Comprehensive Analysis of NAC Transcription Factor Family Uncovers Drought and Salinity Stress Response in Pearl Millet (\u3cem\u3ePennisetum glaucum\u3c/em\u3e)

BACKGROUND: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress response. Currently, no reports are available on the functions of the NAC family in pearl millet. RESULTS: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Thirty-eight and 76 PgNACs were found to be segmental and dispersed duplicated respectively. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (− 073, − 29, and − 151) were found to be membrane-associated transcription factors. Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs were examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet. CONCLUSION: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet

A comparative analysis of single-cell transcriptomic technologies in plants and animals

The development of sequencing methods has resulted in the investigation of many unexplored research areas. Among the different sequencing methods, single-cell transcriptomics is versatile and has completely changed the researchers' perception of biological processes from tissue to single-cell. Single-cell transcriptomic is applied in various fields to reveal cell-cell interaction, phytopathogenic interactions, cell-specific genetic expression, regulatory pathways, and the effects of drugs on cells. Single-cell transcriptomics was initially applied to the model organisms, such as mice and Arabidopsis thaliana, and then later expanded to other non-model species. Recently, single-cell transcriptomics is revolutionizing plant and animal research. The direct application of single-cell transcriptomics has become simple with advanced sequencing methods and data analysis tools available. This review summarizes the latest knowledge on single-cell transcriptomics in plant and animal research. We emphasize various sequencing methods, bioinformatics software development, comparison between plant and animal single-cell transcriptomics studies, and the limitations and future prospectus

Pearl millet transcription factor family characterization data

Presented are datasets derived from analyzing sequences of putative transcription factors and some other proteins in pearl millet (Pennisetum glaucum). These datasets shows families which those protiens belong to, a phylogenetic tree and conserved motifs for each of these family, and their predicted subcellular localization.  </p

Basic statistics for sequenced reads from transcriptome of pearl millet.

<p>Basic statistics for sequenced reads from transcriptome of pearl millet.</p

DEGs involved in phytohormone and MAPK signaling pathway.

<p>The proposed pathways show phytohormone biosynthesis (light orange) and MAPK signaling pathways (light blue). This figure shows only the genes that have been associated with the pathway from transcriptome analysis. Red boxes show plant hormones, blue boxes show the genes up-regulated stress, green arrow shows genes involved in drought tolerance through ubiquitin mediated proteolysis and red arrows shows the direct involvement in the drought tolerance. Light blue lines with a bar denotes inhibition and simple arrows denotes activation. -p indicates de phosphorylation process. Aux/IAA: auxin-responsive protein IAA; GH3: Auxin-responsive GH3 family protein; SAUR: SAUR-like auxin-responsive protein family; CRE: Histidine kinase 2/3/4 (cytokinin receptor); B-ARR: Two-component response regulator ARR-B family; GID1: Alpha/beta-Hydrolases superfamily protein; TF: Phytochrome interacting factor 3 (PIF3); PP2C: Protein phosphatase 2C; SnRK2: Serine/threonine-protein kinase SRK2; ABF: ABA responsive element binding factor; ETR: Ethylene receptor; EIN3: ETHYLENE-INSENSITIVE3-like 3; JAZ: Jasmonate ZIM domain-containing protein; RTE1: Transmembrane protein 222; MKK9: Mitogen-activated protein kinase kinase 9; ChiB: Basic endochitinase B; MAP3K17/18: Mitogen-activated protein kinase kinase kinase 17/18; MAPK1: Mitogen-activated protein kinase 1; MAPK6: Mitogen-activated protein kinase 6; CAT7: Catalase.</p

Annotations of the genes selected for RT-PCR.

<p>Annotations of the genes selected for RT-PCR.</p

DEGs involved in photosynthesis.

<p>Genes up-regulated by drought stress are shown (25 genes in ICMB 843 and 4 in ICMB 863) in green boxes. White boxes indicate the non-drought-responsive genes. This image was generated using the online tool KEGG Mapper–Colour Pathway (<a href="http://www.genome.jp/kegg/tool/map_pathway3.html" target="_blank">http://www.genome.jp/kegg/tool/map_pathway3.html</a>).</p

DEG analysis in comparisons study.

<p>A) Number of DEGs in all combinations with fold change >2 or <-2 and FDR-corrected <i>p</i>value <0.05) Blue and red bars indicate up- and down- regulated respectively. C: control and T and Treated: Drought- treated B) Venn diagram showing an up-regulated (right side) and down regulated (left side) genes in lines ICMB 843 and ICMB 863 under drought treated situation.</p

Heat map showing the number of DEGs enriched in different KEGG pathways.

<p>The bar scale shows the number of DEGs associated with pathways.</p