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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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Dot plot comparison of the elephant CH (μ and γ) region.A dot matrix representing repetitive sequences of elephant CH (μ and γ) genes. Switch regions are indicated by black-squared boxes and marked with arrowheads, and gaps are indicated by grey-squared boxes. Positions of CH genes are indicated as vertical lines. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches.
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pone-0016889-g004: Dot plot comparison of the elephant CH (μ and γ) region.A dot matrix representing repetitive sequences of elephant CH (μ and γ) genes. Switch regions are indicated by black-squared boxes and marked with arrowheads, and gaps are indicated by grey-squared boxes. Positions of CH genes are indicated as vertical lines. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches.

Mentions: Dot matrix analysis of the elephant IgH locus showed there are switch regions upstream of the μ gene and six γ genes (γ1, γ4, γ5, γ6, γ7, and γ8), as in humans and mice [55], [56]. The switch regions of γ2, γ3, and γ9 could not be identified, most likely due to sequence gaps. Structurally, the switch regions, as in other species, are all composed of pentameric repeats (GGGCT and GAGCT). The elephant Sμ region shows substantial nucleotide similarity with those of human, mouse, and pig (Fig. 3). The six elephant Sγ regions are similar, but share little sequence similarity with human and mouse Sγ (Fig. 4 and data not shown).


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)

Dot plot comparison of the elephant CH (μ and γ) region.A dot matrix representing repetitive sequences of elephant CH (μ and γ) genes. Switch regions are indicated by black-squared boxes and marked with arrowheads, and gaps are indicated by grey-squared boxes. Positions of CH genes are indicated as vertical lines. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0016889-g004: Dot plot comparison of the elephant CH (μ and γ) region.A dot matrix representing repetitive sequences of elephant CH (μ and γ) genes. Switch regions are indicated by black-squared boxes and marked with arrowheads, and gaps are indicated by grey-squared boxes. Positions of CH genes are indicated as vertical lines. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches.
Mentions: Dot matrix analysis of the elephant IgH locus showed there are switch regions upstream of the μ gene and six γ genes (γ1, γ4, γ5, γ6, γ7, and γ8), as in humans and mice [55], [56]. The switch regions of γ2, γ3, and γ9 could not be identified, most likely due to sequence gaps. Structurally, the switch regions, as in other species, are all composed of pentameric repeats (GGGCT and GAGCT). The elephant Sμ region shows substantial nucleotide similarity with those of human, mouse, and pig (Fig. 3). The six elephant Sγ regions are similar, but share little sequence similarity with human and mouse Sγ (Fig. 4 and data not shown).

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