Skip to main content
SpringerLink
Log in

In silico annotation of 458 genes identified from comparative analysis of Full length cDNAs and NextGen Sequence of chromosome 2A of hexaploid wheat

  • Original Article
  • Published:
Journal of Plant Biochemistry and Biotechnology Aims and scope Submit manuscript

Abstract

Bread wheat (2n = 6x = 42) is one among the most important staple food crops in the world and plays a crucial role in food security. Owing to its large size of 17 Gb and > 80% repetitive DNA content, the approach used to obtain gold standard rice reference sequence could not be used in wheat. However, flow sorted chromosome arms from specialized cytogenetic stocks were used for shotgun sequencing by International Wheat Genome Sequencing Consortium to obtain a draft sequence. The arm specific genome sequence approach reduced the complexity in several ways. Utilizing a de novo hybrid assembly, generated from shotgun sequence data of chromosome 2AS and 2AL, the present study identified, characterized and annotated genes corresponding to full length cDNAs (FLcDNA) specific to 2A. In the present study, 458 genes corresponding to FLcDNAs were predicted on chromosome 2A. The coding sequences of these genes were characterized using BLASTX search against the NCBI non-redundant database at E-value of 1e-15. Among the 429 genes, putative 413 homologues were identified and their functions were assigned, based on signatures obtained from 13 different databases. GO enrichment annotated these genes to represent diverse molecular functions, cellular localization and biological processes. Forty-five genes could be identified with EC number and assigned to 25 metabolic pathways, of which starch and sucrose metabolism was the most predominant pathway. In silico analysis revealed the presence of gene families on 2A ranging from disease resistance/stress response to signaling and transportation. The results represented annotation for 458 genes of chromosome 2A at nucleotide-, protein-, and process-level. Annotation of genes corresponding to FLcDNAs provides a valuable evidence based resource for characterizing specific pathways, processes and functions for chromosome 2A of wheat.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

Abbreviations

NGS:

NextGen sequencing

FLcDNAs:

Full length cDNAs

EST:

Expressed sequence tags

IWGSC:

International Wheat Genome Sequencing Consortium

References

  • Abe H, Urao T, Ito T et al (2003) Transcriptional activators in abscisic acid signaling. Plant Cell 15:63–78

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Beardmore J, Ride JP, Granger JW (1983) Cellular lignification as a factor in the hypersensitive resistance of wheat to stem rust. Physiol Plant Pathol 22:209–220

    Article  CAS  Google Scholar 

  • Bird PM, Ride JP (1981) The resistance of wheat to Septoria nodorum: fungal development in relation to host lignification. Physiol Plant Pathol 19:289–299

    Article  Google Scholar 

  • Boyd LA, Smith PH, Green RM, Brown JKM (1994) The relationship between the expression of defense-related genes and mildew development in barley. Mol Plant Microbe Interact 7:401–410

    Article  CAS  Google Scholar 

  • Bull J, Mauch F, Hertig C et al (1992) Sequence and expression of a wheat gene that encodes a novel protein associated with pathogen defense. Mol Plant Microbe Interact 5:516–519

    Article  PubMed  CAS  Google Scholar 

  • Carver TLW, Zeyen RJ, Robbins MP, Dearne GA (1992) Effects of the PAL inhibitor, AOPP, on oat, barley and wheat cell responses to appropriate and inappropriate formae specials of Erysiphe graminis DC. Physiol Mol Plant Pathol 41:397–409

    Article  CAS  Google Scholar 

  • Dixon RA, Paiva NL (1995) Stress-lnduced phenylpropanoid metabolism. Plant Cell 7:1085–1097

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ferrer J, Austin MB Jr, Stewart C Jr, Noel JP (2008) Structure and function of enzymes involved in the biosynthesis of phenylpropanoids. Plant Physiol Biochem 46:356–370

    Article  PubMed  CAS  Google Scholar 

  • Flavell RB (1986) Repetitive DNA and chromosome evolution in plants. Philos Trans R Soc Lond B 312:227

    Article  CAS  Google Scholar 

  • Hahlbrock K, Scheel D (1989) Physiology and molecular biology of phenylpropanoid metabolism. Annu Rev Plant Physiol Plant Mol Biol 40:347–369

    Article  CAS  Google Scholar 

  • He Y, Li W, Lv J et al (2012) Ectopic expression of a wheat MYB transcription factor gene, TaMYB73, improves salinity stress tolerance in Arabidopsis thaliana. J Exp Bot 63:1511–1522

    Article  PubMed  CAS  Google Scholar 

  • Hernandez P, Martis M, Dorado G et al (2012) Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69:377–386

    Article  PubMed  CAS  Google Scholar 

  • Jia J, Zhao S, Kong X et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95

    Article  PubMed  CAS  Google Scholar 

  • Ling H-Q, Zhao S, Liu D et al (2013) Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87–90

    Article  PubMed  CAS  Google Scholar 

  • Liu Q, Kasuga M, Sakuma Y et al (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low- temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10:1391–1406

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Moerschbacher BM, Noll U, Gorrichon L, Reisener HJ (1990) Specific inhibition of lignification breaks hypersensitive resistance of wheat to stem rust. Plant Physiol 93:465–470

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Qi LL, Echalier B, Chao S et al (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 712:701–712

    Article  CAS  Google Scholar 

  • Riechmann JL, Ratcliffe OJ (2000) A genomic perspective on plant transcription factors. Curr Opin Plant Biol 3:423–434

    Article  PubMed  CAS  Google Scholar 

  • Stein L (2001) Genome annotation: from sequence to biology. Nat Rev Genet 2:493–503

    Article  PubMed  CAS  Google Scholar 

  • The International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. https://doi.org/10.1126/science.1251788

    Article  Google Scholar 

  • Van Ooijen G, Mayr G, Kasiem MMA et al (2008) Structure—function analysis of the NB-ARC domain of plant disease resistance proteins. J Exp Bot 59:1383–1397

    Article  PubMed  CAS  Google Scholar 

  • Vogt T (2010) Phenylpropanoid biosynthesis. Mol Plant 3:2–20

    Article  PubMed  CAS  Google Scholar 

  • Wicker T, Mayer KFX, Gundlach H et al (2011) Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley and their relatives. Plant Cell 23:1706–1718

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yadav D, Singh NK (2011) Wheat triticin: a potential target for nutritional quality improvement. Asian J Biotechnol 3:1–21

    Article  CAS  Google Scholar 

Download references

Acknowledgements

Contribution of all members of International Wheat Genome Sequencing Consortium (IWGSC) is highly acknowledged. Funding to the corresponding author provided by DBTNew Delhi, India vide file No.F. No.BT/IWGSC/03/TF/2008 is gratefully acknowledged.

Author information

Author notes

  1. Kuldeep Singh

    Present address: ICAR-National Bureau of Plant Genetic Resources, Dev Prakash Shastri Marg, Pusa Campus, New Delhi, India

Authors and Affiliations

  1. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India

    Parampreet Kaur, Inderjit Singh Yadav, Bharat Yadav, O. P. Gupta & Kuldeep Singh

  2. National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India

    Ajay Mahato & Nagendra Kumar Singh

  3. Institute of Experimental Botany, Prague 6, Czech Republic

    J. Dolezel

  4. University of Delhi, South Campus, New Delhi, India

    J. P. Khurana

Authors
  1. Parampreet Kaur
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Inderjit Singh Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bharat Yadav
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ajay Mahato
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. O. P. Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. J. Dolezel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nagendra Kumar Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. J. P. Khurana
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kuldeep Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kuldeep Singh.

Ethics declarations

Conflict of interest

The authors declare no competing interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kaur, P., Yadav, I.S., Yadav, B. et al. In silico annotation of 458 genes identified from comparative analysis of Full length cDNAs and NextGen Sequence of chromosome 2A of hexaploid wheat. J. Plant Biochem. Biotechnol. 28, 25–34 (2019). https://doi.org/10.1007/s13562-018-0460-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13562-018-0460-z

Keywords

Search

Navigation