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Physical map of lncRNAs and lincRNAs linked with stress responsive miRs and genes network of pigeonpea (Cajanus cajan L.)

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Abstract

Pigeonpea (Cajanus cajan L.) is one of economically significant comestible legume crop possessing huge agricultural as well as therapeutic value. Though many reports have been published in identification of lncRNAs from recognized plant models viz., arabidopsis, maize and rice, less has been studied about lncRNAs of legume crops of Fabaceae family. Pigeonpea comprehensive transcriptome assembly data available at Legume Information System was used in this investigation. Chromosome physical maps were drawn by using locations of lncRNAs and lincRNAs in C. cajan (L.) chromosomes. The GO enrichment was extracted for all the neighbouring protein coding genes and more abundant terms were computed for each category of molecular function, biological process and cellular components by Blast2go. The targets and target mimics were predicted using psRNATarget pooled with native scripts in accordance with rules. Sixty-three novel lincRNAs were identified from pigeonpea transcriptome assembly. Stringent in-silico analyses were done to identify novel lincRNAs. Gene ontology and enrichment analysis of identified transcripts were carried out to functionally characterize lincRNAs. The result showed that 43 lincRNAs could perfectly be mapped on pigeonpea genome. We report 50 lncRNA targeting cca-miRs and 36 cca-miRs processed from lncRNAs as pre-miRs. LncRNAs act as eTM for functional mRNAs. Target networks and similar lincRNAs and targets clusters of related species are also elucidated. The results presented here will facilitate future studies to unravel the function of lincRNAs in pigeonpea proposing that the genome-wide computational analysis is a reliable method for identifying new lincRNAs and accelerating the development of biotic and abiotic stress tolerant pigeonpea varieties.

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Abbreviations

APOLO:

Long intergenic noncoding RNA transcribed by RNA polymerases II and V in response to auxin in arabidopsis

ASCO:

Alternative splicing competitor

At4:

Acyl transferase and synonym of Induced by phosphate starvation 1

COOLAIR:

Intronic lncRNA can induce the epigenetic repression of FLC 

DCL5:

Dicer-like 5

Enod40:

EARLYNODULIN40

eRNA:

Enhancer-associated RNA

GO:

Gene ontology

IPS1:

Induced by phosphate starvation 1

iRNA:

Intervening RNA

lincRNA:

Long intergenic non-coding RNAs

lncRNA:

Long non-coding RNAs

MAC3:

Pre-mRNA-processing factor 19 homolog 1

miRNAs:

MicroRNAs

Mt4:

Metallothionein 4

ncRNAs:

Non-coding RNAs

npcRNAs:

Non protein-coding RNAs

PHO2:

Phosphate2

PHO2:

Pi over accumulator

pRNA:

Promoter-associated RNA

PWP2:

Periodic tryptophan protein 2

RhoGAP:

Rho GTPase activation protein

snoRNAs:

Small nucleolar RNAs

TPS:

Trehalose-6-phosphate synthase

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Acknowledgements

We sincerely thank the Director, ICAR-NBPGR, New Delhi, India for providing all the necessary facilities to carry out this work. The authors acknowledge Indian Council of Agricultural Research, New Delhi and Indo- Swiss collaboration in Biotechnology for funding this research.

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Author notes

  1. JeshimaKhan Yasin and BharatKumar Mishra have contributed equally to this work.

Authors and Affiliations

  1. Division of Genomic Resources, ICAR-NBPGR, New Delhi, 110012, India

    Jeshima Khan Yasin & Bharat Kumar Mishra

  2. University of Alabama, Tuscaloosa, USA

    Bharat Kumar Mishra

  3. Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu, India

    M. Arumugam Pillai

  4. Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, PUSA Campus, New Delhi, 110012, India

    Viswanathan Chinnusamy

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  1. Jeshima Khan Yasin
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YJK and VC planned and organized the research; YJK and BKM conducted research; YJK and MAP wrote the manuscript; VC edited the manuscript; all authors read and accepted the final version of the manuscript.

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Supplementary Information

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13562_2021_674_MOESM1_ESM.xlsx

Supplementary material 1. List of identified putative lncRNAs containing source sequences selected after filtering for lincRNA identification. Supplementary material 2. (2a, 2b, 2c) Confirmed lincRNA positions next to functional genes in genome browser. Supplementary material 3. Map positions of identified lincRNAs in Glycine. Supplementary material 4. GO enrichment analysis of genes linked to lincRNAs were mined. Supplementary material 5. GO terms among biological processes. Supplementary material 6. Identified miRs and target sequences. Supplementary material 7. Putative cca-miRs targets from C.cajan. Supplementary material 8. Putative cca-miRs targets from G. max. (XLSX 63 kb)

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Yasin, J.K., Mishra, B.K., Arumugam Pillai, M. et al. Physical map of lncRNAs and lincRNAs linked with stress responsive miRs and genes network of pigeonpea (Cajanus cajan L.). J. Plant Biochem. Biotechnol. 31, 271–292 (2022). https://doi.org/10.1007/s13562-021-00674-0

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