Limits...
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.

Show MeSH

Related in: MedlinePlus

Evolutionary relationships among primates species. (A) phylogenetic tree of the 11 primate species for which the cDNA references were available calculated based on the 1,628 common original ESTs. (B) phylogenetic tree of the old world monkeys and human species calculated based on the 8,788 common assembled ESTs. (C) phylogenetic tree of the old world monkeys and human restricted to the 5’UTR of the transcripts calculated based on the 1,016 common assembled ESTs. (D) phylogenetic tree of the old world monkeys and human restricted to the coding sequence of the transcripts calculated based on the 8,024 common assembled ESTs. (E) phylogenetic tree of the old world monkeys and human restricted to the 3’UTR of the transcripts calculated based on the 2,209 common assembled ESTs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3539953&req=5

Figure 6: Evolutionary relationships among primates species. (A) phylogenetic tree of the 11 primate species for which the cDNA references were available calculated based on the 1,628 common original ESTs. (B) phylogenetic tree of the old world monkeys and human species calculated based on the 8,788 common assembled ESTs. (C) phylogenetic tree of the old world monkeys and human restricted to the 5’UTR of the transcripts calculated based on the 1,016 common assembled ESTs. (D) phylogenetic tree of the old world monkeys and human restricted to the coding sequence of the transcripts calculated based on the 8,024 common assembled ESTs. (E) phylogenetic tree of the old world monkeys and human restricted to the 3’UTR of the transcripts calculated based on the 2,209 common assembled ESTs.

Mentions: Analysis of genomic relationships among species is an important way for studying evolution of genomic features. The relationships of the C. sabaeus EST with the 10 above described primate species for which the cDNA references were available have been quantified. For each one of the 1,628 ESTs aligned on all the cDNA references, multiple sequence alignment scores have been computed. Based on these pairwise alignment scores, an average genomic distance matrix has been computed (Table 5) and a phylogenetic tree constructed (Figure 6A). As it would be expected, the H. sapiens and P. troglodytes are clustered together, as it is also the case for the C. sabaeus and M. mulatta. The G. gorilla, P. abelii, and N. leucogeny were located between these two clusters, and the C. jacchus, M. murinus, O. garnettii, and T. syrichta are segregated from other species. By comparing only to the more related species, phylogenetic trees have also been computed with a higher number of AGM ESTs with all the 14,410 assembled transcripts (Figure 6B). Finally, trees have been constructed for specific sections of the transcripts: 5’UTR regions (Figure 6C), CDS sections (Figure 6D), and 3’UTR regions (Figure 6E). Both the phylogenetic trees restricted on the CDS and 3’UTR sections show a clusterisation of the C. sabaeus with the M. mulatta and a strong segregation with other species. Interestingly, the phylogenetic tree restricted on the 5’UTR sections revealed a different shape. C. sabaeus and the N. leucogeny species clustered together, suggesting distinct selective pressures in the 5’UTR as compared to other regions.


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)

Evolutionary relationships among primates species. (A) phylogenetic tree of the 11 primate species for which the cDNA references were available calculated based on the 1,628 common original ESTs. (B) phylogenetic tree of the old world monkeys and human species calculated based on the 8,788 common assembled ESTs. (C) phylogenetic tree of the old world monkeys and human restricted to the 5’UTR of the transcripts calculated based on the 1,016 common assembled ESTs. (D) phylogenetic tree of the old world monkeys and human restricted to the coding sequence of the transcripts calculated based on the 8,024 common assembled ESTs. (E) phylogenetic tree of the old world monkeys and human restricted to the 3’UTR of the transcripts calculated based on the 2,209 common assembled ESTs.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Evolutionary relationships among primates species. (A) phylogenetic tree of the 11 primate species for which the cDNA references were available calculated based on the 1,628 common original ESTs. (B) phylogenetic tree of the old world monkeys and human species calculated based on the 8,788 common assembled ESTs. (C) phylogenetic tree of the old world monkeys and human restricted to the 5’UTR of the transcripts calculated based on the 1,016 common assembled ESTs. (D) phylogenetic tree of the old world monkeys and human restricted to the coding sequence of the transcripts calculated based on the 8,024 common assembled ESTs. (E) phylogenetic tree of the old world monkeys and human restricted to the 3’UTR of the transcripts calculated based on the 2,209 common assembled ESTs.
Mentions: Analysis of genomic relationships among species is an important way for studying evolution of genomic features. The relationships of the C. sabaeus EST with the 10 above described primate species for which the cDNA references were available have been quantified. For each one of the 1,628 ESTs aligned on all the cDNA references, multiple sequence alignment scores have been computed. Based on these pairwise alignment scores, an average genomic distance matrix has been computed (Table 5) and a phylogenetic tree constructed (Figure 6A). As it would be expected, the H. sapiens and P. troglodytes are clustered together, as it is also the case for the C. sabaeus and M. mulatta. The G. gorilla, P. abelii, and N. leucogeny were located between these two clusters, and the C. jacchus, M. murinus, O. garnettii, and T. syrichta are segregated from other species. By comparing only to the more related species, phylogenetic trees have also been computed with a higher number of AGM ESTs with all the 14,410 assembled transcripts (Figure 6B). Finally, trees have been constructed for specific sections of the transcripts: 5’UTR regions (Figure 6C), CDS sections (Figure 6D), and 3’UTR regions (Figure 6E). Both the phylogenetic trees restricted on the CDS and 3’UTR sections show a clusterisation of the C. sabaeus with the M. mulatta and a strong segregation with other species. Interestingly, the phylogenetic tree restricted on the 5’UTR sections revealed a different shape. C. sabaeus and the N. leucogeny species clustered together, suggesting distinct selective pressures in the 5’UTR as compared to other regions.

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