title: The Medicago sativa gene index 1.2: a web-accessible gene expression atlas for investigating expression differences between Medicago sativa subspecies.
abstract: BACKGROUND
  Alfalfa (Medicago sativa L.) is the primary forage legume crop species in the United States and plays essential economic and ecological roles in agricultural systems across the country. Modern alfalfa is the result of hybridization between tetraploid M. sativa ssp. sativa and M. sativa ssp. falcata. Due to its large and complex genome, there are few genomic resources available for alfalfa improvement.
  
  
  RESULTS
  A de novo transcriptome assembly from two alfalfa subspecies, M. sativa ssp. sativa (B47) and M. sativa ssp. falcata (F56) was developed using Illumina RNA-seq technology. Transcripts from roots, nitrogen-fixing root nodules, leaves, flowers, elongating stem internodes, and post-elongation stem internodes were assembled into the Medicago sativa Gene Index 1.2 (MSGI 1.2) representing 112,626 unique transcript sequences. Nodule-specific and transcripts involved in cell wall biosynthesis were identified. Statistical analyses identified 20,447 transcripts differentially expressed between the two subspecies. Pair-wise comparisons of each tissue combination identified 58,932 sequences differentially expressed in B47 and 69,143 sequences differentially expressed in F56. Comparing transcript abundance in floral tissues of B47 and F56 identified expression differences in sequences involved in anthocyanin and carotenoid synthesis, which determine flower pigmentation. Single nucleotide polymorphisms (SNPs) unique to each M. sativa subspecies (110,241) were identified.
  
  
  CONCLUSIONS
  The Medicago sativa Gene Index 1.2 increases the expressed sequence data available for alfalfa by ninefold and can be expanded as additional experiments are performed. The MSGI 1.2 transcriptome sequences, annotations, expression profiles, and SNPs were assembled into the Alfalfa Gene Index and Expression Database (AGED) at http://plantgrn.noble.org/AGED/ , a publicly available genomic resource for alfalfa improvement and legume research.
authors.affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. Jamie.ORourke@ars.usda.gov.
authors.forename: Jamie A
authors.initials: JA
authors.lastname: O'Rourke
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. fuxxx026@umn.edu.
authors.forename: Fengli
authors.initials: F
authors.lastname: Fu
authors.affiliation: USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. Bruna.Bucciarelli@ars.usda.gov.
authors.forename: Bruna
authors.initials: B
authors.lastname: Bucciarelli
authors.affiliation: USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. yangsh38@hotmail.com.|Present Address: Monsanto Company, Molecular Breeding Technology, Chesterfield, MO, 63167, USA. yangsh38@hotmail.com.
authors.forename: S Sam
authors.initials: SS
authors.lastname: Yang
authors.affiliation: USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. Debby.Samac@ars.usda.gov.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Samac
authors.affiliation: USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. JoAnn.Lamb@ars.usda.gov.
authors.forename: JoAnn F S
authors.initials: JF
authors.lastname: Lamb
authors.affiliation: Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. mjmonteros@noble.org.
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Monteros
authors.affiliation: USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA. michelle.graham@ars.usda.gov.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Graham
authors.affiliation: USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. gronw001@umn.edu.
authors.forename: John W
authors.initials: JW
authors.lastname: Gronwald
authors.affiliation: Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. ndkrom@noble.org.
authors.forename: Nick
authors.initials: N
authors.lastname: Krom
authors.affiliation: Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. jli@noble.org.
authors.forename: Jun
authors.initials: J
authors.lastname: Li
authors.affiliation: Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. xdai@noble.org.
authors.forename: Xinbin
authors.initials: X
authors.lastname: Dai
authors.affiliation: Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA. pzhao@noble.org.
authors.forename: Patrick X
authors.initials: PX
authors.lastname: Zhao
authors.affiliation: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA. vance004@umn.edu.|USDA-ARS-Plant Science Research Unit, St. Paul, MN, 55108, USA. vance004@umn.edu.
authors.forename: Carroll P
authors.initials: CP
authors.lastname: Vance
mesh_terms: D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D000455:Medicago sativa / Q000235:genetics*; D010858:Pigmentation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D059467:Transcriptome / Q000235:genetics