Cargando…

Evolution and expression of the fructokinase gene family in Saccharum

BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fr...

Descripción completa

Detalles Bibliográficos
Autores principales: Chen, Yihong, Zhang, Qing, Hu, Weichang, Zhang, Xingtan, Wang, Liming, Hua, Xiuting, Yu, Qingyi, Ming, Ray, Zhang, Jisen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319016/
https://www.ncbi.nlm.nih.gov/pubmed/28222695
http://dx.doi.org/10.1186/s12864-017-3535-7
_version_ 1782509298095489024
author Chen, Yihong
Zhang, Qing
Hu, Weichang
Zhang, Xingtan
Wang, Liming
Hua, Xiuting
Yu, Qingyi
Ming, Ray
Zhang, Jisen
author_facet Chen, Yihong
Zhang, Qing
Hu, Weichang
Zhang, Xingtan
Wang, Liming
Hua, Xiuting
Yu, Qingyi
Ming, Ray
Zhang, Jisen
author_sort Chen, Yihong
collection PubMed
description BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS: In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress. CONCLUSIONS: Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3535-7) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-5319016
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-53190162017-02-24 Evolution and expression of the fructokinase gene family in Saccharum Chen, Yihong Zhang, Qing Hu, Weichang Zhang, Xingtan Wang, Liming Hua, Xiuting Yu, Qingyi Ming, Ray Zhang, Jisen BMC Genomics Research Article BACKGROUND: Sugarcane is an important sugar crop contributing up to about 80% of the world sugar production. Efforts to characterize the genes involved in sugar metabolism at the molecular level are growing since increasing sugar content is a major goal in the breeding of new sugarcane varieties. Fructokinases (FRK) are the main fructose phosphorylating enzymes with high substrate specificity and affinity. RESULTS: In this study, by combining comparative genomics approaches with BAC resources, seven fructokinase genes were identified in S. spontaneum. Phylogenetic analysis based on representative monocotyledon and dicotyledon plant species suggested that the FRK gene family is ancient and its evolutionary history can be traced in duplicated descending order: SsFRK4, SsFRK6/SsFRK7,SsFRK5, SsFRK3 and SsFRK1/SsFRK2. Among the close orthologs, the number and position of exons in FRKs were conserved; in contrast, the size of introns varied among the paralogous FRKs in Saccharum. Genomic constraints were analyzed within the gene alleles and between S. spontaneum and Sorghum bicolor, and gene expression analysis was performed under drought stress and with exogenous applications of plant hormones. FRK1, which was under strong functional constraint selection, was conserved among the gene allelic haplotypes, and displayed dominant expression levels among the gene families in the control conditions, suggesting that FRK1 plays a major role in the phosphorylation of fructose. FRK3 and FRK5 were dramatically induced under drought stress, and FRK5 was also found to increase its expression levels in the mature stage of Saccharum. Similarly, FRK3 and FRK5 were induced in response to drought stress in Saccharum. FRK2 and FRK7 displayed lower expression levels than the other FRK family members; FRK2 was under strong genomic selection constraints whereas FRK7 was under neutral selection. FRK7 may have become functionally redundant in Saccharum through pseudogenization. FRK4 and FRK6 shared the most similar expression pattern: FRK4 was revealed to have higher expression levels in mature tissues than in premature tissues of Saccharum, and FRK6 presented a slight increase under drought stress. CONCLUSIONS: Our study presents a comprehensive genomic study of the entire FRK gene family in Saccharum, providing the foundations for approaches to characterize the molecular mechanism regulated by the SsFRK family in sugarcane. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3535-7) contains supplementary material, which is available to authorized users. BioMed Central 2017-02-21 /pmc/articles/PMC5319016/ /pubmed/28222695 http://dx.doi.org/10.1186/s12864-017-3535-7 Text en © The Author(s). 2017 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
Chen, Yihong
Zhang, Qing
Hu, Weichang
Zhang, Xingtan
Wang, Liming
Hua, Xiuting
Yu, Qingyi
Ming, Ray
Zhang, Jisen
Evolution and expression of the fructokinase gene family in Saccharum
title Evolution and expression of the fructokinase gene family in Saccharum
title_full Evolution and expression of the fructokinase gene family in Saccharum
title_fullStr Evolution and expression of the fructokinase gene family in Saccharum
title_full_unstemmed Evolution and expression of the fructokinase gene family in Saccharum
title_short Evolution and expression of the fructokinase gene family in Saccharum
title_sort evolution and expression of the fructokinase gene family in saccharum
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319016/
https://www.ncbi.nlm.nih.gov/pubmed/28222695
http://dx.doi.org/10.1186/s12864-017-3535-7
work_keys_str_mv AT chenyihong evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT zhangqing evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT huweichang evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT zhangxingtan evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT wangliming evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT huaxiuting evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT yuqingyi evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT mingray evolutionandexpressionofthefructokinasegenefamilyinsaccharum
AT zhangjisen evolutionandexpressionofthefructokinasegenefamilyinsaccharum