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Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane

BACKGROUND: Sugarcane accumulates very high levels of sucrose in the culm. Elucidation of the molecular mechanisms that allows such high sucrose synthesis and accumulation (up to 650 mM) is made difficult by the complexity of the highly polyploid genome. Here we report the use of RNA Seq data to cha...

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Autores principales: Thirugnanasambandam, Prathima P., Mason, Patrick J., Hoang, Nam V., Furtado, Agnelo, Botha, Frederik C., Henry, Robert J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485122/
https://www.ncbi.nlm.nih.gov/pubmed/31023213
http://dx.doi.org/10.1186/s12870-019-1733-y
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author Thirugnanasambandam, Prathima P.
Mason, Patrick J.
Hoang, Nam V.
Furtado, Agnelo
Botha, Frederik C.
Henry, Robert J.
author_facet Thirugnanasambandam, Prathima P.
Mason, Patrick J.
Hoang, Nam V.
Furtado, Agnelo
Botha, Frederik C.
Henry, Robert J.
author_sort Thirugnanasambandam, Prathima P.
collection PubMed
description BACKGROUND: Sugarcane accumulates very high levels of sucrose in the culm. Elucidation of the molecular mechanisms that allows such high sucrose synthesis and accumulation (up to 650 mM) is made difficult by the complexity of the highly polyploid genome. Here we report the use of RNA Seq data to characterize the sucrose synthase (SuSy) genes expressed in the transcriptome of the mature sugarcane plant. RESULTS: Four SuSy gene families were identified in the sugarcane Iso-Seq long read transcriptome (SUGIT) through gene annotation of transcripts that mapped to reference SuSy genes from sorghum and maize. In total, 38, 19, 14, and 2 transcripts were identified for the four corresponding SuSy genes 1, 2, 4 and 7, respectively. Comparative studies using available SuSy genes from sorghum (1, 2, 4, 6, 7) and maize (1–7) revealed that the sugarcane SuSy genes were interrupted by multiple introns and that they share a highly conserved gene structure. Spatial expression of the four SuSy genes in sugarcane genotypes and in the progenitor species, Saccharum spontaneum and Saccharum officinarum, was studied in the leaf and root tissues and also in three regions of the culm tissue; top, middle and bottom internodes. Expression profiles indicated that all SuSy transcripts were differentially expressed between the top and bottom tissues, with high expression in the top tissues, lower expression in the bottom and moderate expression in the middle, indicating a gradient of SuSy activity in the sugarcane culm. Further, the root tissue had similar expression levels to that of the top internodes while leaf tissues showed lower expression. In the progenitors, SuSy7 was found to be highly expressed in S. officinarum while the other three SuSy genes had moderate expression in both the progenitors. CONCLUSIONS: The high expression of the SuSy genes in sink tissues, the top internodes and the roots suggests functional roles in sucrose utilization to support growth. The SuSy7 gene has not been previously reported in sugarcane. As sugarcane is unique in storing such high amounts of sucrose, it is possible that there are more SuSy genes/isoforms with specific expression patterns to be discovered in this complex system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1733-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-64851222019-05-03 Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane Thirugnanasambandam, Prathima P. Mason, Patrick J. Hoang, Nam V. Furtado, Agnelo Botha, Frederik C. Henry, Robert J. BMC Plant Biol Research Article BACKGROUND: Sugarcane accumulates very high levels of sucrose in the culm. Elucidation of the molecular mechanisms that allows such high sucrose synthesis and accumulation (up to 650 mM) is made difficult by the complexity of the highly polyploid genome. Here we report the use of RNA Seq data to characterize the sucrose synthase (SuSy) genes expressed in the transcriptome of the mature sugarcane plant. RESULTS: Four SuSy gene families were identified in the sugarcane Iso-Seq long read transcriptome (SUGIT) through gene annotation of transcripts that mapped to reference SuSy genes from sorghum and maize. In total, 38, 19, 14, and 2 transcripts were identified for the four corresponding SuSy genes 1, 2, 4 and 7, respectively. Comparative studies using available SuSy genes from sorghum (1, 2, 4, 6, 7) and maize (1–7) revealed that the sugarcane SuSy genes were interrupted by multiple introns and that they share a highly conserved gene structure. Spatial expression of the four SuSy genes in sugarcane genotypes and in the progenitor species, Saccharum spontaneum and Saccharum officinarum, was studied in the leaf and root tissues and also in three regions of the culm tissue; top, middle and bottom internodes. Expression profiles indicated that all SuSy transcripts were differentially expressed between the top and bottom tissues, with high expression in the top tissues, lower expression in the bottom and moderate expression in the middle, indicating a gradient of SuSy activity in the sugarcane culm. Further, the root tissue had similar expression levels to that of the top internodes while leaf tissues showed lower expression. In the progenitors, SuSy7 was found to be highly expressed in S. officinarum while the other three SuSy genes had moderate expression in both the progenitors. CONCLUSIONS: The high expression of the SuSy genes in sink tissues, the top internodes and the roots suggests functional roles in sucrose utilization to support growth. The SuSy7 gene has not been previously reported in sugarcane. As sugarcane is unique in storing such high amounts of sucrose, it is possible that there are more SuSy genes/isoforms with specific expression patterns to be discovered in this complex system. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1733-y) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-25 /pmc/articles/PMC6485122/ /pubmed/31023213 http://dx.doi.org/10.1186/s12870-019-1733-y Text en © The Author(s). 2019 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.
spellingShingle Research Article
Thirugnanasambandam, Prathima P.
Mason, Patrick J.
Hoang, Nam V.
Furtado, Agnelo
Botha, Frederik C.
Henry, Robert J.
Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title_full Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title_fullStr Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title_full_unstemmed Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title_short Analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
title_sort analysis of the diversity and tissue specificity of sucrose synthase genes in the long read transcriptome of sugarcane
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6485122/
https://www.ncbi.nlm.nih.gov/pubmed/31023213
http://dx.doi.org/10.1186/s12870-019-1733-y
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