De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome
Joint Authors
Zhukov, Vladimir A.
Zhernakov, Alexander I.
Kulaeva, Olga A.
Ershov, Nikita I.
Borisov, Alexey Y.
Tikhonovich, Igor A.
Source
International Journal of Genomics
Issue
Vol. 2015, Issue 2015 (31 Dec. 2015), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2015-11-24
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
The large size and complexity of the garden pea (Pisum sativum L.) genome hamper its sequencing and the discovery of pea gene resources.
Although transcriptome sequencing provides extensive information about expressed genes, some tissue-specific transcripts can only be identified from particular organs under appropriate conditions.
In this study, we performed RNA sequencing of polyadenylated transcripts from young pea nodules and root tips on an Illumina GAIIx system, followed by de novo transcriptome assembly using the Trinity program.
We obtained more than 58,000 and 37,000 contigs from “Nodules” and “Root Tips” assemblies, respectively.
The quality of the assemblies was assessed by comparison with pea expressed sequence tags and transcriptome sequencing project data available from NCBI website.
The “Nodules” assembly was compared with the “Root Tips” assembly and with pea transcriptome sequencing data from projects indicating tissue specificity.
As a result, approximately 13,000 nodule-specific contigs were found and annotated by alignment to known plant protein-coding sequences and by Gene Ontology searching.
Of these, 581 sequences were found to possess full CDSs and could thus be considered as novel nodule-specific transcripts of pea.
The information about pea nodule-specific gene sequences can be applied for gene-based markers creation, polymorphism studies, and real-time PCR.
American Psychological Association (APA)
Zhukov, Vladimir A.& Zhernakov, Alexander I.& Kulaeva, Olga A.& Ershov, Nikita I.& Borisov, Alexey Y.& Tikhonovich, Igor A.. 2015. De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. International Journal of Genomics،Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1066038
Modern Language Association (MLA)
Zhukov, Vladimir A.…[et al.]. De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. International Journal of Genomics No. 2015 (2015), pp.1-11.
https://search.emarefa.net/detail/BIM-1066038
American Medical Association (AMA)
Zhukov, Vladimir A.& Zhernakov, Alexander I.& Kulaeva, Olga A.& Ershov, Nikita I.& Borisov, Alexey Y.& Tikhonovich, Igor A.. De Novo Assembly of the Pea (Pisum sativum L.) Nodule Transcriptome. International Journal of Genomics. 2015. Vol. 2015, no. 2015, pp.1-11.
https://search.emarefa.net/detail/BIM-1066038
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1066038