Limits...
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.

Show MeSH
Alignment of nucleotide sequences of seven elephant germline DH families.Seven families representing elephant 87 germline DH segments are aligned. Nucleotides that are the same as the top segment, DH34, are indicated with dots. Dashes mean gaps introduced to make the alignment. DH57 and 62, DH50 and 38, DH74 and 66, and DH47 and 36 are shadowed as they share identical sequences. Coding regions of DH segments are separated from recombination signal sequences (RSSs) (nonamer, spacer, and heptamer).
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3045440&req=5

pone-0016889-g007: Alignment of nucleotide sequences of seven elephant germline DH families.Seven families representing elephant 87 germline DH segments are aligned. Nucleotides that are the same as the top segment, DH34, are indicated with dots. Dashes mean gaps introduced to make the alignment. DH57 and 62, DH50 and 38, DH74 and 66, and DH47 and 36 are shadowed as they share identical sequences. Coding regions of DH segments are separated from recombination signal sequences (RSSs) (nonamer, spacer, and heptamer).

Mentions: In the elephant IgH locus, 87 DH segments were identified and are presented in Figure S4 (S4-1∼S4-10). It should be noted that there might be more DH segments because of the existence of sequence gaps. Except for DH76, which has a 10 bp spacer, all the DH segments are flanked by characteristic heptamers and nonamers separated by 12-bp spacers. The potential coding regions of DH segments are 10–37 bp in length (Figure S4, S4-1∼S4-10). It has been suggested that coding regions of DH segments of humans can be described by the characteristics of their amino acids [57]. Inspection showed that a great number of polar/hydrophobic amino acids or stop codons occur widely in elephant DH coding regions (data not shown). In humans and mice, the germline DH segments can be classified into families based on the extent of sequence similarity [58], [59]. Analysis of nucleotide similarity in the coding regions and flanking RSSs indicated that the 87 elephant DH segments could be divided into seven families. Members within the same family share at least 70% nucleotide identity (data not shown), while some members in a family have completely identical sequences (these are shadowed in Fig. 7). We present the sequence alignment of the seven families in Fig. 7, which shows that each family contains characteristic sequence intervals that are distinct from other families.


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)

Alignment of nucleotide sequences of seven elephant germline DH families.Seven families representing elephant 87 germline DH segments are aligned. Nucleotides that are the same as the top segment, DH34, are indicated with dots. Dashes mean gaps introduced to make the alignment. DH57 and 62, DH50 and 38, DH74 and 66, and DH47 and 36 are shadowed as they share identical sequences. Coding regions of DH segments are separated from recombination signal sequences (RSSs) (nonamer, spacer, and heptamer).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0016889-g007: Alignment of nucleotide sequences of seven elephant germline DH families.Seven families representing elephant 87 germline DH segments are aligned. Nucleotides that are the same as the top segment, DH34, are indicated with dots. Dashes mean gaps introduced to make the alignment. DH57 and 62, DH50 and 38, DH74 and 66, and DH47 and 36 are shadowed as they share identical sequences. Coding regions of DH segments are separated from recombination signal sequences (RSSs) (nonamer, spacer, and heptamer).
Mentions: In the elephant IgH locus, 87 DH segments were identified and are presented in Figure S4 (S4-1∼S4-10). It should be noted that there might be more DH segments because of the existence of sequence gaps. Except for DH76, which has a 10 bp spacer, all the DH segments are flanked by characteristic heptamers and nonamers separated by 12-bp spacers. The potential coding regions of DH segments are 10–37 bp in length (Figure S4, S4-1∼S4-10). It has been suggested that coding regions of DH segments of humans can be described by the characteristics of their amino acids [57]. Inspection showed that a great number of polar/hydrophobic amino acids or stop codons occur widely in elephant DH coding regions (data not shown). In humans and mice, the germline DH segments can be classified into families based on the extent of sequence similarity [58], [59]. Analysis of nucleotide similarity in the coding regions and flanking RSSs indicated that the 87 elephant DH segments could be divided into seven families. Members within the same family share at least 70% nucleotide identity (data not shown), while some members in a family have completely identical sequences (these are shadowed in Fig. 7). We present the sequence alignment of the seven families in Fig. 7, which shows that each family contains characteristic sequence intervals that are distinct from other families.

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