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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.


Mapping of small RNA reads to repetitive regions of Eucalyptus grandis reference genome. Size distribution (in nucleotides – nt) of small RNA reads from smRNA-Seq data based on mapping to repetitive regions of Eucalyptus grandis reference genome per sample: E. globulus A2 developing xylem (gloA2), E. globulus C3 developing xylem (gloC3), BRASUZ BR1 leaves (leaves) and BRASUZ BR1 developing xylem (xylem). Light blue bars represent reads mapped to repetitive regions and dark blue bars, to non-repetitive regions
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Fig4: Mapping of small RNA reads to repetitive regions of Eucalyptus grandis reference genome. Size distribution (in nucleotides – nt) of small RNA reads from smRNA-Seq data based on mapping to repetitive regions of Eucalyptus grandis reference genome per sample: E. globulus A2 developing xylem (gloA2), E. globulus C3 developing xylem (gloC3), BRASUZ BR1 leaves (leaves) and BRASUZ BR1 developing xylem (xylem). Light blue bars represent reads mapped to repetitive regions and dark blue bars, to non-repetitive regions

Mentions: Mapping data was investigated for correlation between sequence size and mapping location in repetitive regions. Mapping data of unique reads from 19 to 26-nt showed sRNA reads located mostly in repeat regions (70.1 % in E. grandis BRASUZ1 leaves, 59.3 % in E. grandis BRASUZ1 xylem, 64.3 % in E. globulus A2 xylem and 64.9 % in E. globulus C3 xylem). Size distribution of mapped reads revealed a general tendency to mapping on repetitive regions irrespective of the sequence size (Fig. 4).Fig. 4


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)

Mapping of small RNA reads to repetitive regions of Eucalyptus grandis reference genome. Size distribution (in nucleotides – nt) of small RNA reads from smRNA-Seq data based on mapping to repetitive regions of Eucalyptus grandis reference genome per sample: E. globulus A2 developing xylem (gloA2), E. globulus C3 developing xylem (gloC3), BRASUZ BR1 leaves (leaves) and BRASUZ BR1 developing xylem (xylem). Light blue bars represent reads mapped to repetitive regions and dark blue bars, to non-repetitive regions
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Mapping of small RNA reads to repetitive regions of Eucalyptus grandis reference genome. Size distribution (in nucleotides – nt) of small RNA reads from smRNA-Seq data based on mapping to repetitive regions of Eucalyptus grandis reference genome per sample: E. globulus A2 developing xylem (gloA2), E. globulus C3 developing xylem (gloC3), BRASUZ BR1 leaves (leaves) and BRASUZ BR1 developing xylem (xylem). Light blue bars represent reads mapped to repetitive regions and dark blue bars, to non-repetitive regions
Mentions: Mapping data was investigated for correlation between sequence size and mapping location in repetitive regions. Mapping data of unique reads from 19 to 26-nt showed sRNA reads located mostly in repeat regions (70.1 % in E. grandis BRASUZ1 leaves, 59.3 % in E. grandis BRASUZ1 xylem, 64.3 % in E. globulus A2 xylem and 64.9 % in E. globulus C3 xylem). Size distribution of mapped reads revealed a general tendency to mapping on repetitive regions irrespective of the sequence size (Fig. 4).Fig. 4

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.