Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L.
The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resource...
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| Format: | Online |
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BlackWell Publishing Ltd
2014
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285118/ |
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pubmed-42851182015-01-26 Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. Sablok, Gaurav Fu, Yuan Bobbio, Valentina Laura, Marina Rotino, Giuseppe L Bagnaresi, Paolo Allavena, Andrea Velikova, Violeta Viola, Roberto Loreto, Francesco Li, Mingai Varotto, Claudio Research Articles The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax. BlackWell Publishing Ltd 2014-06 2014-02-20 /pmc/articles/PMC4285118/ http://dx.doi.org/10.1111/pbi.12159 Text en © 2014 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. http://creativecommons.org/licenses/by-nc/3.0/ This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Sablok, Gaurav Fu, Yuan Bobbio, Valentina Laura, Marina Rotino, Giuseppe L Bagnaresi, Paolo Allavena, Andrea Velikova, Violeta Viola, Roberto Loreto, Francesco Li, Mingai Varotto, Claudio |
| spellingShingle |
Sablok, Gaurav Fu, Yuan Bobbio, Valentina Laura, Marina Rotino, Giuseppe L Bagnaresi, Paolo Allavena, Andrea Velikova, Violeta Viola, Roberto Loreto, Francesco Li, Mingai Varotto, Claudio Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| author_facet |
Sablok, Gaurav Fu, Yuan Bobbio, Valentina Laura, Marina Rotino, Giuseppe L Bagnaresi, Paolo Allavena, Andrea Velikova, Violeta Viola, Roberto Loreto, Francesco Li, Mingai Varotto, Claudio |
| author_sort |
Sablok, Gaurav |
| title |
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| title_short |
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| title_full |
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| title_fullStr |
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| title_full_unstemmed |
Fuelling genetic and metabolic exploration of C3 bioenergy crops through the first reference transcriptome of Arundo donax L. |
| title_sort |
fuelling genetic and metabolic exploration of c3 bioenergy crops through the first reference transcriptome of arundo donax l. |
| description |
The development of inexpensive and highly productive biomass sources of biofuel is a priority in global climate change biology. Arundo donax, also known as the giant reed, is recognized as one of the most promising nonfood bioenergy crops in Europe. Despite its relevance, to date no genomic resources are available to support the characterization of the developmental, adaptive and metabolic traits underlying the high productivity of this nonmodel species. We hereby present the first report on the de novo assembly of bud, culm, leaf and root transcriptomes of A. donax, which can be accessed through a customized BLAST server (http://ecogenomics.fmach.it/arundo/) for mining and exploring the genetic potential of this species. Based on functional annotation and homology comparison to 19 prospective biofuel Poaceae species, we provide the first genomic view of this so far unexplored crop and indicate the model species with highest potential for comparative genomics approaches. The analysis of the transcriptome reveals strong differences in the enrichment of the Gene Ontology categories and the relative expression among different organs, which can guide future efforts for functional genomics or genetic improvement of A. donax. A set of homologs to key genes involved in lignin, cellulose, starch, lipid metabolism and in the domestication of other crops is discussed to provide a platform for possible enhancement of productivity and saccharification efficiency in A. donax. |
| publisher |
BlackWell Publishing Ltd |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285118/ |
| _version_ |
1613173684546043904 |