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Transcriptome dynamics of daily, seasonal and annual cycles in the needles of Douglas-fir (Pseudotsuga menziesii Mirb.)

dataset
posted on 2024-01-26, 23:05 authored by USDA Forest Service
Rhythms of light, temperature, and precipitation provide signals that regulate rhythmic gene expression and growth in trees. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal, seasonal, and circannual needle mRNA accumulation in Douglas-fir, Pseudotsuga menziesii. Using mRNA sequencing, we sampled 101 bp reads from 19 trees and constructed a combined 'pan-transcriptome' reference that includes 199,471 transcripts (PRJNA356432). Using this reference, we mapped RNA-seq reads from samples that capture diurnal variation between two families of trees (12 time points; PRJNA263611), seasonal variation between three families of trees (PRJNA188506), and annual variation between two families of trees (16 time points; PRJNA243096). This study shows that thousands of genes reach peak annual activity during the winter and summer solstices, and that photoperiod and light quality is a dominant driver of daily and annual transcription in Douglas-fir.

Funding

U.S. Department of Agriculture, 2010-65300-20166

History

Data contact name

BioProject Curation Staff

Publisher

National Center for Biotechnology Information

Temporal Extent Start Date

2017-01-18

Theme

  • Non-geospatial

ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

Biological Sciences; biotechnology; genetics

Pending citation

  • No

Public Access Level

  • Public

Accession Number

PRJNA362352

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