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Non-coding RNAs having strong positive interaction with mRNAs reveal their regulatory nature during flowering in a wild relative of pigeonpea (Cajanus scarabaeoides)

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Abstract

In higher plants, flower development is a result of crosstalk between many factors like photoperiod, vernalization, hormone concentration, epigenetic modification etc. and is also regulated by non-coding RNAs (ncRNAs). In the present study, we are reporting the involvement of long non-coding RNAs (lncRNAs) and miRNAs during the process of flower development in Cajanus scarabaeoides, an important wild relative of pigeonpea. The transcriptome of floral and leaf tissues revealed a total of 1672 lncRNAs and 57 miRNAs being expressed during flower development. Prediction analysis of identified lncRNAs showed that 1593 lncRNAs were targeting 3420 mRNAs and among these, 98 were transcription factors (TFs) belonging to 48 groups. All the identified 57 miRNAs were novel, suggesting their genera specificity. Prediction of the secondary structure of lncRNAs and miRNAs followed by interaction analysis revealed that 199 lncRNAs could interact with 47 miRNAs where miRNAs were acting in the root of interaction. Gene Ontology of the ncRNAs and their targets showed the potential role of lncRNAs and miRNAs in the flower development of C. scarabaeoides. Among the identified interactions, 17 lncRNAs were endogenous target mimics (eTMs) for miRNAs that target flowering-related transcription factors. Expression analysis of identified transcripts revealed that higher expression of Csa-lncRNA_1231 in the bud sequesters Csa-miRNA-156b by indirectly mimicking the miRNA and leading to increased expression of flower-specific SQUAMOSA promoter-binding protein-like (SPL-12) TF indicating their potential role in flower development. The present study will help in understanding the molecular regulatory mechanism governing the induction of flowering in C. scarabaeoides.

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Abbreviations

AGO:

Argonaute

ARF:

Auxin responsive factor

BLAST:

Basic local alignment search tool

bp:

Base pairs

cDNA:

Complementary DNA

CMS system:

Cytoplasmic male-sterile system

COG:

Clusters of orthologous groups

eTMs:

Endogenous target mimics

GO:

Gene ontology

kb:

Kilo base

KEGG:

Kyoto encyclopedia of genes and genomes

lincRNAs:

Long intergenic non-coding RNAs

lncRNAs:

Long non-coding RNAs

min:

Minutes

miRNAs:

MicroRNAs

mRNAs:

Messenger RNAs

NATs:

Natural antisense transcripts

ncRNAs:

Non-coding RNAs

Nr database:

Non-redundant protein database

nt:

Nucleotides

ORF’s:

Open reading frames

PCR:

Polymerase chain reaction

pi-RNAs:

Piwi-interacting RNAs

pri-miRNAs:

Primary miRNAs

qRT-PCR:

Quantitative real time PCR

RISC:

RNA-induced silencing complex

r-RNAs:

Ribosomal RNAs

sec:

Seconds

siRNAs:

Small interfering RNAs

snoRNAs:

Small nucleolar RNAs

snRNAs:

Small Nuclear RNAs

SPL:

SQUAMOSA promoter-binding protein like

tasi-RNAs:

Trans-acting small interfering RNAs

TF’s:

Transcription factors

t-RNAs:

Transfer RNAs

UTRs:

Untranslated regions

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Acknowledgements

The authors acknowledge the support received from the Director, ICAR-National Institute for Plant Biotechnology, NewDelhi.

Funding

We acknowledge the financial support received from ICAR-National Institute for Plant Biotechnology, New Delhi, India.

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Authors and Affiliations

  1. ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India

    Antara Das, Swati Saxena, Kuldeep Kumar, Kishor U. Tribhuvan, N. K. Singh & Kishor Gaikwad

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  1. Antara Das
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  2. Swati Saxena
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  3. Kuldeep Kumar
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  4. Kishor U. Tribhuvan
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  5. N. K. Singh
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Contributions

Experiments were designed by KG and NKS; AD and SS conducted experiments; and all authors analyzed, wrote and edited the manuscript. All authors read and approve the final manuscript.

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Correspondence to Kishor Gaikwad.

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Das, A., Saxena, S., Kumar, K. et al. Non-coding RNAs having strong positive interaction with mRNAs reveal their regulatory nature during flowering in a wild relative of pigeonpea (Cajanus scarabaeoides). Mol Biol Rep 47, 3305–3317 (2020). https://doi.org/10.1007/s11033-020-05400-y

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