The major histocompatibility complex (Mhc) class IIB region has greater genomic structural flexibility and diversity in the quail than the chicken

Abstract

Background: The quail and chicken major histocompatibility complex (Mhc) genomic regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated class I, class IIB, natural killer (NK)-receptor-like, lectin-like and BG genes. Therefore, the elucidation of genetic factors that contribute to the greater Mhc diversity in the quail would help to establish it as a model experimental animal in the investigation of avian Mhc associated diseases. AIMS AND APPROACHES: The main aim here was to characterize the genetic and genomic features of the transcribed major quail MhcIIB (CojaIIB) region that is located between the Tapasin and BRD2 genes, and to compare our findings to the available information for the chicken MhcIIB (BLB). We used four approaches in the study of the quail MhcIIB region, (1) haplotype analyses with polymorphic loci, (2) cloning and sequencing of the RT-PCR CojaIIB products from individuals with different haplotypes, (3) genomic sequencing of the CojaIIB region from the individuals with the different haplotypes, and (4) phylogenetic and duplication analysis to explain the variability of the region between the quail and the chicken.

Results: Our results show that the Tapasin-BRD2 segment of the quail Mhc is highly variable in length and in gene transcription intensity and content. Haplotypic sequences were found to vary in length between 4 to 11 kb. Tapasin-BRD2 segments contain one or two major transcribed CojaIIBs that were probably generated by segmental duplications involving c-type lectin-like genes and NK receptor-like genes, gene fusions between two CojaIIBs and transpositions between the major and minor CojaIIB segments. The relative evolutionary speed for generating the MhcIIBs genomic structures from the ancestral BLB2 was estimated to be two times faster in the quail than in the chicken after their separation from a common ancestor. Four types of genomic rearrangement elements (GRE), composed of simple tandem repeats (STR), were identified in the MhcIIB genomic segment located between the Tapasin-BRD2 genes. The GREs have many more STR numbers in the quail than in the chicken that displays strong linkage disequilibrium.

Conclusion: This study suggests that the Mhc classIIB region has a flexible genomic structure generated by rearrangement elements and rapid SNP accumulation probably as a consequence of the quail adapting to environmental conditions and pathogens during its migratory history after its divergence from the chicken.

Figure 1

Comparative gene map of quail and chicken Mhc region and locations of the genetic markers PM1 to PM3. The map shows the comparison of the 180 kb Coja haplotype 1 sequence (AB078884: Shiina et al 2004) and the 92 kb chicken B12 haplotype sequence (AL023516: Kaufman et al 1999). Black and gray boxes indicate the Mhc class I and class IIB loci respectively. White boxes indicate other genes. The labeled vertical arrows indicate the locations of the newly designated genetic markers PM1 – PM3.

Figure 2

Phylogenetic tree of the quail and chicken transcribed MhcIIBs. The dendrogram was constructed from the nucleotide sequences of the β1 extracellular domain regions (exon 2) (270 nucleotides in length) of MhcIIB genes for the 16 CojaIIBs shown in figure S1 the chicken haplotypic BLB sequences on B2 B4 B12 B14 B15 B19 and B21 (AJ248576 AJ248583 AJ248572 AJ248581 AJ248585 AJ248577 AJ248584 AJ248579 AJ248580 AJ248582 AJ248574 AJ248586 AJ248575 and AJ248573) and HLA-DRB1 (AF142457). The HLA-DRB1 sequence used as a species outlier roots the tree. Values near the branch-points of the tree indicate the bootstrap values. Bold letters indicate major transcribed CojaIIBs and BLBs.

Figure 3

Genomic structures of the major transcribed MhcIIB segments in the quail and chicken. The map shows the comparison of the major transcribed MhcIIB segments on five Coja haplotypic sequences (HT1 HT2 HT3 HT4 and HT5) and the chicken B12 haplotype sequence. Gray striped and black boxes indicate the major transcribed MhcIIB moderately transcribed MhcIIB and non-transcribed MhcIIB respectively. White boxes indicate other genes. The numbers in parenthesis are the GenBank accession numbers. The white oval indicates TB1 and the black oval indicates the location of TB2-1 TB2-2 and TB3.

Figure 4

Gene duplication models inferred from the reconstructed phylogenetic trees. The labeled arrows indicate the speciation and gene duplication events for the chicken (C) and quail (Q) lineages. Dotted arrows indicate the evolutionary process for the origin of HT2 and HT5. Gray backgrounds indicate quail and chicken MHCIIB structures at the present-day.