title: Identifying conserved and novel microRNAs in developing seeds of Brassica napus using deep sequencing.
abstract: MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. Members of 59 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally 29 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. Assembled mRNA-seq contigs allowed for a search of putative new precursors and led to the identification of 13 novel miRNA families. Analysis of miRNA population between libraries reveals that several miRNAs and isomiRNAs have different abundance in developing stages compared to mature seeds. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comparative study of the miRNA transcriptome of mature and developing B. napus seeds and provides a basis for future research on individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus.
authors.affiliation: PPGGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, Rio Grande do Sul, Brazil.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: Körbes
authors.forename: Ronei Dorneles
authors.initials: RD
authors.lastname: Machado
authors.forename: Frank
authors.initials: F
authors.lastname: Guzman
authors.forename: Mauricio Pereira
authors.initials: MP
authors.lastname: Almerão
authors.forename: Luiz Felipe Valter
authors.initials: LF
authors.lastname: de Oliveira
authors.forename: Guilherme
authors.initials: G
authors.lastname: Loss-Morais
authors.forename: Andreia Carina
authors.initials: AC
authors.lastname: Turchetto-Zolet
authors.forename: Alexandro
authors.initials: A
authors.lastname: Cagliari
authors.forename: Felipe
authors.initials: F
authors.lastname: dos Santos Maraschin
authors.forename: Marcia
authors.initials: M
authors.lastname: Margis-Pinheiro
authors.forename: Rogerio
authors.initials: R
authors.lastname: Margis
mesh_terms: D029688:Brassica napus / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D017124:Conserved Sequence; D004734:Energy Metabolism / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D026723:Polyadenylation / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D012639:Seeds / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant