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Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus.

Tchitchek N, Jacquelin B, Wincker P, Dossat C, Silva CD, Weissenbach J, Blancher A, Müller-Trutwin M, Benecke A - BMC Genomics (2012)

Bottom Line: For 506 transcripts, sequences were quasi-complete.In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, Bures-sur-Yvette, France.

ABSTRACT

Background: African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution.

Results: We have exhaustively sequenced an Expression Sequence Tag (EST) library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.

Conclusions: The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

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Inter- and intra- species alignment comparisons. (A) 4-set Venn diagram showing the intersections among the 4 sets of original ESTs aligned on the H. sapiens, M. mulatta, P. troglodytes, and P. abelii species, and 2-set Venn diagram showing the intersections between the 2 sets of original ESTs aligned over the C. sabaeus and M. fascicularis species. (B) Idem as A for the distinct transcripts.
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Figure 2: Inter- and intra- species alignment comparisons. (A) 4-set Venn diagram showing the intersections among the 4 sets of original ESTs aligned on the H. sapiens, M. mulatta, P. troglodytes, and P. abelii species, and 2-set Venn diagram showing the intersections between the 2 sets of original ESTs aligned over the C. sabaeus and M. fascicularis species. (B) Idem as A for the distinct transcripts.

Mentions: the original and the assembled ESTs was found for the H. sapiens (∼80% of the original ESTs and ∼60% of the distinct transcripts) probably due to the relatively higher degree of investigation of this genome. The higher frequence as to compared to the ones of NHP is thus due to the broader sequence information from human genomes and does not reflect the biological distances between the species. The C. jacchus, G. gorilla, M. mulatta, N. leucogeny, P. troglodytes species had relatively high-proportions of aligned ESTs (∼63% of the original ESTs and ∼41% of the distinct transcripts), and the M. murinus, O. garnettii, T. syrichta species had equally low-proportions of aligned ESTs (∼18% of the original library and ∼7% of the distinct transcripts). The P. abelii species had an intermediate proportion of aligned ESTs (∼50% of the library and ∼30% of the distinct transcripts). We then performed Venn Diagrams between AGM and cDNA of the NHP species showing the highest proportions of aligned ESTs (M. mulatta, N. leucogeny, P. troglodytes, and H. sapiens), 31,005 of the 37,787 original ESTs and 8,909 of the 14,410 distinct transcrips could been aligned on at least one of the cDNA references (Figures 2A and 2B). 23,450 of the original ESTs (62.05%) were shared between the H. sapiens and M. mulatta species. AGM shared 25,196 sequences (66.67%) with those of M. mulatta, and 17,743 (46.95%) with the four species. The number of mapped ESTs on the C. sabaeus and M. fascicularis draft genomes is highly significant for both the original ESTs and the assembled and singletons ESTs, and almost the totality of the ESTs are commonly mapped ESTs between the two genomes (Figures 2A and 2B). Note that the alignment to the draft genomes was performed using low-specificity alignment parameters and thus is not directly comparable to the alignments of the EST libraries. Overall, while giving different specific alignment information, the number of mapped transcripts and mapped genes for both the 37,787 originals ESTs and the 14,410 distinct transcripts are convergent in the number of mapped genes and proportional with the genomic distances that exist among these species.


Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus.

Tchitchek N, Jacquelin B, Wincker P, Dossat C, Silva CD, Weissenbach J, Blancher A, Müller-Trutwin M, Benecke A - BMC Genomics (2012)

Inter- and intra- species alignment comparisons. (A) 4-set Venn diagram showing the intersections among the 4 sets of original ESTs aligned on the H. sapiens, M. mulatta, P. troglodytes, and P. abelii species, and 2-set Venn diagram showing the intersections between the 2 sets of original ESTs aligned over the C. sabaeus and M. fascicularis species. (B) Idem as A for the distinct transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3539953&req=5

Figure 2: Inter- and intra- species alignment comparisons. (A) 4-set Venn diagram showing the intersections among the 4 sets of original ESTs aligned on the H. sapiens, M. mulatta, P. troglodytes, and P. abelii species, and 2-set Venn diagram showing the intersections between the 2 sets of original ESTs aligned over the C. sabaeus and M. fascicularis species. (B) Idem as A for the distinct transcripts.
Mentions: the original and the assembled ESTs was found for the H. sapiens (∼80% of the original ESTs and ∼60% of the distinct transcripts) probably due to the relatively higher degree of investigation of this genome. The higher frequence as to compared to the ones of NHP is thus due to the broader sequence information from human genomes and does not reflect the biological distances between the species. The C. jacchus, G. gorilla, M. mulatta, N. leucogeny, P. troglodytes species had relatively high-proportions of aligned ESTs (∼63% of the original ESTs and ∼41% of the distinct transcripts), and the M. murinus, O. garnettii, T. syrichta species had equally low-proportions of aligned ESTs (∼18% of the original library and ∼7% of the distinct transcripts). The P. abelii species had an intermediate proportion of aligned ESTs (∼50% of the library and ∼30% of the distinct transcripts). We then performed Venn Diagrams between AGM and cDNA of the NHP species showing the highest proportions of aligned ESTs (M. mulatta, N. leucogeny, P. troglodytes, and H. sapiens), 31,005 of the 37,787 original ESTs and 8,909 of the 14,410 distinct transcrips could been aligned on at least one of the cDNA references (Figures 2A and 2B). 23,450 of the original ESTs (62.05%) were shared between the H. sapiens and M. mulatta species. AGM shared 25,196 sequences (66.67%) with those of M. mulatta, and 17,743 (46.95%) with the four species. The number of mapped ESTs on the C. sabaeus and M. fascicularis draft genomes is highly significant for both the original ESTs and the assembled and singletons ESTs, and almost the totality of the ESTs are commonly mapped ESTs between the two genomes (Figures 2A and 2B). Note that the alignment to the draft genomes was performed using low-specificity alignment parameters and thus is not directly comparable to the alignments of the EST libraries. Overall, while giving different specific alignment information, the number of mapped transcripts and mapped genes for both the 37,787 originals ESTs and the 14,410 distinct transcripts are convergent in the number of mapped genes and proportional with the genomic distances that exist among these species.

Bottom Line: For 506 transcripts, sequences were quasi-complete.In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut des Hautes Études Scientifiques-Centre National de la Recherche Scientifique, Bures-sur-Yvette, France.

ABSTRACT

Background: African Green Monkeys (AGM) are amongst the most frequently used nonhuman primate models in clinical and biomedical research, nevertheless only few genomic resources exist for this species. Such information would be essential for the development of dedicated new generation technologies in fundamental and pre-clinical research using this model, and would deliver new insights into primate evolution.

Results: We have exhaustively sequenced an Expression Sequence Tag (EST) library made from a pool of Peripheral Blood Mononuclear Cells from sixteen Chlorocebus sabaeus monkeys. Twelve of them were infected with the Simian Immunodeficiency Virus. The mononuclear cells were or not stimulated in vitro with Concanavalin A, with lipopolysacharrides, or through mixed lymphocyte reaction in order to generate a representative and broad library of expressed sequences in immune cells. We report here 37,787 sequences, which were assembled into 14,410 contigs representing an estimated 12% of the C. sabaeus transcriptome. Using data from primate genome databases, 9,029 assembled sequences from C. sabaeus could be annotated. Sequences have been systematically aligned with ten cDNA references of primate species including Homo sapiens, Pan troglodytes, and Macaca mulatta to identify ortholog transcripts. For 506 transcripts, sequences were quasi-complete. In addition, 6,576 transcript fragments are potentially specific to the C. sabaeus or corresponding to not yet described primate genes.

Conclusions: The EST library we provide here will prove useful in gene annotation efforts for future sequencing of the African Green Monkey genomes. Furthermore, this library, which particularly well represents immunological and hematological gene expression, will be an important resource for the comparative analysis of gene expression in clinically relevant nonhuman primate and human research.

Show MeSH
Related in: MedlinePlus