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

Mahmodi, Parvaneh; Moeini, Ahmad; Khayam Nekoie, Seyed Mojtaba; Mardi, Mohsen; Hosseini Salekdeh, Ghasem

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

20.1001.1.22520783.1393.4.6.4.8

Main Subjects

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