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Chapter 4 : Specificities as Deduced from Comparative Genomics

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Specificities as Deduced from Comparative Genomics, Page 1 of 2

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Abstract:

This chapter mainly focuses on specific genes of as well as genes missing in but present in other species, with the aim to identify genes that encode particular functions specifically associated with the life-style of . Species-specific comparisons shown in the chapter were based on the BLASTP program, with the pam250 substitution matrix to favor recognition of large similar segment pairs and the seg filter to mask compositionally biased regions in the query sequences. In each considered species, each nonunique protein is assigned to a class of paralogs. Clustering of genes responsible for secondary metabolite synthesis have been already identified in . The survey of the genome led to the identification of a cluster of genes that seems specific to . Among the 377 genes specific to A. fumigatus, 74% encode small proteins (shorter than 150 amino acids), whereas only 8% of the genes in the whole genome encode such small proteins. Genome comparison studies in have shown that species- or genus-specific genes constitute a tiny part of the genome compared to other fungal species. Moreover, the analyses of -specific genes have not been very informative in terms of gene functions and do not highlight any particular pathway which could be unique to this fungus. The chapter confirms that the eight analyzed species are closely related and shows that no major particular event of function loss or gain took place in during its evolution.

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
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Figures

Image of Figure 1.
Figure 1.

Distribution of the sizes of mcl classes of nonunique proteins in (ASFU) species. The horizontal axis indicates the sizes of the mcl families, i.e., the number of proteins per mcl family. On the vertical axis are the occurrences of families per size.

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
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Image of Figure 2.
Figure 2.

Motif distributions in two sets of homologous protein sequences as obtained with the MEME and MAST programs for FKS (A) and chitinases (B). Sequence identifications are preceded by their species code, as indicated in footnotes for Tables 2 and 3 , with additional species corresponding to (HOSA), (SACE), and (ARTH).

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
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Image of Figure 3.
Figure 3.

Locus organization of several genes specific to the genome. The genes indicated by black arrows or bars are specific to , and those indicated by white arrows or bars are nonspecific. Eleven genes specific to are located within a 100kb subtelomeric region of chromosome I (supercontig 98).

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
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Tables

Generic image for table
Table 1.

Specific conservation in each considered species

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
Generic image for table
Table 2.

Gene duplication and conservation in

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
Generic image for table
Table 3.

Shared reciprocal best hits (RBH) between pairs of species

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4
Generic image for table
Table 4.

Trichothecenes: genes in spp. determined to be homologous to family genes

Citation: Gastebois A, Lambou K, Hoi J, Tekaia F. 2009. Specificities as Deduced from Comparative Genomics, p 29-38. In Latgé J, Steinbach W (ed), and Aspergillosis. ASM Press, Washington, DC. doi: 10.1128/9781555815523.ch4

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