Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop
Joint Authors
Al-Ameri, Abdulhafed A.
Al-Qurainy, Fahad
Gaafar, Abdel-Rhman Z.
Khan, Salim
Nadeem, M.
Tarroum, Mohamed
Alshameri, Aref
Ashraf, Muhammad
Source
International Journal of Genomics
Issue
Vol. 2019, Issue 2019 (31 Dec. 2019), pp.1-14, 14 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2019-10-08
Country of Publication
Egypt
No. of Pages
14
Main Subjects
Abstract EN
The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat, drought, and mild salinity.
A complete image on its genic architecture will promote our understanding about gene expression networks and different tolerance mechanisms at the molecular level.
Therefore, whole mRNA sequence approach on the Guar plant was conducted to provide a snapshot of the mRNA information in the cell under salinity, heat, and drought stresses to be integrated with previous transcriptomic studies.
RNA-Seq technology was employed to perform a 2×100 paired-end sequencing using an Illumina HiSeq 2500 platform for the transcriptome of leaves of C.
tetragonoloba under normal, heat, drought, and salinity conditions.
Trinity was used to achieve a de novo assembly followed by gene annotation, functional classification, metabolic pathway analysis, and identification of SSR markers.
A total of 218.2 million paired-end raw reads (~44 Gbp) were generated.
Of those, 193.5M paired-end reads of high quality were used to reconstruct a total of 161,058 transcripts (~266 Mbp) with N50 of 2552 bp and 61,508 putative genes.
There were 6463 proteins having >90% full-length coverage against the Swiss-Prot database and 94% complete orthologs against Embryophyta.
Approximately, 62.87% of transcripts were blasted, 50.46% mapped, and 43.50% annotated.
A total of 4715 InterProScan families, 3441 domains, 74 repeats, and 490 sites were detected.
Biological processes, molecular functions, and cellular components comprised 64.12%, 25.42%, and 10.4%, respectively.
The transcriptome was associated with 985 enzymes and 156 KEGG pathways.
A total of 27,066 SSRs were gained with an average frequency of one SSR/9.825 kb in the assembled transcripts.
This resulting data will be helpful for the advanced analysis of Guar to multi-stress tolerance.
American Psychological Association (APA)
Al-Qurainy, Fahad& Alshameri, Aref& Gaafar, Abdel-Rhman Z.& Khan, Salim& Nadeem, M.& Al-Ameri, Abdulhafed A.…[et al.]. 2019. Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. International Journal of Genomics،Vol. 2019, no. 2019, pp.1-14.
https://search.emarefa.net/detail/BIM-1165716
Modern Language Association (MLA)
Al-Qurainy, Fahad…[et al.]. Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. International Journal of Genomics No. 2019 (2019), pp.1-14.
https://search.emarefa.net/detail/BIM-1165716
American Medical Association (AMA)
Al-Qurainy, Fahad& Alshameri, Aref& Gaafar, Abdel-Rhman Z.& Khan, Salim& Nadeem, M.& Al-Ameri, Abdulhafed A.…[et al.]. Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. International Journal of Genomics. 2019. Vol. 2019, no. 2019, pp.1-14.
https://search.emarefa.net/detail/BIM-1165716
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1165716