Crop Biotechnology

In collaboration with Payame Noor University and Iranian Biotechnology Society

Current Issue

By Issue

By Author

By Subject

Author Index

Keyword Index

About Journal

Aims and Scope

Editorial Board

Publication Ethics

Indexing and Abstracting

Related Links

FAQ

Peer Review Process

Journal Metrics

News

Analysis of Saffron Stigma (Crocus sativus L.) Transcriptome Using SOAPdenovo and Trinity Assembly Software

Document Type : Research Paper

Authors

1 Ph.D. Student of plant breeding, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

2 Associate Professor, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

3 Associate Professor, Faculty of Biological Biotechnology Research Institute of Iran, Karaj, Iran.

Abstract

Saffron (Crocus sativus L.), is the most valuable and popular spice in the word. It is a triploid species of the Iridaceae family. Its long, red, and aromatic stigma distinguishes this species from others in its family. With the rapid advances in next generation sequencing technology, RNA sequencing has risen as a cost-effective and powerful method for transcriptome study. De novo assembly of transcripts provides main solution to transcriptome analysis for organisms without reference genome. Precise sequencing and assembly of transcriptome reliable data are necessary for the downstream analysis. Accordingly, this work was analyzed by two of the most popular software's Trinity and SOAPdenovo for saffron stigma transcriptome to study the effective programs for transcriptome assembly. The results showed that the mean sequence length and the number of unigenes obtained by Trinity were more than SOAPdenovo (Trinity: 689, SOAPdenovo: 624). Translation of the better results produced by the appropriate assembler to protein led to a significant increase in the number of its records obtained at databases. Furthermore, these unigenes might help to identify more metabolite pathways. Assembled unigenes by Trinity had no lacking distance and were about twice the unigenes assembled by SOAPdenovo. As a general conclusion, it seems that selection of an appropriate software and its parameters is not easy without comprehension understanding of different software operation and their setting. Thus, comparison of the different softwares efficiency on the different organisms could provide some practical suggestions and choose an appropriate software.

Keywords

Main Subjects

References
 Anonymous, Government Information Center, http://dolat.ir/NSite/FullStory/News
Bai XL, Rivera-Vega P, Mamidala P, Bonello DA, Herms O (2011) Transcriptomic signatures of ash (Fraxinus spp.) phloem. PloS one 6:e16368.
Bentley DR (2006) Whole-genome re-sequencing. Current opinion in genetics and development 16:545-552.
Cahais VP, Gayral G, Tsagkogeorga J, Melo Ferreira M, Ballenghien L, Weinert Y, Chiari K, Belkhir V, Galtier N (2012) Reference-free transcriptome assembly in non-model animals from next-generation sequencing data. Molecular Ecology Resources 12:834-845.
Conesa AS, Götz JM, García-Gómez J, Terol M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674-3676.
Chikhi R, Medvedev P (2012) Informed and Automated k-Mer Size Selection for Genome Assembly. Oxford University Press. 7:564-673.
Duan JC, Xia G, Zhao J, Kong K (2012) Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics. 13:392-404.
Fernández JA, Pandalai S (2004) Biology, biotechnology and biomedicine of saffron. Recent Research Developments in Plant Science. 2:127-159.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng O (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. 29:644-652.
Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Research. 20:265-272.
Liu M, Qiao G, Jiang J, Yang H, Xie L, Xie J, Zhuo R (2012) Transcriptome sequencing and de novo analysis for ma bamboo (Dendrocalamus latiflorus Munro) using the Illumina platform. PloS one 7:e46766.
Liu T, Zhu S, Tang Q, Chen P, Yu Y, Tang S (2013) De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). BMC Genomics 14:125-136.
Morozova O, Hirst M, Marra MA (2009) Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics. 10:135-151.
Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics. 92:255-264.
Schulz MH, Zerbino DR, Vingron M, Birney E (2012) Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 28:1086-1092.
Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics. 12:131-150.
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I (2009) ABySS: a parallel assembler for short read sequence data. Genome Research. 19:1117-1123.
Wani BA, Hamza AKR, Mohiddin F (2011) Saffron: A repository of medicinal properties. J. Med. Plant Res. 5:2131-2135.
Wu J, Zhang Y, Zhang H, Huang H, Folta KM, Lu J (2010) Whole genome wide expression profiles of Vitis amurensis grape responding to downy mildew by using Solexa sequencing technology. BMC Plant Biology. 10:234.
Xu DL, Long H, Liang JJ, Zhang J, Chen X, Li JL, Pan ZF, Deng GB, Yu MQ (2012) De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. BMC Genomics. 13:133-142.
Zeng J, Liu Y, Liu W, Liu X, Liu F, Huang P, Zhu P, Chen J, Shi M, Guo F (2013) Integration of transcriptome, proteome and metabolism data reveals the alkaloids biosynthesis in Macleaya cordata and Macleaya microcarpa. PloS one 8:e53409.
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.
Zhao QY, Wang Y, Kong YM, Luo D, Li X, an Hao P (2011) Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 12:S2.
Zheng X, Pan C, Diao Y, You Y, Yang C, Hu C (2013) Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae). BMC Genomics 14:490-501.
Crop Biotechnology
Volume 4, Issue 6 - Serial Number 6
October 2014
Pages 35-46
Files
Share
How to cite
Statistics