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Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves.

Leyva-Pérez Mde L, Valverde-Corredor A, Valderrama R, Jiménez-Ruiz J, Muñoz-Merida A, Trelles O, Barroso JB, Mercado-Blanco J, Luque F - DNA Res. (2014)

Bottom Line: After 5 days, the plants were found to have completely recovered.After long-term exposure to cold, a large proportion of gene down-regulation was found, including photosynthesis and plant growth genes.Up-regulated genes after long-term cold exposure were related to organelle fusion, nucleus organization, and DNA integration, including retrotransposons.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Experimental, Universidad de Jaén, Jaén, Spain.

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Related in: MedlinePlus

Percentage of different genes that mapped in OlePic as reference at different minimun e-values. The cDNA sequences of AS8 and olive-related plant species were mapped to OlePic by using the blastn algorithm from blast/2.2.20 software.
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DSU033F3: Percentage of different genes that mapped in OlePic as reference at different minimun e-values. The cDNA sequences of AS8 and olive-related plant species were mapped to OlePic by using the blastn algorithm from blast/2.2.20 software.

Mentions: The transcriptome was assembled from a total of 741,674,755 high-quality paired-end reads (149.77 Gb; Supplementary Table S2). Each sample was separately assembled using the ABySS-pe software with a k-mer = 64. Finally, all samples were re-assembled together with the ABySS single-end using a k-mer = 63. The final transcriptome (OlePic) contains 157,799 unigenes with an N50 length of 700 bases, an average length of 544 bases, a maximal length of 11,114 bases, 46% GC, and 0% undetermined. The distribution by length of the unigenes generated in the assembly is shown in Fig. 2A. The result shows that although OlePic has a higher number of assembled transcripts, the distribution by length is similar to the currently available, most complete olive transcriptome AS8. In addition, OlePic is enriched in longer contigs than AS8 in a similar way as the Mimulus guttatus one, the available plant transcriptome most phylogenetically related to Olive tree.37 On the other hand, mapping analysis with bowtie2 showed that, on average, 65% of original reads aligned with OlePic end to end and 83.5% aligned locally. It can therefore be concluded that the vast majority of the reads sequenced are represented in this new transcriptome. Another common assessment of the quality of the assembled database is provided by the coverage. The minimum k-mer coverage for each unigene was 400 (Fig. 2B), and 88% of contigs were covered for >1,000 k-mer of 63 bases. Regarding cold stress, all reads derived from the cold experiment samples were mapped end to end to the assembly (Fig. 2C). In addition, 73.3% of unigenes were covered for reads obtained in this study (115,644 unigenes). From these unigenes, 82.5% were covered by more than at least 50 reads. The OlePic transcripts’ similarity and transcriptome coverage with olive AS8 transcriptome and other phylogenetically related species (monkey flower,37 tomato,38 grapevine39 and rose gum40) were measured by blastn algorithm from BLAST software at different expectation values (Fig. 3). Consistently with the established phylogenetic relationships, the percentage of cDNA sequences with hits in OlePic was proportional to the different species phylogenetic likelihood.Figure 2.


Early and delayed long-term transcriptional changes and short-term transient responses during cold acclimation in olive leaves.

Leyva-Pérez Mde L, Valverde-Corredor A, Valderrama R, Jiménez-Ruiz J, Muñoz-Merida A, Trelles O, Barroso JB, Mercado-Blanco J, Luque F - DNA Res. (2014)

Percentage of different genes that mapped in OlePic as reference at different minimun e-values. The cDNA sequences of AS8 and olive-related plant species were mapped to OlePic by using the blastn algorithm from blast/2.2.20 software.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4379972&req=5

DSU033F3: Percentage of different genes that mapped in OlePic as reference at different minimun e-values. The cDNA sequences of AS8 and olive-related plant species were mapped to OlePic by using the blastn algorithm from blast/2.2.20 software.
Mentions: The transcriptome was assembled from a total of 741,674,755 high-quality paired-end reads (149.77 Gb; Supplementary Table S2). Each sample was separately assembled using the ABySS-pe software with a k-mer = 64. Finally, all samples were re-assembled together with the ABySS single-end using a k-mer = 63. The final transcriptome (OlePic) contains 157,799 unigenes with an N50 length of 700 bases, an average length of 544 bases, a maximal length of 11,114 bases, 46% GC, and 0% undetermined. The distribution by length of the unigenes generated in the assembly is shown in Fig. 2A. The result shows that although OlePic has a higher number of assembled transcripts, the distribution by length is similar to the currently available, most complete olive transcriptome AS8. In addition, OlePic is enriched in longer contigs than AS8 in a similar way as the Mimulus guttatus one, the available plant transcriptome most phylogenetically related to Olive tree.37 On the other hand, mapping analysis with bowtie2 showed that, on average, 65% of original reads aligned with OlePic end to end and 83.5% aligned locally. It can therefore be concluded that the vast majority of the reads sequenced are represented in this new transcriptome. Another common assessment of the quality of the assembled database is provided by the coverage. The minimum k-mer coverage for each unigene was 400 (Fig. 2B), and 88% of contigs were covered for >1,000 k-mer of 63 bases. Regarding cold stress, all reads derived from the cold experiment samples were mapped end to end to the assembly (Fig. 2C). In addition, 73.3% of unigenes were covered for reads obtained in this study (115,644 unigenes). From these unigenes, 82.5% were covered by more than at least 50 reads. The OlePic transcripts’ similarity and transcriptome coverage with olive AS8 transcriptome and other phylogenetically related species (monkey flower,37 tomato,38 grapevine39 and rose gum40) were measured by blastn algorithm from BLAST software at different expectation values (Fig. 3). Consistently with the established phylogenetic relationships, the percentage of cDNA sequences with hits in OlePic was proportional to the different species phylogenetic likelihood.Figure 2.

Bottom Line: After 5 days, the plants were found to have completely recovered.After long-term exposure to cold, a large proportion of gene down-regulation was found, including photosynthesis and plant growth genes.Up-regulated genes after long-term cold exposure were related to organelle fusion, nucleus organization, and DNA integration, including retrotransposons.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Biología Experimental, Universidad de Jaén, Jaén, Spain.

Show MeSH
Related in: MedlinePlus