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Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae.

Pappas Mde C, Pappas GJ, Grattapaglia D - BMC Genomics (2015)

Bottom Line: In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets.Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

View Article: PubMed Central - PubMed

Affiliation: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. marilia.pappas@embrapa.br.

ABSTRACT

Background: Micro RNAs are a class of small non coding RNAs of 20-24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing.

Results: In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.

Conclusions: The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

No MeSH data available.


Enrichment of protein domains in predicted micro RNA targets. Count of protein domains in messenger RNA targets predicted by psRNATarget. Protein domains typical from disease resistance genes family TIR-NB-LRR (*) are the most abundant
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Fig5: Enrichment of protein domains in predicted micro RNA targets. Count of protein domains in messenger RNA targets predicted by psRNATarget. Protein domains typical from disease resistance genes family TIR-NB-LRR (*) are the most abundant

Mentions: Prediction of transcripts targeted by miRNAs adds another level of in silico confirmation, providing clues about potential biological processes being regulated. Target prediction was performed for all mapped sequence candidates with a compatible precursor secondary structure using psRNATarget [61]. The Eucalyptus transcript database from Phytozome was used for reverse complementary matching between smRNA-Seq data and potential target transcripts. Functional annotation of targets was retrieved from the BioMart tool available in Phytozome. The number of predicted targets for each miRNA candidate varied from one to twenty transcripts. The enrichment for specific protein domains in predicted target mRNAs is shown in Fig. 5 and indicates the prevalence of signature domains for NB-LRR (NB-ARC, leucine rich repeat) disease resistance genes, ion transporters, SBP (squamosa binding proteins) transcription factors and PPR (pentatricopeptide repeat) proteins. Predicted targets also include transcripts related to wood formation such as cellulose synthases and cytochrome P450 which is involved both in biosynthetic and detoxification pathways.Fig. 5


Genome-wide discovery and validation of Eucalyptus small RNAs reveals variable patterns of conservation and diversity across species of Myrtaceae.

Pappas Mde C, Pappas GJ, Grattapaglia D - BMC Genomics (2015)

Enrichment of protein domains in predicted micro RNA targets. Count of protein domains in messenger RNA targets predicted by psRNATarget. Protein domains typical from disease resistance genes family TIR-NB-LRR (*) are the most abundant
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4696225&req=5

Fig5: Enrichment of protein domains in predicted micro RNA targets. Count of protein domains in messenger RNA targets predicted by psRNATarget. Protein domains typical from disease resistance genes family TIR-NB-LRR (*) are the most abundant
Mentions: Prediction of transcripts targeted by miRNAs adds another level of in silico confirmation, providing clues about potential biological processes being regulated. Target prediction was performed for all mapped sequence candidates with a compatible precursor secondary structure using psRNATarget [61]. The Eucalyptus transcript database from Phytozome was used for reverse complementary matching between smRNA-Seq data and potential target transcripts. Functional annotation of targets was retrieved from the BioMart tool available in Phytozome. The number of predicted targets for each miRNA candidate varied from one to twenty transcripts. The enrichment for specific protein domains in predicted target mRNAs is shown in Fig. 5 and indicates the prevalence of signature domains for NB-LRR (NB-ARC, leucine rich repeat) disease resistance genes, ion transporters, SBP (squamosa binding proteins) transcription factors and PPR (pentatricopeptide repeat) proteins. Predicted targets also include transcripts related to wood formation such as cellulose synthases and cytochrome P450 which is involved both in biosynthetic and detoxification pathways.Fig. 5

Bottom Line: In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets.Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

View Article: PubMed Central - PubMed

Affiliation: Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil. marilia.pappas@embrapa.br.

ABSTRACT

Background: Micro RNAs are a class of small non coding RNAs of 20-24 nucleotides transcribed as single stranded precursors from MIR gene loci. Initially described as post-transcriptional regulators involved in development, two decades ago, miRNAs have been proven to regulate a wide range of processes in plants such as germination, morphology and responses to biotic and abiotic stress. Despite wide conservation in plants, a number of miRNAs are lineage specific. We describe the first genome wide survey of Eucalyptus miRNAs based on high throughput sequencing.

Results: In addition to discovering small RNA sequences, MIR loci were mapped onto the reference genome and interspecific variability investigated. Sequencing was carried out for the two most world widely planted species, E. grandis and E. globulus. To maximize discovery, E. grandis samples were from BRASUZ1, the same tree whose genome provided the reference sequence. Interspecific analysis reinforces the variability in small RNA repertoire even between closely related species. Characterization of Eucalyptus small RNA sequences showed 95 orthologous to conserved miRNAs and 193 novel miRNAs. In silico target prediction confirmed 163 novel miRNAs and degradome sequencing experimentally confirmed several hundred targets. Experimental evidence based on the exclusive expression of a set of small RNAs across 16 species within Myrtaceae further highlighted variable patterns of conservation and diversity of these regulatory elements.

Conclusions: The description of miRNAs in Eucalyptus contributes to scientific knowledge of this vast genre, which is the most widely planted hardwood crop in the tropical and subtropical world, adding another important element to the annotation of Eucalyptus grandis reference genome.

No MeSH data available.