Skip to main content
SpringerLink
Log in

De novo Transcriptome Analysis of Apical Meristem of Jatropha spp. Using 454 Pyrosequencing Platform, and Identification of SNP and EST-SSR Markers

  • Original Paper
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

A high-throughput sequencing by 454 pyrosequencing was performed on the transcriptomes of apical meristem tissue of two Jatropha curcas accessions and four jatropha-related species. J. curcas accession (acc.) CN produced 45.61 Mb data from 127,094 reads with 11,579 contigs and 15,645 singletons, while acc. M10 produced 54.52 Mb data from 142,447 reads with 10,964 contigs and 12,069 singletons. J. integerrima acc. KL gave 20.91 Mb from 71,541 reads with 4,551 contigs and 5,144 singletons, while acc. KY gave 48.74 Mb from 149,392 reads with 8,440 contigs and 8,299 singletons. J. multifida (acc. JM) gave 66.72 Mb from 191,654 reads with 17,444 contigs and 13,965 singletons, and J. podagrica (acc. JP) gave 73.28 Mb from 165,228 reads with 14,070 contigs and 16,572 singletons. BLASTX search of all contigs revealed that 1,683 unique proteins were orthologous across all four Jatropha spp. From 432 EST-SSR primer pairs designed and tested on these six accessions, 269 markers showed polymorphism and produced a total of 862 alleles. Based on sequence alignments between J. curcas accessions with low and high phorbol esters (PEs), 20 candidate SNPs were identified in four coding sequences including one gene relating to biosynthesis pathways of PEs. These expressed sequence tag-sample sequence repeat (EST-SSR) markers and candidate single nucleotide polymorphisms (SNPs) will be useful for jatropha breeding in the future.

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

Similar content being viewed by others

References

  • Achten WMJ, Verchot L, Franken YJ, Mathijs E, Singh VP, Aerts R, Muys B (2008) Review: Jatropha bio-diesel production and use. Biomass Bioenergy 32:1063–1084

    Article  CAS  Google Scholar 

  • Arreguín JCV, Laclette EI, Moraila BJ, Martínez O, Calzada JPV, Estrella LH, Estrella AH (2009) Deep sampling of the Palomero maize transcriptome by a high throughput strategy of pyrosequencing. BMC Genomics 10:299–308

    Article  Google Scholar 

  • Benbouza H, Jacquemin JM, Baudoin JP, Mergeai G (2006) Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamide gels. Biotechnol Agron Soc Environ 10:77–81

    CAS  Google Scholar 

  • Brooker J (2009) Methods for detoxifying oil seed crops (Patent WO/2010/070264)

  • Carvalhoa CR, Clarindoa WR, Praca MM, Araújoa FS, Carels N (2008) Genome size, base composition and karyotype of Jatropha curcas L., an important biofuel plant. Plant Sci 174:613–617

    Article  Google Scholar 

  • Costa GGL, Cardoso KC, Del Bem LEV, Lima AC, Cunha MAS, Camposde LL, Vicentini R, Papes F, Moreira RC, Yunes JA, Campos FAP, Silva MF (2010) Transcriptome analysis of the oil-richseed of the bioenergy crop Jatropha curcas L. BMC Genomics 11:462–470

    Article  PubMed  PubMed Central  Google Scholar 

  • Deng X, Fang Z, Liu YH (2010) Ultrasonic transesterification of Jatropha curcas L. oil to biodiesel by a two-step process. Energy Convers Manag 51:2802–2807

    Article  CAS  Google Scholar 

  • Deschamps S, Campbell MA (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Mol Breed 25:553–570

    Article  CAS  Google Scholar 

  • Galun E (2007) Plant patterning: structural and molecular genetic aspects. World Scientific, Singapore

  • Guo S, Zheng Y, Joung JG, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genomics 11:384–396

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jha TB, Mukherjee P, Datta MM (2007) Somatic embryogenesis in Jatropha curcas Linn., an important biofuel plant. Plant Biotechnol Rep 1:135–140

    Article  Google Scholar 

  • King AJ, He W, Cuevas JA, Freudenberger M, Ramiaramanana DI, Graham IA (2009) Potential of Jatropha curcas as a source of renewable oil and animal feed. J Exp Bot 60:2897–2905

    Article  CAS  PubMed  Google Scholar 

  • King AJ, Montes LR, Clarke JG, Affleck J, Li Y, Witsenboer H, van der Vossen E, van der Linde P, Tripathi Y, Tavares E, Shukla P, Rajasekaran T, van Loo EN, Graham IA (2013) Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity. Plant Biotechnol J 11:986–996

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • King AJ, Li Y, Graham IA (2011) Profiling the developing Jatropha curcas L. seed transcriptome by pyrosequencing. Bioenerg Res 4:211–221

    Article  Google Scholar 

  • Kumar S, Blaxter ML (2010) Comparing de novo assemblers for 454 transcriptome data. BMC Genomics 11:571–582

    Article  PubMed  PubMed Central  Google Scholar 

  • Menezes RG, Rao NG, Karanth SS, Kamath A, Manipady S, Pillay VV (2006) Jatropha curcas poisoning. Indian J Pediatr 73:634

    Article  PubMed  Google Scholar 

  • Natarajan P, Kanagasabapathy D, Gunadayalan G, Panchalingam J, Shree N, Sugantham PA, Singh KK, Madasamy P (2010) Gene discovery from Jatropha curcas by sequencing of ESTs from normalized and full-length enriched cDNA library from developing seeds. BMC Genomics 11:606–612

    Article  PubMed  PubMed Central  Google Scholar 

  • Natarajan P, Parani M (2011) De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GSFLX titanium platform of 454 pyrosequencing. BMC Genomics 12:191–102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Plant Biol 5:94–100

    CAS  Google Scholar 

  • Roth C, Liberles DA (2006) A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol 6:12

    Article  PubMed  PubMed Central  Google Scholar 

  • Saetae D, Kleekayai T, Jayasena V, Suntornsuk W (2011) Functional properties of protein isolate obtained from physic nut (Jatropha curcas L.) seed cake. Food Sci Biotechnol 20:29–37

    Article  CAS  Google Scholar 

  • Sato S, Hirakawa H, Isobe S, Fukai E, Watanabe A, Kato M, Kawashima U, Minami C, Muraki A, Nakazaki N, Takahashi C, Nakayama S, Kishida Y, Kohara M, Yamada M, Tsuruoka H, Sasamoto S, Tabata S, Aizu T, Toyoda A, Shin-I T, Minakuchi Y, Kohara Y, Fujiyama A, Tsuchimoto S, Kajiyama S, Makigano E, Ohmido N, Shibagaki N, Cartagene JA, Wada N, Kohinata T, Atefeh A, Yuasa S, Matsunaga S, Fukui K (2011) Sequence analysis of the genome of an oil bearing tree, Jatropha curcas L. DNA Res 18:65–76

    Article  CAS  PubMed  Google Scholar 

  • Stukenbrock EH, McDonald BA (2009) Population genetics of fungal and oomycete effectors involved in gene-for-gene interactions. Mol Plant Microbe Interact 22:371–380

    Article  CAS  PubMed  Google Scholar 

  • Sujatha M (2006) Genetic improvement of Jatropha curcas L.: possibilities and prospects. Indian J Agrofor 8:58–65

    Google Scholar 

  • Tanya P, Taeprayoon P, Hadkam Y, Srinives P (2011) Genetic diversity among jatropha and jatropha-related species based on ISSR markers. Plant Mol Biol Report 29:252–264

    Article  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    Article  CAS  PubMed  Google Scholar 

  • Wei X, Sujatha M, Aizhong L (2012) Review: genetic diversity in the Jatropha genus and its potential application. CAB Rev 7:1–15

    Google Scholar 

  • Wicker T, Schlagenhauf E, Graner A, Close TJ, Keller B, Stein N (2006) 454 sequencing put to the test using the complex genome of barley. BMC Genomics 7:275–285

    Article  PubMed  PubMed Central  Google Scholar 

  • Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W (2010) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Res Notes 3:42

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Li J, Zhao XQ, Wang J, Wong KSG, Yu J (2006) KaKs_calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4:259–263

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by a joint Royal Golden Jubilee PhD Scholarship between the Thailand Research Fund and Kasetsart University, the Chair Professor Project of Thailand’s National Science and Technology Development Agency (Grant no. P-11-00599), and the Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand.

Author information

Authors and Affiliations

  1. Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand

    Kularb Laosatit

  2. Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand

    Patcharin Tanya, Prakit Somta & Peerasak Srinives

  3. Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand

    Patcharin Tanya & Peerasak Srinives

  4. National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand

    Panthita Ruang-areerate, Chutima Sonthirod & Sithichoke Tangphatsornruang

  5. Special Research Unit in Microalgal Molecular Genetics and Functional Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand

    Piyada Juntawong

Authors
  1. Kularb Laosatit
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Patcharin Tanya
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prakit Somta
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Panthita Ruang-areerate
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chutima Sonthirod
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Sithichoke Tangphatsornruang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Piyada Juntawong
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Peerasak Srinives
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Peerasak Srinives.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

SNP in scaffold Jcr4S00160 coding for steroid binding proteins. Steroid binding proteins involve with the basic five-carbon unit isopentyldiphosphate (IPP), the initial substrate for PE synthesis (JPEG 533 kb)

Table S1

(DOCX 16 kb)

Table S2

(DOCX 13 kb)

Table S3

(DOCX 13 kb)

Table S4

(DOCX 55 kb)

Table S5

(DOCX 11 kb)

Table S6

(DOCX 14 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Laosatit, K., Tanya, P., Somta, P. et al. De novo Transcriptome Analysis of Apical Meristem of Jatropha spp. Using 454 Pyrosequencing Platform, and Identification of SNP and EST-SSR Markers. Plant Mol Biol Rep 34, 786–793 (2016). https://doi.org/10.1007/s11105-015-0961-z

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-015-0961-z

Keywords

Search

Navigation