Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries

Abdulaziz M. Al-Swailem, Maher M. Shehata, Faisel M. Abu-Duhier, Essam J. Al-Yamani, Khalid A. Al-Busadah, Mohammed S. Al-Arawi, Ali Y. Al-Khider, Abdullah N. Al-Muhaimeed, Fahad H. Al-Qahtani, Manee M. Manee, Badr M. Al-Shomrani, Saad M. Al-Qhtani, Amer S. Al-Harthi, Kadir C. Akdemir, Mehmet S. Inan, Hasan H. Otu

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF) analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and ∼40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/), hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism.

Original languageEnglish (US)
Article numbere10720
JournalPloS one
Volume5
Issue number5
DOIs
StatePublished - Sep 17 2010

Fingerprint

Camelus
Camelus dromedarius
Expressed Sequence Tags
camels
expressed sequence tags
Genes
open reading frames
organisms
Open Reading Frames
nucleotide sequences
Complementary DNA
start codon
genome
genes
chimerism
Genome
Protein Databases
Gene Ontology
Initiator Codon
Public Sector

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Al-Swailem, A. M., Shehata, M. M., Abu-Duhier, F. M., Al-Yamani, E. J., Al-Busadah, K. A., Al-Arawi, M. S., ... Otu, H. H. (2010). Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries. PloS one, 5(5), [e10720]. https://doi.org/10.1371/journal.pone.0010720

Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries. / Al-Swailem, Abdulaziz M.; Shehata, Maher M.; Abu-Duhier, Faisel M.; Al-Yamani, Essam J.; Al-Busadah, Khalid A.; Al-Arawi, Mohammed S.; Al-Khider, Ali Y.; Al-Muhaimeed, Abdullah N.; Al-Qahtani, Fahad H.; Manee, Manee M.; Al-Shomrani, Badr M.; Al-Qhtani, Saad M.; Al-Harthi, Amer S.; Akdemir, Kadir C.; Inan, Mehmet S.; Otu, Hasan H.

In: PloS one, Vol. 5, No. 5, e10720, 17.09.2010.

Research output: Contribution to journalArticle

Al-Swailem, AM, Shehata, MM, Abu-Duhier, FM, Al-Yamani, EJ, Al-Busadah, KA, Al-Arawi, MS, Al-Khider, AY, Al-Muhaimeed, AN, Al-Qahtani, FH, Manee, MM, Al-Shomrani, BM, Al-Qhtani, SM, Al-Harthi, AS, Akdemir, KC, Inan, MS & Otu, HH 2010, 'Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries', PloS one, vol. 5, no. 5, e10720. https://doi.org/10.1371/journal.pone.0010720
Al-Swailem AM, Shehata MM, Abu-Duhier FM, Al-Yamani EJ, Al-Busadah KA, Al-Arawi MS et al. Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries. PloS one. 2010 Sep 17;5(5). e10720. https://doi.org/10.1371/journal.pone.0010720
Al-Swailem, Abdulaziz M. ; Shehata, Maher M. ; Abu-Duhier, Faisel M. ; Al-Yamani, Essam J. ; Al-Busadah, Khalid A. ; Al-Arawi, Mohammed S. ; Al-Khider, Ali Y. ; Al-Muhaimeed, Abdullah N. ; Al-Qahtani, Fahad H. ; Manee, Manee M. ; Al-Shomrani, Badr M. ; Al-Qhtani, Saad M. ; Al-Harthi, Amer S. ; Akdemir, Kadir C. ; Inan, Mehmet S. ; Otu, Hasan H. / Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedaries. In: PloS one. 2010 ; Vol. 5, No. 5.
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