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Noncoding RNA. 2018 Oct 8;4(4). pii: E27. doi: 10.3390/ncrna4040027.

Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes.

Author information

1
Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. monica.danilevicz@gmail.com.
2
Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil. kcm.eid@gmail.com.
3
Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil. thiago.venancio@gmail.com.
4
Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil. lfranco@jbrj.gov.br.
5
Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil. sergio@jbrj.gov.br.
6
Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil. mcardoso@jbrj.gov.br.
7
Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. flaviabqi@gmail.com.
8
Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. hemerly@bioqmed.ufrj.br.
9
Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. prosdocimi@bioqmed.ufrj.br.
10
Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil. paulof@bioqmed.ufrj.br.

Abstract

Long non-coding RNAs (lncRNAs) are involved in multiple regulatory pathways and its versatile form of action has disclosed a new layer in gene regulation. LncRNAs have their expression levels modulated during plant development, and in response to stresses with tissue-specific functions. In this study, we analyzed lncRNA from leaf samples collected from the legume Copaifera langsdorffii Desf. (copaíba) present in two divergent ecosystems: Cerrado (CER; Ecological Station of Botanical Garden in Brasília, Brazil) and Atlantic Rain Forest (ARF; Rio de Janeiro, Brazil). We identified 8020 novel lncRNAs, and they were compared to seven Fabaceae genomes and transcriptomes, to which 1747 and 2194 copaíba lncRNAs were mapped, respectively, to at least one species. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. A few selected lncRNA were confirmed by RT-qPCR in the samples from both biomes; Additionally, the analysis of the lncRNA sequences predicted that some might act as microRNA (miRNA) targets or decoys. The emerging studies involving lncRNAs function and conservation have shown their involvement in several types of biotic and abiotic stresses. Thus, the conservation of lncRNAs among Fabaceae species considering their rapid turnover, suggests they are likely to have been under functional conservation pressure. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii in two different biomes.

KEYWORDS:

Copaifera; adaptive response; epigenetics; lncRNA conservation; novel lncRNA

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