as well as the content of soluble sugars by quantitative ¹H nuclear magnetic resonance spectroscopy. A general increase in the transcript levels of genes involved in the transport of soluble carbohydrates was observed. Alkaline-neutral and Acid Invertases transcripts, related to the synthesis of glucose and fructose, were up-regulated in ripe fruits of NaCl-stressed plants without a change in the content of D-glucose and D-fructose. The increases in sucrose and D-sorbitol contents were likely the result of the up-regulation of the transcription of Sucrose-Synthase- and Sorbitol-Dehydrogenase-encoding genes.

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

The existing research on dairy cow mammary gland genes is extensive, but there have been few reports about dynamic changes in dairy cow mammary gland genes as milk yield decrease. For the first time, transcriptome analysis based on short time-series expression miner (STEM) and histological observations were performed using the Holstein dairy cow mammary gland to explore gene expression patterns in this process of decrease (at peak, mid-, and late lactation). Histological observations suggested that the number of mammary acinous cells at peak/mid-lactation was significantly higher than that at mid-/late lactation, and the lipid droplets area secreted by dairy cows was almost unaltered across the three stages of lactation (p > 0.05). Totals of 882 and 1439 genes were differentially expressed at mid- and late lactation, respectively, compared to peak lactation. Function analysis showed that differentially expressed genes (DEGs) were mainly related to apoptosis and energy metabolism (fold change ≥ 2 or fold change ≤ 0.5, p-value ≤ 0.05). Transcriptome analysis based on STEM identified 16 profiles of differential gene expression patterns, including 5 significant profiles (false discovery rate, FDR ≤ 0.05). Function analysis revealed DEGs involved in milk fat synthesis were downregulated in Profile 0 and DEGs in Profile 12 associated with protein synthesis. These findings provide a foundation for future studies on the molecular mechanisms underlying mammary gland development in dairy cows.

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

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.

Physiological and molecular responses for long term salinity stress in common fig (Ficus carica L.)

Salinity stress in increasingly becoming a major challenge in current and expanding agricultural ecosystems. Unlike temporal abiotic stresses, plants are usually exposed to salinity stress for an entire lifespan. Therefore, a long term effect (10 weeks) of continuous salinity exposure was investigated for three common fig landraces (Zraki, Mwazi, and Khdari). Both relative water content and chlorophyll content decreased with elevated salinity stress, while stem length barely changed. The most prominent decline was observed in root biomass. The data would align common fig to moderately tolerant threshold slop with a C₅₀ range of 100 to 150 mM NaCl. A high and significant correlation was evident between root biomass and chlorophyll content (85%). Concurrently, differential expression of putative salinity responsive genes in common fig were determined; signal peptide peptidase-like 2B (FcSPPL2B), dehydration responsive element binding protein (FcDREB), calcineurin B-like protein (CBL)-CBL-interacting serine/threonine-protein kinase 11 (FcCIPK11), sorbitol dehydrogenase (FcSORD) and dehydrin (FcDHN). The data were discussed for each gene in respect of its potential role in salinity stress mitigation. The combined physiological and molecular data would conclude Zraki as the most salinity tolerant genotype. The major implication of the data emphasizes the tremendous genotype by environment (salinity stress) interaction in common fig.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at (10.1007/s12298-020-00921-z).

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

Due to DNA heterozygosity and repeat content, assembly of non-model plant genomes is challenging. Herein, we report a high-quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single-molecule, real-time sequencing. The fig genome is ~333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome-wide analysis of N⁶ -methyladenine and N⁴ -methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non-methylated genes. Furthermore, the characterization of N⁶ -methyladenine sites led to the identification of ANHGA, a species-specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high-quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.