title: Genome-wide identification of the Phaseolus vulgaris sRNAome using small RNA and degradome sequencing.
abstract: BACKGROUND
  MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21, the most used miRNA database, and no phasiRNAs have been identified for the model legume Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs for this organism and, particularly, we suggest new protagonists in the symbiotic nodulation events.
  
  
  RESULTS
  We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs: those known to play crucial roles in the establishment of nodules, and novel miRNAs present only in common bean, suggesting a specific role for these sequences. In addition, we identified 125 loci that potentially produce phased small RNAs, with 47 of them having all the characteristics of being triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study.
  
  
  CONCLUSIONS
  We provide here a set of new small RNAs that contribute to the broader knowledge of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we present here the probable functional regulation associated with the sRNAome and, particularly, in N2-fixing symbiotic nodules.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico. formey@ccg.unam.mx.
authors.forename: Damien
authors.initials: D
authors.lastname: Formey
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico. liniguez@lcg.unam.mx.
authors.forename: Luis Pedro
authors.initials: LP
authors.lastname: Iñiguez
authors.affiliation: Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico. ppelaez@ibt.unam.mx.
authors.forename: Pablo
authors.initials: P
authors.lastname: Peláez
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA. yongfang.li@okstate.edu.
authors.forename: Yong-Fang
authors.initials: YF
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, 74078, USA. ramanjulu.sunkar@okstate.edu.
authors.forename: Ramanjulu
authors.initials: R
authors.lastname: Sunkar
authors.affiliation: Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico. federico@ibt.unam.mx.
authors.forename: Federico
authors.initials: F
authors.lastname: Sánchez
authors.affiliation: Departamento de Biología Molecular de Plantas, Instituto de Biotecnología (UNAM), Av. Universidad 2001, Cuernavaca, 62210, Morelos, Mexico. jlreyes@ibt.unam.mx.
authors.forename: José Luis
authors.initials: JL
authors.lastname: Reyes
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Av. Universidad 1001, Cuernavaca, 62210, Morelos, Mexico. gina@ccg.unam.mx.
authors.forename: Georgina
authors.initials: G
authors.lastname: Hernández
mesh_terms: D017124:Conserved Sequence; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D035683:MicroRNAs / Q000032:analysis / Q000378:metabolism; D027805:Phaseolus / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D018749:RNA, Plant / Q000032:analysis* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000032:analysis / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant; D034741:RNA, Small Interfering