Identification of the Hevea brasiliensisAP2/ERF superfamily by RNA sequencing

Abstract

BackgroundRubber tree (Hevea brasiliensis) laticifers are the source of natural rubber. Rubber production depends on endogenous and exogenous ethylene (ethephon). AP2/ERF transcription factors, and especially Ethylene-Response Factors, play a crucial role in plant development and response to biotic and abiotic stresses. This study set out to sequence transcript expressed in various tissues using next-generation sequencing and to identify AP2/ERF superfamily in the rubber tree.ResultsThe 454 sequencing technique was used to produce five tissue-type transcript libraries (leaf, bark, latex, embryogenic tissues and root). Reads from all libraries were pooled and reassembled to improve mRNA lengths and produce a global library. One hundred and seventy-three AP2/ERF contigs were identified by in silico analysis based on the amino acid sequence of the conserved AP2 domain from the global library. The 142 contigs with the full AP2 domain were classified into three main families (20 AP2 members, 115 ERF members divided into 11 groups, and 4 RAV members) and 3 soloist members. Fifty-nine AP2/ERF transcripts were found in latex. Alongside the microRNA172 already described in plants, eleven additional microRNAs were predicted to inhibit Hevea AP2/ERF transcripts.ConclusionsHevea has a similar number of AP2/ERF genes to that of other dicot species. We adapted the alignment and classification methods to data from next-generation sequencing techniques to provide reliable information. We observed several specific features for the ERF family. Three HbSoloist members form a group in Hevea. Several AP2/ERF genes highly expressed in latex suggest they have a specific function in Hevea. The analysis of AP2/ERF transcripts in Hevea presented here provides the basis for studying the molecular regulation of latex production in response to abiotic stresses and latex cell differentiation.

The Hevea brasiliensis AP2/ERF superfamily: from ethylene signalling to latex harvesting and physiological disease response

“…Marka-marka tersebut disarikan dari Putranto et al (2015aPutranto et al ( , 2015b (Khandelwal et al, 2008) Taken together, the result of differential gene expression analysis by Duan et al (2013) and Putranto et al (2015a) has brought into conclusion that HbERF-IXc4 and HbERF-IXc5 could have a major role in the regulation of latex production as they were highly expressed in bark during latex harvesting. The ERF group VIII contains an ERF-associated amphiphilic repression (EAR)-motif known as the transcriptional repressors (Ohta et al, 2001).…”

“…Based on known previous knowledge in model plants such as Arabidopsis thaliana and Oryza sativa, these transcription factors were involved in the hormonal response of various biotic and abiotic aspects. Duan et al (2013) have classified 142 members of Hevea AP2/ERF superfamily based on the AP2 domain sequence from full length transcripts of RNA sequencing from rubber clone PB 260. The authors have classified HbERF family into 10 functional groups.…”

“…In regard to known function and well-characterized AP2/ERF superfamily, the Arabidopsis database was selected as comparison to Hevea brasiliensis. Duan et al (2013) was also used this database to construct the classification of Hevea AP2/ERF transcription factors. The bibliographic and phylogenetic analyses were able to reveal the potential functions of these GEMs (Putranto et al, 2015a.…”

“…The CBF/DREB1 genes have been extensively characterized in plants linked to the cold stress (Kurepin et al, 2013;Rehman & Mahmood, 2015). In Hevea, a small number of Cold Binding Factor/Dehydration Responsive Element Binding 1 (CBF/DREB1) genes were identified (Duan et al, 2013). This could be explained by a minor adaptation of Hevea tree to the cold zone.…”

“…In Arabidopsis, the miR319b targeted transcript isoform of RAP2.12 containing an intron in order to inactivate the gene (Sobkowiak et al, 2012). In Hevea, several microRNAs including the well-known miR172 were predicted to target AP2/ERF transcripts (Duan et al, 2013). Although the inhibition mode was being achieved mainly by cleavage of target RNA messenger, translation inhibitions has been predicted for two genes .…”