De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

Muñoz‐Mérida, Antonio; González-Plaza, Juan José; Cañada, Andrés; Blanco, Ana María; García-López, Maria del Carmen; Rodrı́guez, José Manuel; Pedrola, Laia; Sicardo, M. Dolores; Hernández, M. Luisa; Rosa, Raúl de la; Belaj, Angjelina; Gil-Borja, Mayte; Luque, Francisco; Martínez-Rivas, José Manuel; Pisano, David G.; Trelles, Oswaldo; Valpuesta, Victoriano; Beuzón, Carmen R.

doi:10.1093/dnares/dss036

Cited by 76 publications

(92 citation statements)

References 38 publications

(44 reference statements)

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“…To examine evidence for past wholegenome duplication, CDS and protein sequences (one transcript per gene) were taken from our ash genome annotation, and downloaded from Phytozome version 10.3 for tomato (S. lycopersicum), monkey flower (M. guttatus) and grape (V. vinifera), the CoGe database for bladderwort (U. gibba) and http://coffee-genome.org for coffee (C. canephora). For olive (O. europaea) we predicted open reading frames from transcriptome data 63 . BLAST alignments were further filtered to retain pairs for which the shorter sequence was at least 50% of the longer sequence, and the alignment was at least 50% of the shorter sequence.…”

Section: Methodsmentioning

confidence: 99%

Genome sequence and genetic diversity of European ash trees

Sollars

Harper

Kelly

et al. 2016

Nature

170

227

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Ash trees (genus. Here we sequence the genome of a low-heterozygosity Fraxinus excelsior tree from Gloucestershire, UK, annotating 38,852 protein-coding genes of which 25% appear ash specific when compared with the genomes of ten other plant species. Analyses of paralogous genes suggest a whole-genome duplication shared with olive (Olea europaea, Oleaceae). We also re-sequence 37 F. excelsior trees from Europe, finding evidence for apparent long-term decline in effective population size. Using our reference sequence, we reanalyse association transcriptomic data 3 , yielding improved markers for reduced susceptibility to ash dieback. Surveys of these markers in British populations suggest that reduced susceptibility to ash dieback may be more widespread in Great Britain than in Denmark. We also present evidence that susceptibility of trees to H. fraxineus is associated with their iridoid glycoside levels. This rapid, integrated, multidisciplinary research response to an emerging health threat in a non-model organism opens the way for mitigation of the epidemic.

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Section: Methodsmentioning

confidence: 99%

Genome sequence and genetic diversity of European ash trees

Sollars

Harper

Kelly

et al. 2016

Nature

170

227

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“…Moreover, clustering of transcript and metabolite profiles is becoming a powerful technique for identifying candidate genes (29 -32). Large expressed sequence tag collections from high secoiridoid-accumulating olive fruits and leaves (33)(34)(35)(36) are a valuable resource for the identification of candidate transcripts in secoiridoid biosynthesis. With the exception of a geraniol synthase involved in the synthesis of geraniol from geranyl-diphosphate (15), up to now no secoiridoid biosynthetic genes have been biochemically characterized in olive.…”

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confidence: 99%

Identification and Characterization of the Iridoid Synthase Involved in Oleuropein Biosynthesis in Olive (Olea europaea) Fruits

Alagna

Geu‐Flores

Kries

et al. 2016

Journal of Biological Chemistry

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The secoiridoids are the main class of specialized metabolites present in olive (Olea europaea L.) fruit. In particular, the secoiridoid oleuropein strongly influences olive oil quality because of its bitterness, which is a desirable trait. In addition, oleuropein possesses a wide range of pharmacological properties, including antioxidant, anti-inflammatory, and anti-cancer activities. In accordance, obtaining high oleuropein varieties is a main goal of molecular breeding programs. Here we use a transcriptomic approach to identify candidate genes belonging to the secoiridoid pathway in olive. From these candidates, we have functionally characterized the olive homologue of iridoid synthase (OeISY), an unusual terpene cyclase that couples an NAD (P)H-dependent 1,4-reduction step with a subsequent cyclization, and we provide evidence that OeISY likely generates the monoterpene scaffold of oleuropein in olive fruits. OeISY, the first pathway gene characterized for this type of secoiridoid, is a potential target for breeding programs in a high value secoiridoid-accumulating species.Olive (Olea europaea L.) produces a range of secondary metabolites that strongly affect the taste and nutritional properties of olive oil and fruits. The most abundant of these secondary metabolites are the secoiridoids, monoterpenoids with a 3,4-dihydropyran skeleton. These compounds are present as oleosidic secoiridoids or oleosides that have an exocyclic olefinic functionality (1) and possess a tyrosine-derived component (see Fig.

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“…9). These sequences were reported in the annotation of functional olive transcriptome (Muñoz-Mérida et al, 2013;de la O Leyva-Pérezet al, 2014 andGuerra et al, 2015). The BLASTN search of the RAPD fragment A13 600 revealed some hits with high percentage of identity (94%) and query coverage (21%).…”

Section: Sequence Analysis Of Some Polymorphic Pcr Bandsmentioning

confidence: 83%

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Alsamman¹,

Adawy²,

Ibrahim³

et al. 2017

Plant Omics

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The Selective Amplification of Start Codon Polymorphic Loci (SASPL) has been developed as a new PCR-based molecular marker. SASPL was validated for the analysis of varietal diversity on ten olive varieties. Validation included in vitro comparison against RAPD, SCoT and SAMPL markers. Assessment of these techniques included primer selectivity, genome coverage and the ability to target genic regions through in silico PCR analysis. Candidate PCR fragments were further sequenced to annotate non-identified genes in olive. Eight SASPL primers were compared to 24 RAPD, 39 SCoT and 12 SAMPL primers. The TA produced by the RAPD, SCoT, SAMPL and the eight SASPL primers were 359, 642, 571 and 269 amplicons, respectively. The highest average number of TA was revealed by SAMPL (47.6), average of PA (18.1) and genetic similarity (GS) (96%) among the olive varieties. On the other hand, SASPL analysis provided higher average number of TA (33.6), average of PA (16.2) and GS (93%) than SCoT and RAPD. The highest average of (PIC) (0.2909) was exhibited by SASPL analysis and the lowest average (0.2038) was revealed by SCoT. The highest number of UB (111) was revealed by SCoT and the lowest UB (43) was obtained by SASPL. Across the four marker types, variety Maraki was characterized by the highest number of unique markers (74). Meanwhile, the variety Manzanillo was characterized by the lowest number of unique markers (8). In addition, in the in silico analysis SASPL exhibited the highest chromosomal coverage (0.59%) and targeted genes (1090) using the lowest number of primers. Additionally, the average area covered by the SASPL primers (354kb) was larger than SCoT and SAMPL. RAPD analysis provided the lowest potential, chromosomal coverage (0.04%) and number of targeted genes (17) compared to SASPL, SCoT and SAMPL analysis. The total coverage of the genome, revealed by combined data was higher (1.21%) than that of each technique separately. Meanwhile, the difference between the actual and the total genomic regions covered by the combined data was about 652kb. Our results suggested that the newly developed SASPL marker is the most adequately and each of the studied marker target different genomic areas, while some areas are shared. Two SCoT and one RAPD fragment were sequenced and showed a high similarity to genes of high physiological functions; such as cyclic plant-specific DNA-binding transcription factor, SANT domain and Copia-type retrotransposon.

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De Novo Assembly and Functional Annotation of the Olive (Olea europaea) Transcriptome

Cited by 76 publications

References 38 publications

Genome sequence and genetic diversity of European ash trees

Genome sequence and genetic diversity of European ash trees

Identification and Characterization of the Iridoid Synthase Involved in Oleuropein Biosynthesis in Olive (Olea europaea) Fruits

Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

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