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Dee R. Denver - One of the best experts on this subject based on the ideXlab platform.
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Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:BackgroundPerennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation.ResultsWe identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter.ConclusionsOur study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cyclic gene expression variation in douglas fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cycles of gene expression variation in douglas fir Needles
bioRxiv, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x109 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
Richard Cronn - One of the best experts on this subject based on the ideXlab platform.
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Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:BackgroundPerennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation.ResultsWe identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter.ConclusionsOur study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cyclic gene expression variation in douglas fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cycles of gene expression variation in douglas fir Needles
bioRxiv, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x109 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
Amina Rangoonwala - One of the best experts on this subject based on the ideXlab platform.
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remote sensing and the optical properties of the narrow cylindrical leaves of juncus roemerianus
IEEE Transactions on Geoscience and Remote Sensing, 2004Co-Authors: E.w. Ramsey, Amina RangoonwalaAbstract:To develop a more complete foundation for remote sensing of the marsh grass Juncus roemerianus, we measured the optical properties of its cylindrical leaves at sites of different canopy height, biomass composition and amount, and connectivity to ocean flushing. To measure the leaf optical properties, we adapted a technique used for Conifer Needles. After establishing the reliability and limits of the adapted technique to the wider J.roemerianus leaves, mean transmittance and reflectance spectra were compared to associated leaf diameters from two dates in 1999 and 2002 and at each site. Transmittance was inversely related to leaf diameter. Mean transmittance and reflectance generated from reoccupation of many field sites in 2002 indicated little or no difference in transmittance between years, a slight reflectance difference in the visible (<2%) and a slightly higher reflectance difference in the near infrared (NIR) (<4%). Site comparison indicated limited ability to separate leaf transmittance but not reflectance by marsh type (e.g., low, medium, high) or biomass. Excluding one outlier, we found leaf transmittances could be adequately represented as 1% /spl plusmn/ 0.2% in the visible and 9% /spl plusmn/ 1% in the NIR and leaf reflectances represented from 14% to 16% in the visible and 71% to 75% in the NIR (the reflectance ranges represent 1999 and 2002 means). Reflectance and transmittance spectra associated with the dead J. roemerianus leaves displayed a spectrally flat increase from the visible to the NIR wavelengths. In total, we documented the atypical optical properties of the cylindrical J. roemerianus leaves and showed that to a first approximation, single means could represent leaf transmittance and visible leaf reflectance across all marsh zones and, after accounting for sample standardization, possibly the NIR reflectance as well.
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remote sensing and the optical properties of the narrow cylindrical leaves of juncus roemerianus
IEEE Transactions on Geoscience and Remote Sensing, 2004Co-Authors: E.w. Ramsey, Amina RangoonwalaAbstract:To develop a more complete foundation for remote sensing of the marsh grass Juncus roemerianus, we measured the optical properties of its cylindrical leaves at sites of different canopy height, biomass composition and amount, and connectivity to ocean flushing. To measure the leaf optical properties, we adapted a technique used for Conifer Needles. After establishing the reliability and limits of the adapted technique to the wider J.roemerianus leaves, mean transmittance and reflectance spectra were compared to associated leaf diameters from two dates in 1999 and 2002 and at each site. Transmittance was inversely related to leaf diameter. Mean transmittance and reflectance generated from reoccupation of many field sites in 2002 indicated little or no difference in transmittance between years, a slight reflectance difference in the visible (<2%) and a slightly higher reflectance difference in the near infrared (NIR) (<4%). Site comparison indicated limited ability to separate leaf transmittance but not reflectance by marsh type (e.g., low, medium, high) or biomass. Excluding one outlier, we found leaf transmittances could be adequately represented as 1% /spl plusmn/ 0.2% in the visible and 9% /spl plusmn/ 1% in the NIR and leaf reflectances represented from 14% to 16% in the visible and 71% to 75% in the NIR (the reflectance ranges represent 1999 and 2002 means). Reflectance and transmittance spectra associated with the dead J. roemerianus leaves displayed a spectrally flat increase from the visible to the NIR wavelengths. In total, we documented the atypical optical properties of the cylindrical J. roemerianus leaves and showed that to a first approximation, single means could represent leaf transmittance and visible leaf reflectance across all marsh zones and, after accounting for sample standardization, possibly the NIR reflectance as well.
Peter C. Dolan - One of the best experts on this subject based on the ideXlab platform.
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Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:BackgroundPerennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation.ResultsWe identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter.ConclusionsOur study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cyclic gene expression variation in douglas fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cycles of gene expression variation in douglas fir Needles
bioRxiv, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x109 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
Sanjuro Jogdeo - One of the best experts on this subject based on the ideXlab platform.
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Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:BackgroundPerennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation.ResultsWe identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter.ConclusionsOur study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cyclic gene expression variation in douglas fir Needles
BMC Genomics, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal cycles and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1 × 109 reads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily and annual variation. We identified 12,042 diurnally-cyclic transcripts, 9299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 circannual transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light intensity at diurnal scales and photoperiod at annual scales, with approximately half of transcripts reaching maximum expression +/− 2 h from sunrise and sunset, and +/− 20 days from winter and summer solstices. Comparisons with published studies from other Conifers shows congruent behavior in clock genes with Japanese cedar (Cryptomeria), and a significant preservation of gene expression patterns for 2278 putative orthologs from Douglas-fir during the summer growing season, and 760 putative orthologs from spruce (Picea) during the transition from fall to winter. Our study highlight the extensive diurnal and circannual transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts show a significant diurnal cycle, and 58.7% show a significant circannual cycle. Remarkably, thousands of genes reach their annual peak activity during winter dormancy. Our study establishes the fine-scale timing of daily and annual maximum gene expression for diverse needle genes in Douglas-fir, and it highlights the potential for using this information for evaluating hypotheses concerning the daily or seasonal timing of gene activity in temperate-zone Conifers, and for identifying cyclic transcriptome components in other Conifer species.
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transcription through the eye of a needle daily and annual cycles of gene expression variation in douglas fir Needles
bioRxiv, 2017Co-Authors: Richard Cronn, Peter C. Dolan, Sanjuro Jogdeo, J. Bradley St. Clair, Jill L. Wegrzyn, David B Neale, Dee R. DenverAbstract:Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In Conifers, Needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in Conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) Needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x109 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in Conifer Needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.