Figure 1.
Fourteen BG genes of the B12 haplotype are present as two singletons (BG0 on chromosome 2, and BG1 in the BF-BL region or classical MHC on chromosome 16) and a cluster of twelve genes in the BG region on chromosome 16 (BG2-BG13, all in the same transcriptional orientation but separated into clusters V and VI by a region containing a kinesin motor protein gene, a C-type lectin gene, and an unassigned gene called LOC4255771).
The genes are depicted with their introns, exons and intragenic regions to scale (except for regions with dotted lines) and in the orientation as typically shown for the chicken MHC and surrounding regions. The BG0 gene was discovered as a cDNA from a CB (B12) chicken caecal tonsil library, but the sequence of the gene is based on the whole genome shotgun sequence (release 2.1), located at positions 100590000–100600000 on chromosome 2.
Figure 2.
Individual BG genes of the B12 haplotype have striking expression patterns, as assessed by RT-PCR from cells and tissues using what were expected to be “universal primers” followed by cloning and sequencing.
At the top, the heading of columns indicates the genes (with their present names along with alternative names previously used) in the same orientation as in Figure 1, and sequences labelled I and II apparently picked up from the B4 haplotype during derivation of CB congenic line chickens from the B12 haplotype of C line chickens. Also shown are the number of independent PCR reactions, and the number of total BG clones sequenced. On the left, the labels for rows describe the isolated cells and tissues from which the RNA was derived, along with separation techniques and treatments that were carried out (as described in Materials and Methods). Values in the table indicate the number of sequences found by RT-PCR, cloning and sequencing for each gene. After the work was well underway, it was realised that the primers were not “universal”, and therefore presence and absence of BG0 and BG2 were determined by specific primers (designated by a number for the sequences, followed by a plus or minus); NT indicates not tested. The coloured boxes indicate the results for presumed haemopoietic (blue) and tissue (green) genes. To be clear, complete separation of these expression patterns in tissues is not expected: all tissues contain blood vessels, some tissues contain tissue-resident macrophages and some tissues contain primary or secondary lymphoid tissue.
Figure 3.
The two cosmid clusters are contiguous with the orientation cluster VI-cluster V, followed by the TRIM and BF-BL regions, as assessed by fibre-FISH and sequence comparison.
A. Fibre-FISH of DNA from Con A-stimulated C-B12 spleen cells (B12 haplotype) with a BF-BL probe (cosmid c4.5 in white), a cluster V probe (cosmid cG43 in red) and a cluster VI probe (cosmid cG24 in green), with the image of red hydridisation shifted above for clarity. Note the single spot of hybridisation at the inner edge of the white hybridisation, which indicates the BG1 gene and correctly orients the BG region. B. Detailed comparison of two BG region probes indicates orientation of the two clusters. Upper panel, on top are the gene sequences for BG2-BG13 (as depicted in Figure 1), and to the left are the sequences for the two probes (cG43 for cluster V in red and cG24 for cluster VI in green), with a dot plot showing sequence identity (dottup program set to 150 nucleotide word size, as described in Materials and Methods). Lower panel, interpretation of hybridisation patterns expected based on the dot plot, compared to two representative examples of actual fibre-FISH, with cG43 in green and cG24 in red.
Figure 4.
Phylogenetic analysis reveals six kinds of BG genes in the B12 haplotype: The two singletons each separately, and the twelve BG genes of the BG region in four groups indicating the presence of hybrid genes.
Left, relationships of whole BG gene sequences (from 500 bp upstream to near the end of the 3′UTR as determined by the predicted polyadenylation site) as assessed by phylogenetic analysis (numbers at nodes indicate boot strap values determined from 1000 replicates). Right, relationships of different regions of BG genes indicated by colour, as determined by separate phylogenetic analyses in Figure 5.
Figure 5.
Phylogenetic analysis of nucleotide sequences for different regions of BG genes indicates separate evolutionary histories, consistent with recombination and/or deletion leading to hybrid genes in the BG region.
The proximal promoters (500 bp upstream of the presumed transcriptional start site) and 5′UTRs fall into two well-supported groups that correlate with hemopoietic (blue) and tissue (green) expression as determined in Figure 2 (the separation of the BG0, BG1 and BG2 are due to short deletions in the 5′UTR, as seen by sequence alignment in Figure 6). In contrast, short branches with generally poor bootstrap support characterise the signal sequences and variable Ig-like regions. Transmembrane regions fall into two groups (as seen by sequence alignment in Figure 7), except for BG0. 3′UTRs fall into two well-supported groups, except for the two singletons, which include sequence of apparently distinct evolutionary origin at the very 3′ end.
Figure 6.
Sequence alignments for the 5'UTR of B12 BG genes, showing the separation into genes expressed in hemopoietic cells and in tissues.
A large gap in genes expressed in hemopoietic cells was presumably created by deletion between two direct repeats indicated by boxes, and smaller gaps are found in the genes expressed in tissues.
Figure 7.
Sequence relationships for the connecting peptide to transmembrane region of B12 BG genes show two groups, those which have histidine and lysine near the N-terminus of the transmembrane region, and those with a leucine and threonine (arrows).
A helical wheel shows that one side of an alpha helix through transmembrane region is primarily composed of larger residues (F, phenylalanine; I, isoleucine; L, leucine; W, tryptophan) along with a smaller residue (S, serine), while the other side is composed of smaller residues (A, alanine; G glycine; T, threonine; V, valine). This arrangement suggests that one side of the helix forms a flattened surface for interaction as a dimer, with the signature charged residue (K, lysine) near the edge of this interaction zone.
Figure 8.
The presence of hybrid BG genes in the B12 haplotype shows no obvious pattern, consistent with a random process of recombination in the centre of the genes.
The 14 BG genes of the B12 haplotype (as in Figure 1) are depicted with coloured boxes illustrating presumed origin (as in Figure 5). See Figure S11 for an alternative view.
Figure 9.
Comparison of cosmid cluster VI from the B12 haplotype with the BQ haplotype from a red junglefowl, showing regions of virtual identity separated by two large indels, one in the middle of the sequences and the other where the red junglefowl haplotype (but not the B12 haplotype) continues into the TRIM region.
Genomic organisation on bottom line is from cluster VI of this paper (accession number KC955130) compared to two sequences from the BQ haplotype, middle line from the WGS sequence assembly (nucleotides 166492–252491 on chromosome 16) and top line from the sequence of a BAC from the same individual chicken (accession number AB268588.1). Note that there exist differences between the WGS and BAC sequences, and further that the WGS assembly has regions of unknown sequence with only approximate length. WGS-NA indicates genes not annotated by ENSEMBL at the time of this analysis.
Figure 10.
The BG regions of six haplotypes are located in the same orientation from the BF-BL region, but vary in size and composition, as assessed by fibre-FISH using probes corresponding to the cosmids cG43 from BG cluster V (red), cG24 from BG cluster VI (green) and c4.5 from BF-BL cluster I (white).
Each panel is representative of several fibre-FISH experiments with genomic DNA from B2 (IS2 cell line), B4 (identical in BF-BL region with B13, UG5 cell line), B12 (Con A-stimulated spleen cells), B15 (TG15 cell line), B19 (IS19 cell line) and B21 (TG21 cell line).