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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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Phylogenetic analysis of the 112 elephant VH genes.A phylogenetic tree of nucleotide sequences of 112 elephant VH segments was constructed. The seven identified VH gene families are labeled with Arabic numerals. The credibility value for each node is shown.
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pone-0016889-g005: Phylogenetic analysis of the 112 elephant VH genes.A phylogenetic tree of nucleotide sequences of 112 elephant VH segments was constructed. The seven identified VH gene families are labeled with Arabic numerals. The credibility value for each node is shown.

Mentions: A total of 112 VH segments were identified in the elephant IgH locus. 51 of them appear to be potentially functional, because they have leader exons, normal open reading frames (ORF), downstream RSSs, and V gene domain (framework regions (FRs) and complementarity determining regions (CDRs)). The remaining 61 segments contain either in-frame stop codons or frameshifts, and are thus designated as pseudogenes. In addition, there are 17 partial segments of about 200 bp in length, which are regarded as truncated VH sequences. There are gaps above 10 kb in the elephant genome among the VH gene segments (Fig. 1), suggesting that there might be more VH segments. To examine the relationships among the elephant germline VH segments, pseudogenes as well as functional genes were used to construct a phylogenetic tree (Fig. 5). The seven identified VH gene families (1, 2, 3, 4, 5, 6, and 7) were confirmed to be homologous with the corresponding human VH gene families. The elephant VH4 family contains the most members (72 VH segments), which could be further divided into three groups (Fig. 5). We chose representative VH sequences from elephant and other mammals, covering almost all VH families identified, to construct phylogenetic trees (Fig. 6). The elephant VH genes clearly fall into the three previously known VH clans.


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)

Phylogenetic analysis of the 112 elephant VH genes.A phylogenetic tree of nucleotide sequences of 112 elephant VH segments was constructed. The seven identified VH gene families are labeled with Arabic numerals. The credibility value for each node is shown.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0016889-g005: Phylogenetic analysis of the 112 elephant VH genes.A phylogenetic tree of nucleotide sequences of 112 elephant VH segments was constructed. The seven identified VH gene families are labeled with Arabic numerals. The credibility value for each node is shown.
Mentions: A total of 112 VH segments were identified in the elephant IgH locus. 51 of them appear to be potentially functional, because they have leader exons, normal open reading frames (ORF), downstream RSSs, and V gene domain (framework regions (FRs) and complementarity determining regions (CDRs)). The remaining 61 segments contain either in-frame stop codons or frameshifts, and are thus designated as pseudogenes. In addition, there are 17 partial segments of about 200 bp in length, which are regarded as truncated VH sequences. There are gaps above 10 kb in the elephant genome among the VH gene segments (Fig. 1), suggesting that there might be more VH segments. To examine the relationships among the elephant germline VH segments, pseudogenes as well as functional genes were used to construct a phylogenetic tree (Fig. 5). The seven identified VH gene families (1, 2, 3, 4, 5, 6, and 7) were confirmed to be homologous with the corresponding human VH gene families. The elephant VH4 family contains the most members (72 VH segments), which could be further divided into three groups (Fig. 5). We chose representative VH sequences from elephant and other mammals, covering almost all VH families identified, to construct phylogenetic trees (Fig. 6). The elephant VH genes clearly fall into the three previously known VH clans.

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