Data of RNA sequencing of pearl millet panicles treated with a high temperature

Pearl millet (Pennisetum glaucum) is a cereal crop that can grow and set seeds even under drought, high temperatures and nutrient-poor conditions. Panicles of two pearl millet cultivars that differ in seed-setting rates were exposed to two different high-temperature treatments at three different developmental stages with three replicates, and RNA was prepared from these panicles. The resulting RNA samples were subjected to sequencing with the Illumina NovaSeq 6000 sequencer. The obtained data were 150-base-paired-end reads and were approximately 5 Gb/sample in total. These read data were deposited as those for a project in the NCBI (National Center for Biotechnology Information) BioProject database.


Value of The Data
• These data can be used to obtain expression levels of genes in pearl millet panicles exposed to a high temperature • These data can also help narrow down genes that determine differences in seed-setting rates under high temperatures between pearl millet cultivars • Pearl millet researchers and breeders will benefit from these data • Researchers and breeders for other crops can also benefit from these data.

Background
Pearl millet ( Pennisetum glaucum ) is in general tolerant to a high temperature as well as to drought and nutrient-poor conditions.Nevertheless, seed-setting rates of pearl millet can be decreased by 40 °C or a higher temperature, and its extent differs between cultivars.For example, the cultivar ICMB00333 can maintain the seed-setting rate under a high temperature, whereas ICMB00555 cannot.Such a high temperature can be reached during the seed-setting stage in regions where pearl millet is cultivated.It is therefore relevant to pearl millet production to identify or develop cultivars that can maintain its seed-setting rate under a high temperature and to understand mechanisms underlying such high temperature tolerance [1] .In pearl millet, only pistils are visible at the booting and panicle emergence stages, and the anther emergence stage follows them.The high temperature-dependent decrease of seed-setting rates of pearl millet is more severe when a high temperature is imposed at the booting or panicle emergence stage than when it is imposed at a later stage.This suggests that the pistils at early developmental stages are more sensitive to a high temperature than those at later stages and pollen grains [2] .The numbers of the DEGs detected."booting", "heading" and "anther-emerging" correspond to the booting, panicle emergence and anther emergence stages, respectively, when the panicles were treated with 42 °C.For "air", a growth chamber was used to impose 42 °C, and for "water", a water bath was used.The DEGs were obtained on the basis of TPM as the normalized expression level for each gene as described in "EXPERIMENTAL DESIGN, MATERIALS AND METHODS".The exact numbers of the DEGs are presented in the figure.

Data Description
Seed-setting rates of ICMB00333 and ICMB00555 plants were assessed after they were grown and exposed to 42 °C under a controlled condition in the laboratory.The resulting data were deposited in the figshare repository ( https://doi.org/10.6084/m9.figshare.24532792).Panicles of these cultivars were exposed to 42 °C water or air at the booting, panicle emergence or anther emergence stage, and subjected to RNA sequencing (RNA-Seq).The resulting reads were deposited in the NCBI Sequence Read Archive (SRA) database ( https://www.ncbi.nlm.nih.gov/sra ) and are available with the NCBI BioProject accession number PRJNA926343.These are summarized in Table 1 .The reads were mapped to the pearl millet reference genome [3] .Resulting read counts and transcripts per million (TPM) for each gene (or transcript) and a list of differentially expressed genes (DEGs) (i.e., genes either upregulated or downregulated by the 42 °C treatment) as well as the seed-setting rates of ICMB00333 and ICMB00555 were deposited in figshare ( https://doi.org/10.6084/m9.figshare.24532792, Table 2 ).The numbers of DEGs are presented in Fig. 1 .

Plant materials and high temperature treatments
Seeds of ICMB00333 and ICMB00555 were sown on a mixture of equal volumes of soil and vermiculite in perforated pots.Plants were grown in a growth chamber under the 12-hour 28 °C day/12-hour 20 °C night condition until they reached the booting, panicle emergence or anther emergence stage.For the 42 °C treatment in a growth chamber, the plants in a control group

RNA extraction, sequencing and data analyses
The florets sampled were ground in liquid nitrogen with a mortar and pestle to fine powders.Total RNA was extracted from them with the NucleoSpin RNA Plant kit (Macherey-Nagel, Düren, Germany).The resulting RNA samples were sent to Novogen Co. (Beijing, China) for mRNA sequencing by Illumina NovaSeq 60 0 0 to obtain 150-base-paired-end reads for approximately 5Gb/sample.The resulting clean reads were mapped to the pearl millet reference genome [3] by Bowtie 2 with the -very-sensitive" option [4] .Read counts for each gene were then obtained by featureCounts [5] .TPM were obtained from these read counts by a custom Perl script.Genes with TPM more than two times greater or smaller under the 42 °C condition than under the 28 °C condition were extracted as DEGs.Scripts used for these analyses can be provided upon request.

Limitations
None.

Figure 1 .
Figure 1.The numbers of the DEGs detected."booting", "heading" and "anther-emerging" correspond to the booting, panicle emergence and anther emergence stages, respectively, when the panicles were treated with 42 °C.For "air", a growth chamber was used to impose 42 °C, and for "water", a water bath was used.The DEGs were obtained on the basis of TPM as the normalized expression level for each gene as described in "EXPERIMENTAL DESIGN, MATERIALS AND METHODS".The exact numbers of the DEGs are presented in the figure.
°C day/20 °C night condition until they reached the booting, panicle head-emerging or anther-emerging stage.Their panicles were then exposed to 42 °C in either the growth chamber or water.RNA samples were prepared from florets in these panicles and subjected to RNA sequencing (RNA-Seq) with the Illumina NovaSeq 60 0 0 sequencer.

Table 1
Samples and the SRA accession numbers associated with PRJNA926343.

Table 2
Data deposited in figshare.for 48 hours under the same condition, and the other plants were grown for 48 hours under 12-hour 42 °C day/12-hour 30 °C night condition.For the 42 °C treatment in a water bath, panicles of the plants at one of the above developmental stages were incubated in either 28 °C or 42 °C water in a water bath for 30 seconds.Florets in the middle part of the panicles of these plants were sampled immediately after the above treatments were finished, and stored at -80 °C until they were used for RNA extraction.