De-novo transcriptome assembly for discovery of putative microsatellite markers and transcription factors in black pepper (Piper nigrum)

ANKITA NEGI; RAHUL SINGH JASROTIA; SARIKA JAISWAL; U B ANGADI; M A IQUEBAL; JOHNSON GEORGE K; ANIL RAI; DINESH KUMAR

doi:10.56093/ijas.v89i7.91657

Authors

ANKITA NEGI Research Scholar, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
RAHUL SINGH JASROTIA Research Scholar, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
SARIKA JAISWAL Senior Scientist,ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
U B ANGADI Principal Scientist, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
M A IQUEBAL Senior Scientist, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
JOHNSON GEORGE K Principal Scientist, ICAR-IISR, Kerala.
ANIL RAI Principal Scientist, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India
DINESH KUMAR Principal Scientist, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110 012, India

https://doi.org/10.56093/ijas.v89i7.91657

Keywords:

Black pepper, de novo assembly, Markers, RNA-sequence, Transcription factors Black pepper (Piper nigrum L.) (2n = 52), a trailing woody flowering vine belongs to Piperaceae family. Genus piper has more than 1000 species (Jaramillo and Manos 2001). It is c

Abstract

Black pepper (Piper nigrum L.) (2n= 52; Piperaceae), is a perennial, trailing woody flowering vine having global importance with widespread dietary, medicinal, and preservative uses. It is one of the highly traded high cost spice germplasms cultivated for its fruit. Unlike model species, the whole genome sequence information and genomic resources of black pepper are still unavailable in public domain. Crop production is highly affected by abiotic and biotic stresses. Hence transcriptome profiling has permitted a significant enhancement in discovery and expression profiling of genes and functional genomic studies in black pepper. Stress responsive transcriptomic data of various black pepper genotypes were obtained from public domain (SRA database, NCBI) for the de novo transcriptome assembly, identification of transcription factors and mining of putative simple sequence repeat markers. De novo transcriptome assembly was done with SOAP denovo-trans assembler, which generated 53690 transcripts. A total of 14005 transcription factors with BLAST and 39685 without BLAST hits were identified. A total of 4770 putative SSR markers were identified using de novo transcriptome assembly. Myeloblastosis (MYB) related proteins, Basic helix-loop-helix (BHLH), NAC, WRKY and ERF transcriptional factors found in this study are reported to be associated with plant tolerance against stress condition. These SSR markers can be valuable and facilitate advancements in genetic and molecular studies in the endeavour of better productivity of P. nigrum germplasm, especially in the era of rising abiotic stress.

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References

Ahmad N, Fazal H, Abbasi B H, Rashid M, Mahmood T and Fatima N. 2010. Efficient regeneration and antioxidant potential in regenerated tissues of Piper nigrum L. Plant Cell, Tissue and Organ Culture (PCTOC) 102(1): 129–34. DOI: https://doi.org/10.1007/s11240-010-9712-x

Altschul S F, Gish W, Miller W, Myers E W and Lipman D J. 1990. Basic local alignment search tool. Journal of Molecular Biology 215(3): 403–10. DOI: https://doi.org/10.1016/S0022-2836(05)80360-2

Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data.

Bolger A M, Lohse M and Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15): 2114–20. DOI: https://doi.org/10.1093/bioinformatics/btu170

Conesa A, Gotz S, Garcia-Gomez J M, Terol J, Talon M and Robles M. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18): 3674–6. DOI: https://doi.org/10.1093/bioinformatics/bti610

FAOSTAT: Production, Crops, Millet, data. Food and Agriculture Organization. 2017.

Gulcin I. 2005. The antioxidant and radical scavenging activities of black pepper (Piper nigrum) seeds. International Journal of Food Sciences and Nutrition 56(7): 491–9. DOI: https://doi.org/10.1080/09637480500450248

Huang X and Madan A. 1999. CAP3: A DNA sequence assembly program. Genome Research 9(9): 868–77. DOI: https://doi.org/10.1101/gr.9.9.868

Huang X, Yan H D, Zhang X Q, Zhang J, Frazier T P, Huang D J, Lu L,Huang L, Liu W, Pneg Y, Ma X D and Yan Y. 2016. De novo transcriptome analysis and molecular marker development of two hemarthria species. Front Plant Science 7: 496. DOI: https://doi.org/10.3389/fpls.2016.00496

Jaramillo M A and Manos P S. 2001. Phylogeny and patterns of floral diversity in the genus Piper (Piperaceae). American Journal of Botany, 88(4): 706–16. DOI: https://doi.org/10.2307/2657072

Jin J, Tian F, Yang D C, Meng Y Q, Kong L, Luo J and Gao G. 2016. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research 45(D1): 1040–45 DOI: https://doi.org/10.1093/nar/gkw982

Krishnamoorthy B and Parthasarathy V A. 2011. Improvement of black pepper. Plant Sciences Reviews 2010, 37. DOI: https://doi.org/10.1079/PAVSNNR20105003

Kujur A, Bajaj D, Saxena M S, Tripathi S, Upadhyaya H D, Gowda C L L, Singh S, Jain M, Tyagi A K and Parida S K. 2013.

Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Research 20(4): 355–74. DOI: https://doi.org/10.1093/dnares/dst015

Lan Thi Hoang X, Du Nhi N H, Binh Anh Thu N, Phuong Thao N and Phan Tran L S. 2017. Transcription factors and their roles in signal transduction in plants under abiotic stresses. Current genomics 18(6): 483–497. DOI: https://doi.org/10.2174/1389202918666170227150057

Liu Q, Wang Z, Xu X, Zhang H and Li C. 2015. Genome-wide analysis of C2H2 Zinc-finger family transcription factors and their responses to abiotic stresses in poplar (Populus trichocarpa). PloS One 10(8): e0134753. DOI: https://doi.org/10.1371/journal.pone.0134753

Pandey S P and Somssich I E. 2009. The role of WRKY transcription factors in plant immunity. Plant Physiology 150(4): 1648–55. DOI: https://doi.org/10.1104/pp.109.138990

Quijano-Abril M A, Callejas-Posada R and Miranda-Esquivel D R. 2006. Areas of endemism and distribution patterns for neotropical Piper species (Piperaceae). Journal of Biogeography 33(7): 1266–78. DOI: https://doi.org/10.1111/j.1365-2699.2006.01501.x

Shin D, Moon S J, Han S, Kim B G, Park S R, Lee S K and Yi B Y. 2011. Expression of StMYB1R-1, a novel potato single MYB-like domain transcription factor, increases drought tolerance. Plant Physiology 155(1): 421–32. DOI: https://doi.org/10.1104/pp.110.163634

Taxak P C, Khanna S M, Bharadwaj C, Gaikwad K, Kaur S, Chopra M, Tandon G, Jaiswal S, Iquebal M A, Rai A, Kumar D, Srinivasan and Jain P K. 2017. Transcriptomic signature of fusarium toxin in chickpea unveiling wilt pathogenicity pathways and marker discovery. Physiological and Molecular Plant Pathology 100: 163–77. DOI: https://doi.org/10.1016/j.pmpp.2017.09.006

Thiel T, Michalek W, Varshney R and Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 106(3): 411–22. DOI: https://doi.org/10.1007/s00122-002-1031-0

Tian B, Lin Z B, Ding Y and Ma Q H. 2006. Cloning and characterization of a cDNA encoding Ran binding protein from wheat: Full Length Research Paper. DNA Sequence 17(2): 136–42. DOI: https://doi.org/10.1080/10425170600609306

Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth B C, Remm M and Rozen S G. 2012. Primer3—new capabilities and interfaces. Nucleic Acids Research 40(15): 115. DOI: https://doi.org/10.1093/nar/gks596

Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S and Zhou X. 2014. SOAP denovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 30(12): 1660–6. DOI: https://doi.org/10.1093/bioinformatics/btu077