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A preliminary analysis of the immunoglobulin genes in the African elephant (Loxodonta africana).

Guo Y, Bao Y, Wang H, Hu X, Zhao Z, Li N, Zhao Y - PLoS ONE (2011)

Bottom Line: The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene.These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex.Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China.

ABSTRACT
The genomic organization of the IgH (Immunoglobulin heavy chain), Igκ (Immunoglobulin kappa chain), and Igλ (Immunoglobulin lambda chain) loci in the African elephant (Loxodonta africana) was annotated using available genome data. The elephant IgH locus on scaffold 57 spans over 2,974 kb, and consists of at least 112 V(H) gene segments, 87 D(H) gene segments (the largest number in mammals examined so far), six J(H) gene segments, a single μ, a δ remnant, and eight γ genes (α and ε genes are missing, most likely due to sequence gaps). The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene. Two different transcriptional orientations were determined for these V(κ) gene segments. In contrast, the Igλ locus on scaffold 68 includes 15 V(λ) gene segments, all with the same transcriptional polarity as the downstream J(λ)-C(λ) cluster. These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex. Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.

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The elephant IgH locus.The elephant IgH locus is localized to scaffold 57. The length is approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′γ segment. Filled bars: potentially functional VH genes; open bars: VH pseudogenes: open bars and V-p; thin bars: truncated VH segments and V-t; DH: diversity genes; JH: joining genes; μ: IgM coding gene; δ: IgD remnant; and γ: IgG coding gene. VH and DH genes are numbered based on the families to which they belong and their positions in the locus. The number before the dash (VHn or DHn) indicates the family, while the number after dash represents the genomic position. JH genes are numbered based on the order of their locations in the locus. Double slashes indicate gaps >10 kb. Alpha and epsilon genes are not displayed on the map, but this does not imply their absence in the elephant IgH locus.
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pone-0016889-g001: The elephant IgH locus.The elephant IgH locus is localized to scaffold 57. The length is approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′γ segment. Filled bars: potentially functional VH genes; open bars: VH pseudogenes: open bars and V-p; thin bars: truncated VH segments and V-t; DH: diversity genes; JH: joining genes; μ: IgM coding gene; δ: IgD remnant; and γ: IgG coding gene. VH and DH genes are numbered based on the families to which they belong and their positions in the locus. The number before the dash (VHn or DHn) indicates the family, while the number after dash represents the genomic position. JH genes are numbered based on the order of their locations in the locus. Double slashes indicate gaps >10 kb. Alpha and epsilon genes are not displayed on the map, but this does not imply their absence in the elephant IgH locus.

Mentions: The public elephant genome assembly used in this study was loxAfr3, which is an assembly of the genome of the African Elephant (Loxodonta africana), sequenced to 7× coverage. The high genome coverage of this assembly confers a high reliability on the gene analysis. BLAST searching localized the elephant IgH locus to genomic scaffold 57. It spans approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′ γ gene (Fig. 1). A single μ and eight γ genes were identified in this scaffold. Neither ε nor α genes could be found, most likely due to sequence gaps.


A preliminary analysis of the immunoglobulin genes in the African elephant (Loxodonta africana).

Guo Y, Bao Y, Wang H, Hu X, Zhao Z, Li N, Zhao Y - PLoS ONE (2011)

The elephant IgH locus.The elephant IgH locus is localized to scaffold 57. The length is approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′γ segment. Filled bars: potentially functional VH genes; open bars: VH pseudogenes: open bars and V-p; thin bars: truncated VH segments and V-t; DH: diversity genes; JH: joining genes; μ: IgM coding gene; δ: IgD remnant; and γ: IgG coding gene. VH and DH genes are numbered based on the families to which they belong and their positions in the locus. The number before the dash (VHn or DHn) indicates the family, while the number after dash represents the genomic position. JH genes are numbered based on the order of their locations in the locus. Double slashes indicate gaps >10 kb. Alpha and epsilon genes are not displayed on the map, but this does not imply their absence in the elephant IgH locus.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3045440&req=5

pone-0016889-g001: The elephant IgH locus.The elephant IgH locus is localized to scaffold 57. The length is approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′γ segment. Filled bars: potentially functional VH genes; open bars: VH pseudogenes: open bars and V-p; thin bars: truncated VH segments and V-t; DH: diversity genes; JH: joining genes; μ: IgM coding gene; δ: IgD remnant; and γ: IgG coding gene. VH and DH genes are numbered based on the families to which they belong and their positions in the locus. The number before the dash (VHn or DHn) indicates the family, while the number after dash represents the genomic position. JH genes are numbered based on the order of their locations in the locus. Double slashes indicate gaps >10 kb. Alpha and epsilon genes are not displayed on the map, but this does not imply their absence in the elephant IgH locus.
Mentions: The public elephant genome assembly used in this study was loxAfr3, which is an assembly of the genome of the African Elephant (Loxodonta africana), sequenced to 7× coverage. The high genome coverage of this assembly confers a high reliability on the gene analysis. BLAST searching localized the elephant IgH locus to genomic scaffold 57. It spans approximately 2,974 kb from the most 5′ VH segment (VH2-112p) to the most 3′ γ gene (Fig. 1). A single μ and eight γ genes were identified in this scaffold. Neither ε nor α genes could be found, most likely due to sequence gaps.

Bottom Line: The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene.These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex.Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of AgroBiotechnology, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China.

ABSTRACT
The genomic organization of the IgH (Immunoglobulin heavy chain), Igκ (Immunoglobulin kappa chain), and Igλ (Immunoglobulin lambda chain) loci in the African elephant (Loxodonta africana) was annotated using available genome data. The elephant IgH locus on scaffold 57 spans over 2,974 kb, and consists of at least 112 V(H) gene segments, 87 D(H) gene segments (the largest number in mammals examined so far), six J(H) gene segments, a single μ, a δ remnant, and eight γ genes (α and ε genes are missing, most likely due to sequence gaps). The Igκ locus, found on three scaffolds (202, 50 and 86), contains a total of 153 V(κ) gene segments, three J(κ) segments, and a single C(κ) gene. Two different transcriptional orientations were determined for these V(κ) gene segments. In contrast, the Igλ locus on scaffold 68 includes 15 V(λ) gene segments, all with the same transcriptional polarity as the downstream J(λ)-C(λ) cluster. These data suggest that the elephant immunoglobulin gene repertoire is highly diverse and complex. Our results provide insights into the immunoglobulin genes in a placental mammal that is evolutionarily distant from humans, mice, and domestic animals.

Show MeSH