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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.


Conservation of miR159a. Multiple sequence alignment of Eucalyptus grandis miR159a (egr-miR159a) and plant miR159a sequences from miRBase (sequence id as in miRBase)
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Fig3: Conservation of miR159a. Multiple sequence alignment of Eucalyptus grandis miR159a (egr-miR159a) and plant miR159a sequences from miRBase (sequence id as in miRBase)

Mentions: Conserved miRNAs were often observed among 21-nt reads with highest counts. MiR159a was consistently the most abundant 21-nt sequence in three out of four samples – E. grandis BRASUZ1 leaves (40 %) (Fig. 2a) and developing xylem (10.5 %) (Fig. 2b), and E. globulus C3 developing xylem (18.2 %) (Fig. 2d). In the E. globulus A2 xylem sample, miR159a (6.99 %) was outnumbered by miR172g (9.16 %), but was the second most abundant 21-nt read (Fig. 2c). MiR159a is a highly conserved miRNA as seen by alignment of Eucalyptus miR159a with all plant orthologs present in miRBase (Fig. 3). MiR166 and miR396 are other conserved miRNAs that are featured among the top fifteen 21-nt reads in all four samples. A broad search for conserved miRNAs was carried out and is discussed further.Fig. 3


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)

Conservation of miR159a. Multiple sequence alignment of Eucalyptus grandis miR159a (egr-miR159a) and plant miR159a sequences from miRBase (sequence id as in miRBase)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig3: Conservation of miR159a. Multiple sequence alignment of Eucalyptus grandis miR159a (egr-miR159a) and plant miR159a sequences from miRBase (sequence id as in miRBase)
Mentions: Conserved miRNAs were often observed among 21-nt reads with highest counts. MiR159a was consistently the most abundant 21-nt sequence in three out of four samples – E. grandis BRASUZ1 leaves (40 %) (Fig. 2a) and developing xylem (10.5 %) (Fig. 2b), and E. globulus C3 developing xylem (18.2 %) (Fig. 2d). In the E. globulus A2 xylem sample, miR159a (6.99 %) was outnumbered by miR172g (9.16 %), but was the second most abundant 21-nt read (Fig. 2c). MiR159a is a highly conserved miRNA as seen by alignment of Eucalyptus miR159a with all plant orthologs present in miRBase (Fig. 3). MiR166 and miR396 are other conserved miRNAs that are featured among the top fifteen 21-nt reads in all four samples. A broad search for conserved miRNAs was carried out and is discussed further.Fig. 3

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.