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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 IgL locus.The elephant Igκ locus is distributed over three scaffolds (202, 50, and 86), and the Igλ locus is located on scaffold 68. Overall configurations are drawn approximately to scale. The potentially functional Vκ and Vλ genes are shown as filled bars, while pseudogenes are represented by open bars and indicated with the letter p. Double slashes indicate gaps >10 kb. The unidirectional arrowheads below Vκ gene segments on scaffold 86 indicate that their transcriptional direction is opposite to downstream Jκ segments. However, the unidirectional arrowheads on scaffolds 202 and 50 do not represent different transcriptional directions from the identified Jκ gene segment; they merely indicate a transcriptional direction different from that of the remaining Vκ gene segments in the scaffold.
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pone-0016889-g009: The elephant IgL locus.The elephant Igκ locus is distributed over three scaffolds (202, 50, and 86), and the Igλ locus is located on scaffold 68. Overall configurations are drawn approximately to scale. The potentially functional Vκ and Vλ genes are shown as filled bars, while pseudogenes are represented by open bars and indicated with the letter p. Double slashes indicate gaps >10 kb. The unidirectional arrowheads below Vκ gene segments on scaffold 86 indicate that their transcriptional direction is opposite to downstream Jκ segments. However, the unidirectional arrowheads on scaffolds 202 and 50 do not represent different transcriptional directions from the identified Jκ gene segment; they merely indicate a transcriptional direction different from that of the remaining Vκ gene segments in the scaffold.

Mentions: Immunoglobulin κ chain genes of elephant were identified on three scaffolds: 202, 50, and 86. A schematic diagram is shown in Fig. 9. Of the 153 germline Vκ segments from the three scaffolds, 53 were regarded as potentially functional genes and 100 as pseudogenes. Based on sequence similarity analysis, 142 of the Vκ segments can be assigned to eight families (Vκ1∼Vκ8) (Table S3), which contain 2, 31, 2, 102, 1, 1, 2, and 1 members, respectively. The remaining 11 Vκ pseudogenes could not be assigned to any family because they share less than 70% nucleotide similarity with any other Vκ gene segment. A phylogenetic tree of the elephant Vκ functional genes is shown in Fig.10. The six elephant Vκ families (Vκ1∼Vκ6) correspond to the six human Vκ gene families. In addition, scaffold 86 includes 24 Vκ segments showing the same transcriptional orientation as the Jκ and Cκ, and 18 Vκ segments showing a reverse transcriptional direction. Three Jκ segments and one Cκ gene on scaffold 86 are displayed in Figure S5. In addition, Vκ segments located on scaffolds 202 and 50 also possess two different transcriptional directions.


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 IgL locus.The elephant Igκ locus is distributed over three scaffolds (202, 50, and 86), and the Igλ locus is located on scaffold 68. Overall configurations are drawn approximately to scale. The potentially functional Vκ and Vλ genes are shown as filled bars, while pseudogenes are represented by open bars and indicated with the letter p. Double slashes indicate gaps >10 kb. The unidirectional arrowheads below Vκ gene segments on scaffold 86 indicate that their transcriptional direction is opposite to downstream Jκ segments. However, the unidirectional arrowheads on scaffolds 202 and 50 do not represent different transcriptional directions from the identified Jκ gene segment; they merely indicate a transcriptional direction different from that of the remaining Vκ gene segments in the scaffold.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3045440&req=5

pone-0016889-g009: The elephant IgL locus.The elephant Igκ locus is distributed over three scaffolds (202, 50, and 86), and the Igλ locus is located on scaffold 68. Overall configurations are drawn approximately to scale. The potentially functional Vκ and Vλ genes are shown as filled bars, while pseudogenes are represented by open bars and indicated with the letter p. Double slashes indicate gaps >10 kb. The unidirectional arrowheads below Vκ gene segments on scaffold 86 indicate that their transcriptional direction is opposite to downstream Jκ segments. However, the unidirectional arrowheads on scaffolds 202 and 50 do not represent different transcriptional directions from the identified Jκ gene segment; they merely indicate a transcriptional direction different from that of the remaining Vκ gene segments in the scaffold.
Mentions: Immunoglobulin κ chain genes of elephant were identified on three scaffolds: 202, 50, and 86. A schematic diagram is shown in Fig. 9. Of the 153 germline Vκ segments from the three scaffolds, 53 were regarded as potentially functional genes and 100 as pseudogenes. Based on sequence similarity analysis, 142 of the Vκ segments can be assigned to eight families (Vκ1∼Vκ8) (Table S3), which contain 2, 31, 2, 102, 1, 1, 2, and 1 members, respectively. The remaining 11 Vκ pseudogenes could not be assigned to any family because they share less than 70% nucleotide similarity with any other Vκ gene segment. A phylogenetic tree of the elephant Vκ functional genes is shown in Fig.10. The six elephant Vκ families (Vκ1∼Vκ6) correspond to the six human Vκ gene families. In addition, scaffold 86 includes 24 Vκ segments showing the same transcriptional orientation as the Jκ and Cκ, and 18 Vκ segments showing a reverse transcriptional direction. Three Jκ segments and one Cκ gene on scaffold 86 are displayed in Figure S5. In addition, Vκ segments located on scaffolds 202 and 50 also possess two different transcriptional directions.

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