title: Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits.
abstract: Long non-coding RNAs (lncRNAs) have recently been found to widely exist in eukaryotes and play important roles in key biological processes. To extend our knowledge of lncRNAs in crop plants we performed both non-directional and strand-specific RNA-sequencing experiments to profile non-coding transcriptomes of various rice and maize organs at different developmental stages. Analysis of more than 3 billion reads identified 22 334 long intergenic non-coding RNAs (lincRNAs) and 6673 pairs of sense and natural antisense transcript (NAT). Many lincRNA genes were associated with epigenetic marks. Expression of rice lincRNA genes was significantly correlated with that of nearby protein-coding genes. A set of NAT genes also showed expression correlation with their sense genes. More than 200 rice lincRNA genes had homologous non-coding sequences in the maize genome. Much more lincRNA and NAT genes were derived from conserved genomic regions between the two cereals presenting positional conservation. Protein-coding genes flanking or having a sense-antisense relationship to these conserved lncRNA genes were mainly involved in development and stress responses, suggesting that the associated lncRNAs might have similar functions. Integrating previous genome-wide association studies (GWAS), we found that hundreds of lincRNAs contain trait-associated SNPs (single nucleotide polymorphisms [SNPs]) suggesting their putative contributions to developmental and agriculture traits.
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Huan
authors.initials: H
authors.lastname: Wang
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Qi-Wen
authors.initials: QW
authors.lastname: Niu
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Hui-Wen
authors.initials: HW
authors.lastname: Wu
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Liu
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore City, 117604, Singapore.
authors.forename: Jian
authors.initials: J
authors.lastname: Ye
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Niu
authors.initials: N
authors.lastname: Yu
authors.affiliation: Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
authors.forename: Nam-Hai
authors.initials: NH
authors.lastname: Chua
mesh_terms: D000383:Agriculture; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development
chemical_list: D062085:RNA, Long Noncoding
keywords: NAT; Oryza sativa L. ssp. Japonica cultivar Nipponbare; RNA-seq; Zea mays L. ssp. mays; conservation; lincRNA