title: Transcriptomic analysis of a psammophyte food crop, sand rice (Agriophyllum squarrosum) and identification of candidate genes essential for sand dune adaptation.
abstract: BACKGROUND
  Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been historically consumed by local populations in the desert regions of northwest China. Sand rice is a potential food crop resilient to ongoing climate change; however, partly due to the scarcity of genetic information, this species has undergone only little agronomic modifications through classical breeding during recent years.
  
  
  RESULTS
  We generated a deep transcriptomic sequencing of sand rice, which uncovers 67,741 unigenes. Phylogenetic analysis based on 221 single-copy genes showed close relationship between sand rice and the recently domesticated crop sugar beet. Transcriptomic comparisons also showed a high level of global sequence conservation between these two species. Conservation of sand rice and sugar beet orthologs assigned to response to salt stress gene ontology term suggests that sand rice is also a potential salt tolerant plant. Furthermore, sand rice is far more tolerant to high temperature. A set of genes likely relevant for resistance to heat stress, was functionally annotated according to expression levels, sequence annotation, and comparisons corresponding transcriptome profiling results in Arabidopsis.
  
  
  CONCLUSIONS
  The present work provides abundant genomic information for functional dissection of the important traits in sand rice. Future screening the genetic variation among different ecotypes and constructing a draft genome sequence will further facilitate agronomic trait improvement and final domestication of sand rice.
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. zhaopengshan@lzb.ac.cn.|Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. zhaopengshan@lzb.ac.cn.
authors.forename: Pengshan
authors.initials: P
authors.lastname: Zhao
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. scapella@crg.eu.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. scapella@crg.eu.|Yeast and Basidiomycete Research Group, CBS Fungal Biodiversity Centre, Uppsalalaan 8, 3584, LT, Utrecht, The Netherlands. scapella@crg.eu.
authors.forename: Salvador
authors.initials: S
authors.lastname: Capella-Gutiérrez
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. shiy05@gmail.com.|Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. shiy05@gmail.com.
authors.forename: Yong
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. zhaox@lzb.ac.cn.|Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. zhaox@lzb.ac.cn.
authors.forename: Xin
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. guoxiong@lzb.ac.cn.|Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. guoxiong@lzb.ac.cn.
authors.forename: Guoxiong
authors.initials: G
authors.lastname: Chen
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003, Barcelona, Spain. toni.gabaldon@crg.eu.|Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain. toni.gabaldon@crg.eu.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain. toni.gabaldon@crg.eu.
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.affiliation: Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. maxiaofei@lzb.ac.cn.|Shapotou Desert Research and Experimental Station, Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, 730000, People's Republic of China. maxiaofei@lzb.ac.cn.
authors.forename: Xiao-Fei
authors.initials: XF
authors.lastname: Ma
mesh_terms: D000222:Adaptation, Physiological; D027703:Amaranthaceae / Q000235:genetics* / Q000502:physiology*; D057231:Climate Change; D018556:Crops, Agricultural; D005502:Food; D005523:Food Supply; D020869:Gene Expression Profiling; D017343:Genes, Plant / Q000235:genetics*; D006358:Hot Temperature; D058977:Molecular Sequence Annotation