Dataset Information

Cloning and characterization of auxin efflux carrier genes EcPIN1a and EcPIN1b from finger millet Eleusine coracana L.

ABSTRACT: Auxin signaling events in plants play important role in developmental regulation as well as gravitropic responses and plays crucial role in the development of root, lateral root and root hairs. The gene that is known to be most important in the development of root, lateral root and root hairs is commonly known as auxin efflux carrier (PIN). Being commonly known as orphan plant, the genome sequence of Eleusine coracana is not known yet, and hence it was very difficult to conduct advanced research in root development in this plant. As PIN gene plays crucial role in root development, to have some advanced study we proposed to clone the PIN genes from E. coracana. We cloned two PIN genes in E. coracana and named them as EcPIN1a and EcPIN1b. The coding sequence (CDS) of EcPIN1a was 1779 bp and EcPIN1b was 1788 bp long that encodes for 593 and 596 amino acids, respectively. In-silico analysis shows the presence of transmembrane domain in EcPIN1a and EcPIN1b protein. Multiple sequence alignment of EcPIN1a and EcPIN1b protein shows the presence of several conserved motifs. Phylogenetic analysis of EcPIN1a and EcPIN1b grouped with the PIN gene of monocot plant Oryza sativa. This shows that EcPIN genes were monocot specific, and closely match with the PIN genes of O. sativa. The transcript analysis of EcPIN1a gene in leaf tissue shows gradual up-regulation from 7th to 28th days of developmental time period while the transcript level was found to be lower in root tissue. The transcript abundance of EcPIN1b was not detected. Gradual up-regulation of EcPIN1a gene in developmental stages signifies its important role in root development in E. coracana.

SUBMITTER: Mohanta TK

PROVIDER: S-EPMC5428087 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Cloning and characterization of auxin efflux carrier genes EcPIN1a and EcPIN1b from finger millet Eleusine coracana L.

Mohanta Tapan Kumar TK Bae Hanhong H

3 Biotech 20170425 1

Auxin signaling events in plants play important role in developmental regulation as well as gravitropic responses and plays crucial role in the development of root, lateral root and root hairs. The gene that is known to be most important in the development of root, lateral root and root hairs is commonly known as auxin efflux carrier (PIN). Being commonly known as orphan plant, the genome sequence of Eleusine coracana is not known yet, and hence it was very difficult to conduct advanced research ...[more]

PMID: 28444595

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Project description:BackgroundThe nucleotide binding site leucine rich repeat (NBLRR) genes significantly regulate defences against phytopathogens in plants. The genome-wide identification and analysis of NBLRR genes have been performed in several species. However, the detailed evolution, structure, expression of NBLRRs and functional response to Magnaporthe grisea are unknown in finger millet (Eleusine coracana (L.) Gaertn.).ResultsThe genome-wide scanning of the finger millet genome resulted in 116 NBLRR (EcNBLRRs1-116) encompassing 64 CC-NB-LRR, 47 NB-LRR and 5 CCR-NB-LRR types. The evolutionary studies among the NBLRRs of five Gramineae species, viz., purple false brome (Brachypodium distachyon (L.) P.Beauv.), finger millet (E. coracana), rice (Oryza sativa L.), sorghum (Sorghum bicolor L. (Moench)) and foxtail millet (Setaria italica (L.) P.Beauv.) showed the evolution of NBLRRs in the ancestral lineage of the target species and subsequent divergence through gene-loss events. The purifying selection (Ka/Ks < 1) shaped the expansions of NBLRRs paralogs in finger millet and orthologs among the target Gramineae species. The promoter sequence analysis showed various stress- and phytohormone-responsive cis-acting elements besides growth and development, indicating their potential role in disease defence and regulatory mechanisms. The expression analysis of 22 EcNBLRRs in the genotypes showing contrasting responses to Magnaporthe grisea infection revealed four and five EcNBLRRs in early and late infection stages, respectively. The six of these nine candidate EcNBLRRs proteins, viz., EcNBLRR21, EcNBLRR26, EcNBLRR30, EcNBLRR45, EcNBLRR55 and EcNBLRR76 showed CC, NB and LRR domains, whereas the EcNBLRR23, EcNBLRR32 and EcNBLRR83 showed NB and LRR somains.ConclusionThe identification and expression analysis of EcNBLRRs showed the role of EcNBLRR genes in assigning blast resistance in finger millet. These results pave the foundation for in-depth and targeted functional analysis of EcNBLRRs through genome editing and transgenic approaches.

Project description:Drought is one of the most significant abiotic stresses that affects the growth and productivity of crops worldwide. Finger millet [Eleusine coracana (L.) Gaertn.] is a C4 crop with high nutritional value and drought tolerance. However, the drought stress tolerance genetic mechanism of finger millet is largely unknown. In this study, transcriptomic (RNA-seq) and proteomic (iTRAQ) technologies were combined to investigate the finger millet samples treated with drought at different stages to determine drought response mechanism. A total of 80,602 differentially expressed genes (DEGs) and 3,009 differentially expressed proteins (DEPs) were identified in the transcriptomic and proteomic levels, respectively. An integrated analysis, which combined transcriptome and proteome data, revealed the presence of 1,305 DEPs were matched with the corresponding DEGs (named associated DEGs-DEPs) when comparing the control to samples which were treated with 19 days of drought (N1-N2 comparison group), 1,093 DEGs-DEPs between control and samples which underwent rehydration treatment for 36 hours (N1-N3 comparison group) and 607 DEGs-DEPs between samples which were treated with drought for 19 days and samples which underwent rehydration treatment for 36 hours (N2-N3 comparison group). Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 80 DEGs-DEPs in the N1-N2 comparison group, 49 DEGs-DEPs in the N1-N3 comparison group, and 59 DEGs-DEPs in the N2-N3 comparison group, which were associated with drought stress. The DEGs-DEPs which were drought tolerance-related were enriched in hydrolase activity, glycosyl bond formation, oxidoreductase activity, carbohydrate binding and biosynthesis of unsaturated fatty acids. Co-expression network analysis revealed two candidate DEGs-DEPs which were found to be centrally involved in drought stress response. These results suggested that the coordination of the DEGs-DEPs was essential to the enhanced drought tolerance response in the finger millet.

Dataset Information

Cloning and characterization of auxin efflux carrier genes EcPIN1a and EcPIN1b from finger millet Eleusine coracana L.

Publications

Cloning and characterization of auxin efflux carrier genes EcPIN1a and EcPIN1b from finger millet Eleusine coracana L.

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