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      Comparative transcriptomics between high and low rubber producing Taraxacum kok-saghyz R. plants

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          Abstract

          Background

          Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential production of NR will contribute to elucidate which genes are involved in the synthesis, regulation and accumulation of this natural polymer and could help to develop Tks into a rubber crop.

          Results

          We measured rubber content in the latex of 90 individual Tks plants from 9 accessions, observing a high degree of variability. We carried out de novo root transcriptome sequencing, assembly, annotation and comparison of gene expression of plants with the lower (LR plants) and the higher rubber content (HR plants). The transcriptome analysis also included one plant that did not expel latex, in principle depleted of latex transcripts. Moreover, the transcription of some genes well known to play a major role in rubber biosynthesis, was probed by qRT-PCR. Our analysis showed a high modulation of genes involved in the synthesis of NR between LR and HR plants, and evidenced that genes involved in sesquiterpenoids, monoterpenoids and phenylpropanoid biosynthesis are upregulated in LR plants.

          Conclusions

          Our results show that a higher amount of rubber in the latex in HR plants is positively correlated with high expression levels of a number of genes directly involved in rubber synthesis showing that NR production is highly controlled at transcriptional level. On the other hand, lower amounts of rubber in LR plants is related with higher expression of genes involved in the synthesis of other secondary metabolites that, we hypothesize, may compete towards NR biosynthesis. This dataset represents a fundamental genomic resource for the study of Tks and the comprehension of the synthesis of NR and other biochemically and pharmacologically relevant compounds in the Taraxacum genus.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-018-5287-4) contains supplementary material, which is available to authorized users.

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          Most cited references 59

          • Record: found
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          Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

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            • Record: found
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            Mapping and quantifying mammalian transcriptomes by RNA-Seq.

            We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.
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              • Record: found
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              Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.

              We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.
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                Author and article information

                Contributors
                francesco.panara@enea.it
                loredana.lopez@enea.it
                loretta.daddiego@enea.it
                elio.fantini@enea.it
                paolo.facella@enea.it
                gaetano.perrotta@enea.it
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                4 December 2018
                4 December 2018
                2018
                : 19
                Affiliations
                ISNI 0000 0000 9864 2490, GRID grid.5196.b, Trisaia Research Center, , ENEA, Italian National Agency for New Technologies Energy and Sustainable Economic Development, ; MT, 75026 Rotondella, Italy
                Article
                5287
                10.1186/s12864-018-5287-4
                6280347
                30514210
                © The Author(s). 2018

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                Categories
                Research Article
                Custom metadata
                © The Author(s) 2018

                Genetics

                natural rubber, taraxacum kok-saghyz, russian dandelion, transcriptomics

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