title: Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum.
abstract: BACKGROUND
  Sugarcane is an economically important crop contributing to about 80% of the world sugar production. Increasing efforts in molecular biological studies have been performed for improving the sugar yield and other relevant important agronomic traits. However, due to sugarcane's complicated genomes, it is still challenging to study the genetic basis of traits, such as sucrose accumulation. Sucrose transporters (SUTs) are critical for both phloem loading in source tissue and sucrose uptaking in sink tissue, and are considered to be the control points for regulating sucrose storage. However, no genomic study for sugarcane sucrose transporter (SsSUT) families has been reported up to date.
  
  
  RESULTS
  By using comparative genomics and bacterial artificial chromosomes (BACs), six SUT genes were identified and characterized in S. spontaenum. Phylogenetic analyses revealed that the two pairs SsSUTs (SsSUT1/SsSUT3 and SsSUT5/SsSUT6) could be clustered together into two separate monocot specific SUT groups, while SsSUT2 and SsSUT4 were separated into the other two groups, with members from both dicot and monocot species. Gene structure comparison demonstrated that the number and position of exons/introns in SUTs were highly conserved among the close orthologs; in contrast, there were variations among the paralogous SUTs in Sacchuarm. Though with the high polyploidy level, gene allelic haplotype comparative analysis showed that the examined four SsSUT members exhibited conservations of gene structures and amino acid sequences among the allelic haplotypes accompanied by variations of intron sizes. Gene expression analyses were performed for tissues from seedlings under drought stress and mature plants of three Saccharum species (S.officinarnum, S.spotaneum and S.robustum). Both SUT1 and SUT4 expressed abundantly at different conditions. SUT2 had similar expression level in all of the examined tissues, but SUT3 was undetectable. Both of SUT5 and SUT6 had lower expression level than other gene member, and expressed stronger in source leaves and are likely to play roles in phloem loading. In the seeding plant leave under water stress, four genes SUT1, SUT2, SUT4 and SUT5 were detectable. In these detectable genes, SUT1 and SUT4 were down regulated, while, SUT2 and SUT5 were up regulated.
  
  
  CONCLUSIONS
  In this study, we presented the first comprehensive genomic study for a whole gene family, the SUT family, in Saccharum. We speculated that there were six SUT members in the S. spotaneum genome. Out of the six members, SsSUTs, SsSUT5 and SsSUT6 were recent duplication genes accompanied by rapid evolution, while, SsSUT2 and SsSUT4 were the ancient members in the families. Despite the high polypoidy genome, functional redundancy may not exist among the SUTs allelic haplotypes supported by the evidence of strong purifying selection of the gene allele. SUT3 could be a low active member in the family because it is undetectable in our study, but it might not be a pseudogene because it harbored integrated gene structure. SUT1 and SUT4 were the main members for the sucrose transporter, while, these SUTs had sub-functional divergence in response to sucrose accumulation and plant development in Saccharum.
authors.affiliation: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. 297160480@qq.com.
authors.forename: Qing
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. 654919671@qq.com.
authors.forename: Weichang
authors.initials: W
authors.lastname: Hu
authors.affiliation: Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. fanzhu2@illinois.edu.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhu
authors.affiliation: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. 849473519@qq.com.
authors.forename: Liming
authors.initials: L
authors.lastname: Wang
authors.affiliation: TexasA&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, 75252, USA. qyu@ag.tamu.edu.
authors.forename: Qingyi
authors.initials: Q
authors.lastname: Yu
authors.affiliation: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology (HIST), Fujian Agriculture and Forestry University, Fuzhou, 350002, China. rming@life.illinois.edu.|Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. rming@life.illinois.edu.
authors.forename: Ray
authors.initials: R
authors.lastname: Ming
authors.affiliation: Center for Genomics and Biotechnology, 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.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
mesh_terms: D000483:Alleles; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D023061:Gene Order; D006239:Haplotypes; D026901:Membrane Transport Proteins / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics*; D031786:Saccharum / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D026901:Membrane Transport Proteins; D010940:Plant Proteins; C078729:sucrose transport protein, plant
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