DOI: 10.5061/dryad.x69p8czwp
title: High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

description: Background Photoperiodic changes in diel cycles of gene expression are
 pervasive in plants. The timing of circadian regulators, together with
 light signals, regulate multiple photoperiod-dependent responses such as
 growth, flowering or tuber formation. However, for most genes, the
 importance of cyclic mRNA levels is less clear. We analyzed the diel
 transcriptome of modern cultivated potato, a highly heterozygous
 autotetraploid. Clonal propagation and limited meiosis have led to the
 accumulation of deleterious alleles, making tetraploid potato an ideal
 model system to investigate the conservation of cyclic expression and
 cyclic genes during artificial selection and clonal propagation. Results
 Our results indicate that rhythmic alleles of cultivated potato were more
 highly expressed than non-rhythmic genes and were highly co-expressed not
 only under diel cycles but also across tissues, developmental stages, and
 stress conditions. Moreover, the smaller ratio of non-synonymous to
 synonymous differences within rhythmic versus non-rhythmic allelic groups
 indicates that cyclic genes, in general, have more conserved core
 functions than non-cyclic genes. In accordance with this observation,
 fully rhythmic allelic groups were highly enriched in photosynthesis and
 ribosome biogenesis genes, which have core functions in plants.
 Furthermore, we investigated differences in cyclic expression patterns
 between photoperiod identifying potential regulators of the strong
 photoperiodic change in phase of expression for ribosome biogenesis and
 pathogen response genes. Finally, analyses of genes involved in tuber
 formation suggests that the regulation of CO gene transcription is not the
 only factor enabling tuberization under long days in modern cultivated
 potato. Conclusions This study not only provides high quality diel
 transcriptomic datasets of cultivated potato but also provides important
 insight on the role of allelic diversity in rhythmic expression in plants.
   
description: # High resolution diel transcriptomes of autotetraploid potato reveal
 expression and sequence conservation among rhythmic genes #### Principle
 Investigator Contact Information ``` Name: Eva M. Farre Institution:
 Michigan State University Email: farre@msu.edu ``` ## Dataset Overview
 This repository contains the large datasets used in the manuscript titled
 'High resolution diel transcriptomes of autotetraploid potato reveal
 expression and sequence conservation among rhythmic genes' by Feke et
 al., accepted in the BMC Genomics. The code used to generate the plots on
 the publication can be found here:
 [https://github.com/efarre/Autotetraploid_potato_diel_transcriptome/tree/main](https://github.com/efarre/Autotetraploid_potato_diel_transcriptome/tree/main). This repository contains the allelic groups for *S. tuberosum* cv. Atlantic used in this study (Dataset S1). It contains the normalized expression of *S. tuberosum* cv. Atlantic leaf tissue under short and long days, and tuber tissue under short days (Dataset S2). As well as the normalized expression of the Atlantic Developmental Gene Expression Atlas(Datasets S3 and S4). It also includes the rhythmic expression analysis results under diel conditions for leaf and tuber tissue (Datasets S5, S6, S7). The repository also contains the pairwise allelic expression correlations of the diel expression datasets (Datasets S8 and S9) and the Atlantic Developmental Gene Expression Atlas (Datasets S10 and S11), as well as the results of the differential expression anlysis between photoperiods of leaf tissue (Dataset S12) and between leaf and tuber tissues (Dataset S13). Dataset S14 contains the MapMan functional annnotation results. ## Description of the data and file structure #### File: Dataset_S1_Allelic_groups.csv **Description:** Synthenic allelic groups in *Solanum tuberosum* cv. Atlantic v3 and S. tuberosum Group Phureja DM 1-3 516 R44 (DM) v6.1. ##### Variables * Syntelog: allelic groups * geneID: gene ID #### File: Dataset_S2_Diel_expression_rlog_long.csv **Description:** Gene expression in Atlantic leaves under short (12 h light/12 h dark) and long days (16 h light/8 h dark) and tubers under short days normalized using DEseq, rlog values are provided. Original data from BioProjects PRJNA957457 (short day) and PRJNA1093480 (long day). ##### Variables * geneID: based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * ZT: time after dawn * SD: short day, light period ZT0-ZT12 * LD: long day, light period ZT0-ZT16 * Expression: in rlog (generated using DEseq) #### File: Dataset_S3_Expression_of_Tissue_samples_from_the_Developmental_Gene_Expression_Atlas.csv **Description:** Gene expression was normalized using DEseq and rlog values are provided. Atlantic Developmental Gene Expression Atlas data were obtained from NCBI under BioProject PRJNA753086. Plant growth and tissue harvest methods are described in doi: [https://doi.org/10.1101/2025.06.26.661617](https://doi.org/10.1101/2025.06.26.661617). ##### Variables * geneID: based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Sample column labels: Samplename_replicate. Abbreviations: * R#: replicate number * TuberS#: tuber developmental stages S1-S4 were collected for this experiment. * YL: young leaf: * ImmFruit: immature fruit. #### File: Dataset_S4_Expression_of_Stress_samples_from_the_Developmental_Gene_Expression_Atlas.csv **Description:** Gene expression was normalized using DEseq and rlog values are provided. Atlantic Developmental Gene Expression Atlas data were obtained from NCBI under BioProject PRJNA753086. Plant growth and tissue harvest methods are described in doi: [https://doi.org/10.1101/2025.06.26.661617](https://doi.org/10.1101/2025.06.26.661617). ##### Variables * geneID: based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Sample column labels: SampleName_replicate. Abbreviations: * R#: replicate number * Meja: methyl jasmonate * BTH: benzothiodiazole #### File: Dataset_S5_Leaf_short_day_cycling_parameters_as_determined_per_JTK.csv **Description:** Rhythmic parameters determined using JTK implemented in MetaCycle using rlog normalized data from short day time course in leaf tissue. ##### Variables * CycID: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * BH.Q:Benjamini–Hochberg q-value * ADJ.P: Adjusted p=value * PER: period * LAG: phase * AMP: amplitude #### File: Dataset_S6_Leaf_long_day_cycling_parameters_as_determined_per_JTK.csv **Description:** Rhythmic parameters determined using JTK implemented in MetaCycle using rlog normalized data from long day time course in leaf tissue. ##### Variables * CycID: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * BH.Q: Benjamini–Hochberg q-value * ADJ.P: Adjusted p=value * PER: period * LAG: phase * AMP: amplitude #### File: Dataset_S7_Tuber_short_day_cycling_parameters_as_determined_per_JTK.csv **Description:** Rhythmic parameters determined using JTK implemented in MetaCycle using rlog normalized data from short day time course in tuber tissue. ##### Variables * CycID: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * BH.Q:Benjamini–Hochberg q-value * ADJ.P: Adjusted p=value * PER: period * LAG: phase * AMP: amplitude #### File: Dataset_S8_Pairwise_allelic_expression_correlations_in_short_days.csv **Description:** The Pearson correlation of the z-scored expression values (rlog) was calculated for each pair of alleles. Leaf short day expression data from Dataset S2 was used to generate these correlations. ##### Variables * Syntelog: allelic group * Haplotype_1: allele 1, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Haplotype_2: allele 2, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Correlation: Pearson correlation, no correlation value is provided for pairs in which one haplotype is not expressed. #### File: Dataset_S9_Pairwise_allelic_expression_correlations_in_long_days.csv **Description:** The Pearson correlation of the z-scored expression values (rlog) was calculated for each pair of alleles.Leaf long day expression data from Dataset S2 was used to generate these correlations. ##### Variables * Syntelog: allelic group * Haplotype_1: allele 1, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Haplotype_2: allele 2, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Correlation: Pearson correlation, no correlation value is provided for pairs in which one haplotype is not expressed. #### File: Dataset_S10_Pairwise_allelic_expression_correlations_in_Tissue_samples_from_the_Developmental_Gene_Expression_Atlas.csv **Description:** The Pearson correlation of the z-scored expression values (rlog) was calculated for each pair of alleles. The rlog expression values are from Dataset S3. Atlantic Developmental Gene Expression Atlas data were obtained from NCBI under BioProject PRJNA753086. Plant growth and tissue harvest methods are described in doi: [https://doi.org/10.1101/2025.06.26.661617](https://doi.org/10.1101/2025.06.26.661617). ##### Variables * Syntelog: allelic group * Haplotype_1: allele 1, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Haplotype_2: allele 2, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Correlation: Pearson correlation, no correlation value is provided for pairs in which one haplotype is not expressed. #### File: Dataset_S11_Pairwise_allelic_expression_correlations_in_Stress_samples_from_the_Developmental_Gene_Expression_Atlas.csv **Description:** The Pearson correlation of the z-scored expression values (rlog) was calculated for each pair of alleles.The rlog expression values are from Dataset S4. Atlantic Developmental Gene Expression Atlas data were obtained from NCBI under BioProject PRJNA753086. Plant growth and tissue harvest methods are described in doi: [https://doi.org/10.1101/2025.06.26.661617](https://doi.org/10.1101/2025.06.26.661617). ##### Variables * Syntelog: allelic group * Haplotype_1: allele 1, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Haplotype_2: allele 2, gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * Correlation: Pearson correlation, no correlation value is provided for pairs in which one haplotype is not expressed. #### File: Dataset_S12_Differential_expression_short_vs._long_day_determined_by_DEseq.csv **Description:** Differential gene expression between short and long days in leaves as determined by DEseq. For this analysis, the time component of RNAseq samples was disregarded. Note that genes with a lower than a threshold value of counts or outlier expression values have no output in DEseq (empty cells). ##### Variables * V1: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * baseMean: The average of the normalized count values, dividing by size factors, taken over all samples. * log2FoldChange: the effect size estimate. This value indicates how much the gene or transcript's expression seems to have changed between the comparison and control groups. This value is reported on a logarithmic scale to base 2 * lfcSE: The standard error estimate for the log2 fold change estimate * stat: The value of the test statistic for the gene or transcript. * pvalue: P-value of the test for the gene or transcript. * padj: Adjusted P-value for multiple testing for the gene or transcript. #### File: Dataset_S13_Differential_expression_leaf_vs._tuber_under_short_days_determined_by_DEseq.csv **Description:** Differential gene expression between leaf and tuber in short days as determined by DEseq. For this analysis, the time component of RNAseq samples was disregarded. Note that genes with a lower than a threshold value of counts or outlier expression values have no output in DEseq (empty cells). ##### Variables * V1: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * baseMean: The average of the normalized count values, dividing by size factors, taken over all samples. * log2FoldChange: he effect size estimate. This value indicates how much the gene or transcript's expression seems to have changed between the comparison and control groups. This value is reported on a logarithmic scale to base 2 * lfcSE: The standard error estimate for the log2 fold change estimate * stat: The value of the test statistic for the gene or transcript. * pvalue: P-value of the test for the gene or transcript. * padj: Adjusted P-value for multiple testing for the gene or transcript. #### File: Dataset_S14_Functional_annotation_of_Atlantic_using_MapMan.txt **Description:** Mercator4 v7.0 ([www.plabipd.de/mercator_main.html](http://www.plabipd.de/mercator_main.html)) and the S. tuberosum cv. Atlantic v3 high confidence representative gene models from SpudDB were used. ##### Variables * BINCODE: Code for functional group * NAME: Name of functional group * IDENTIFIER: gene ID based on Atlantic Genome Assembly (v3) ([https://spuddb.uga.edu](https://spuddb.uga.edu)) * DESCRIPTION: description of functional group * TYPE: The type of the item (T=Transcript, M=Metabolite, P=Protein, E= Enzyme)