title: Characterization of the small RNA component of leaves and fruits from four different cucurbit species.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are a class of non-coding small RNAs involved in post-transcriptional regulation of gene expression critical for plant growth and development, stress responses and other diverse biological processes in plants. The Cucurbitaceae or cucurbit family represents some of economically important species, particularly those with edible and medicinal fruits. Genomic tools for the molecular analysis of members of this family are just emerging. Partial draft genome sequence became available recently for cucumber and watermelon facilitating investigation of the small RNA component of the transcriptomes in cucurbits.
  
  
  RESULTS
  We generated four small RNA libraries from bottle gourd (Lagenaria siceraria), Cucurbita moschata, Cucurbita pepo, and, watermelon (Citrullus lanatus var. lanatus) in order to identify conserved and novel lineage specific miRNAs in these cucurbits. Deep sequencing of small RNA libraries from these species resulted in 1,597,263, 532,948, 601,388, and 493,384 unique sRNA reads from bottle gourd, moschata, pepo and watermelon, respectively. Sequence analysis of these four libraries resulted in identification of 21 miRNA families that are highly conserved and 8 miRNA families that are moderately conserved in diverse dicots. We also identified 4 putative novel miRNAs in these plant species. Furthermore, the tasiRNAs were identified and their biogenesis was determined in these cucurbits. Small RNA blot analysis or q-PCR analyses of leaf and fruit tissues of these cucurbits showed differential expression of several conserved miRNAs. Interestingly, the abundance of several miRNAs in leaves and fruits of closely related C. moschata and C. pepo was also distinctly different. Target genes for the most conserved miRNAs are also predicted.
  
  
  CONCLUSIONS
  High-throughput sequencing of small RNA libraries from four cucurbit species has provided a glimpse of small RNA component in their transcriptomes. The analysis also showed considerable variation within four cucurbit species with regards to expression of individual miRNAs.
authors: Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
authors: Guru
authors: G
authors: Jagadeeswaran
authors: Padma
authors: P
authors: Nimmakayala
authors: Yun
authors: Y
authors: Zheng
authors: Kanchana
authors: K
authors: Gowdu
authors: Umesh K
authors: UK
authors: Reddy
authors: Ramanjulu
authors: R
authors: Sunkar
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D019662:Cucurbitaceae / Q000235:genetics*; D005638:Fruit / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D056426:Genetic Loci / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009928:Organ Specificity / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D034741:RNA, Small Interfering / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering