title: Evolution and expression of the fructokinase gene family in Saccharum.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.|College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
authors.forename: Yihong
authors.initials: Y
authors.lastname: Chen
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Weichang
authors.initials: W
authors.lastname: Hu
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.|Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Xingtan
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
authors.forename: Liming
authors.initials: L
authors.lastname: Wang
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.|College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
authors.forename: Xiuting
authors.initials: X
authors.lastname: Hua
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.|Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, 75252, USA.
authors.forename: Qingyi
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.affiliation: Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjisen@126.com.|College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. zjisen@126.com.|Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. zjisen@126.com.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D019143:Evolution, Molecular; D005091:Exons; D005631:Fructokinases / Q000737:chemistry / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D006239:Haplotypes; D007438:Introns; D005810:Multigene Family; D010802:Phylogeny; D000072417:Protein Domains / Q000235:genetics; D031786:Saccharum / Q000235:genetics*
chemical_list: D005631:Fructokinases; C046173:fructokinase
keywords: Fructokinase gene family; Gene evolution; Gene expression; Polyploidy; Saccharum