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The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants.

ABSTRACT: Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 47,775 were annotated using BLASTX analysis performed against the NR protein database subset with 11,853 transcripts representing putative full-length CDS. Bioinformatic analyses revealed 1,011 transcripts encoding transcription factors, mainly from the BHLH, MYB-related, C2H2, MYB, and ERF families, and 6,411 EST-SSR regions. Single-nucleotide variants of SNPs and indels were identified among the 8 samples at a frequency of 0.5 and 0.04 variants per Kb, respectively. Finally, the assembled transcripts were screened to identify genes related to the biosynthesis of t-anethole, a compound well-known for its nutraceutical and medical properties. For each of the 11 genes encoding structural enzymes in the t-anethole biosynthetic pathway, we identified at least one transcript showing a significant match. Overall, our work represents a treasure trove of information exploitable both for marker-assisted breeding and for in-depth studies on thousands of genes, including those involved in t-anethole biosynthesis.

SUBMITTER: Palumbo F

PROVIDER: S-EPMC6041299 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants.

Palumbo Fabio F Vannozzi Alessandro A Vitulo Nicola N Lucchin Margherita M Barcaccia Gianni G

Scientific reports 20180711 1

Fennel is a plant species of both agronomic and pharmaceutical interest that is characterized by a shortage of genetic and molecular data. Taking advantage of NGS technology, we sequenced and annotated the first fennel leaf transcriptome using material from four different lines and two different bioinformatic approaches: de novo and genome-guided transcriptome assembly. A reference transcriptome for assembly was produced by combining these two approaches. Among the 79,263 transcripts obtained, 4 ...[more]

PMID: 29993007

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Project description:BackgroundWith the increasing demands in livestock and poultry breeding and the growing number of food-borne diseases, it is necessary to practice food safety and develop strategies to produce healthy livestock. Fennel (Foeniculum vulgare Mill.) has been used as an additive in poultry production by some researchers, but there are few studies on the systemic beneficial effects of dietary fennel seed powder supplementation on broilers. Therefore, this study aimed to investigate the effect of dietary fennel seed powder supplementation on feed intake, the apparent metabolic rate of nutrients, intestinal morphology, and carcass traits in Cobb broilers.MethodsA single-factor experimental design was used. In total, 160 1-day-old Cobb broiler chicks were randomly assigned to four treatments, with four replicates each (n = 10/replicate). Broilers in the control (CN) group were fed a basal diet without fennel seed powder, and broilers in the treatment groups were fed a basal diet supplemented with 0.15% (LF), 0.30% (MF), or 0.45% (HF) fennel seed powder, respectively. Feeding trials lasted for 42 days under the conditions of ad libitum access to feed and water, and 24-h illumination. During the third and sixth weeks, digestive and metabolic assays were carried out. When the broilers were 42 days old, one chicken with a weight close to the average was selected from each repetition, euthanized by an intravenous injection of 5% sodium pentobarbital, and carcass traits were measured and intestinal samples were collected for morphological assessment.ResultsThere was no significant difference in growth performance of broilers (P > 0.05). The breast muscle percentage, fat width and fat width index, breast muscle area, and breast muscle area index of broilers in the LF group were higher than those in other groups (P < 0.05). Jejunum weight and length were higher in MF than in CN and LF broilers (P < 0.05). Additionally, duodenal villi height, ileal villi height, and ileal wall thickness were higher in MF than in CN broilers (P < 0.05). There were no significant differences in nutrient utilization among all groups (P > 0.05), except that the ash apparent metabolic rate in MF broilers at 21 days of age was higher than that in LF broilers (P < 0.05). In conclusion, dietary supplementation with a moderate concentration of fennel affects carcass performance, and intestinal morphology, and promotes the growth and development of broilers.

Project description:Non-specific lipid transfer proteins (nsLTPs) are cationic proteins involved in intracellular lipid shuttling in growth and reproduction, as well as in defense against pathogenic microbes. Even though the primary and spatial structures of some nsLTPs from different plants indicate their similar features, they exhibit distinct lipid-binding specificities signifying their various biological roles that dictate further structural study. The present study determined the complete amino acid sequence, in silico 3D structure modeling, and the antiproliferative activity of nsLTP1 from fennel (Foeniculum vulgare) seeds. Fennel is a member of the family Umbelliferae (Apiaceae) native to southern Europe and the Mediterranean region. It is used as a spice medicine and fresh vegetable. Fennel nsLTP1 was purified using the combination of gel filtration and reverse-phase high-performance liquid chromatography (RP-HPLC). Its homogeneity was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry. The purified nsLTP1 was treated with 4-vinyl pyridine, and the modified protein was then digested with trypsin. The complete amino acid sequence of nsLTP1 established by intact protein sequence up to 28 residues, overlapping tryptic peptides, and cyanogen bromide (CNBr) peptides. Hence, it is confirmed that fennel nsLTP1 is a 9433 Da single polypeptide chain consisting of 91 amino acids with eight conserved cysteines. Moreover, the 3D structure is predicted to have four α-helices interlinked by three loops and a long C-terminal tail. The lipid-binding property of fennel nsLTP1 is examined in vitro using fluorescent 2-p-toluidinonaphthalene-6-sulfonate (TNS) and validated using a molecular docking study with AutoDock Vina. Both of the binding studies confirmed the order of binding efficiency among the four studied fatty acids linoleic acid > linolenic acid > Stearic acid > Palmitic acid. A preliminary screening of fennel nsLTP1 suppressed the growth of MCF-7 human breast cancer cells in a dose-dependent manner with an IC50 value of 6.98 µM after 48 h treatment.

Dataset Information

The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants.

Publications

The leaf transcriptome of fennel (Foeniculum vulgare Mill.) enables characterization of the t-anethole pathway and the discovery of microsatellites and single-nucleotide variants.

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