Background The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a purebred Duroc female pig established using older clone-based sequencing methods was incomplete, and unresolved redundancies, short-range order and orientation errors, and associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0). Both assemblies are of substantially higher (>90-fold) continuity and accuracy than Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read assemblies provide an unprecedented view of the genetic make-up of this important agricultural and biomedical model species. We propose that the improved Duroc assembly (Sscrofa11.1) become the reference genome for genomic research in pigs.

The Y chromosome provides a unique opportunity to study mutational processes within the human genome, decoupled from the confounding eVects of interchromosomal recombination. It has been suggested that the increased density of certain dispersed repeats on the Y could account for the high frequency of causative microdeletions relative to single nucleotide mutations in infertile males. Previously we localised breakpoints of an AZFa microdeletion close to two highly homologous complete human endogenous retroviral sequences (HERV), separated by 700 kb. Here we show, by sequencing across the breakpoint, that the microdeletion occurs in register within a highly homologous segment between the HERVs. Furthermore, we show that recurrent double crossovers have occurred between the HERVs, resulting in the loss of a 1.5 kb insertion from one HERV, an event underlying the first ever Y chromosomal polymorphism described, the 12f2 deletion. This event produces a substantially longer segment of absolute homology and as such may result in increased predisposition to further intrachromosomal recombination. Intrachromosomal crosstalk between these two HERV sequences can thus result in either homogenising sequence conversion or a microdeletion causing male infertility. This represents a major subclass of AZFa deletions. (J Med Genet 2000;37:752-758)

Protocadherins are members of the cadherin superfamily involved in cell-cell interactions critical in the development of the central nervous system. This paper describes the isolation, sequence, and expression analysis of two novel protocadherin genes from the hominid specific Yp11.2/Xq21.3 block of homology between the sex chromosomes. The X-(PCDHX) and Y-linked (PCDHY) genes share 98.1% nucleotide and 98.3% amino acid identity and have an identical gene structure of six exons. The open reading frames of PCDHX and PCDHY encode proteins of 1025 and 1037 amino acids respectively and specify seven extracellular cadherin domains. Small differences in amino acid sequence affect regions that potentially have a large impact on function: thus, the X and Y genes may be differentiated in this respect. Sequence analysis of cDNA clones shows that both the X and Y loci are transcribed. RT-PCR expression analysis of mRNA from a variety of tissues and cell lines has demonstrated that both transcripts are expressed predominantly in the brain, with differential regional expression. From studies in the NTERA pluripotential cell line (which differentiates along neuronal and spermatogenic pathways in response to retinoic acid), it emerges that the X and Y-linked genes are regulated differently. This indicates that PCDHX and PCDHY possess different promoter regions. These findings suggest a role for PCDHX and PCDHY in the brain, consistent with the involvement of protocadherins in segmental brain morphogenesis and function. The implications of Y-linked genes expressed predominantly in tissues and organs other than the testis are considered within the context of the concept of sexual selection.

Pulsed-field gel electrophoresis and "cosmid walking" have been used to establish a molecular map of the human major histocompatibility complex (MIC). We have isolated -230 kilobases (kb) of genomic DNA in overlapping cosmid clones covering the genes for the second and fourth components ofcomplement (C2 and C4, respectively), factor B, and steroid 21-hydroxylase, and --=82 kb of genomic DNA surrounding the genes for the tumor necrosis factors a and (. Single-copy hybridization probes isolated from these cosmid clusters and probes for the known MHC gene loci were hybridized to Southern blots of genomic DNA that had been digested with infrequently cutting restriction endonucleases and separated on pulsed-field gels. The data obtained allowed the construction of a long-range genomic restriction map and indicated that the MHC spans 3800 kb. This map orients the MHC class III gene cluster with respect to the DR subregion; the C2 gene is on the telomeric side of the 21-hydroxylase B gene. In addition we have defined the positions of the genes for the tumor necrosis factors a and .8 in the human MHC. Genes for the a chain of DR and 21-hydroxylase B are separated by at least 300 kb, while the distance between the genes for C2 and tumor necrosis factor a is 390 kb. The HLA-B locus lies -250 kb on the telomeric side of the tumor necrosis factor genes.The human major histocompatibility complex (MHC) is located on the short arm ofchromosome 6 in the distal portion of the 6p21.3 band (1). It consists of three major linked gene clusters. The class I and class II regions each encode highly polymorphic families of cell-surface glycoproteins involved in immune regulation. The class I loci consist of at least 17 highly related genes (2) that include those encoding the classical transplantation antigens (HLA-A, -B, and -C). The class II region (HLA-D) is arranged into four subregions DP, DZ/DO, DQ, and DR, each containing at least one a-and ,8-chain pair of genes (3). The class III region contains the genes encoding the serum complement proteins factor B and the second and fourth components of complement (C2 and C4, respectively), as well as two copies of the steroid 21-hydroxylase (21-OHase) genes that are closely linked to the two C4 loci, C4A and C4B (4, 5). Analysis of recombinant HLA haplotypes in family studies has established that the class I loci are telomeric to the class II genes. Within the class II region the DP subregion maps on the centromeric side of DQ and DR. Located between the HLA-DR and HLA-B loci are the class III genes, but the orientation and distance of these genes relative to the class I and class II genes have not been determined. The possibility that a number of other genes may reside within the MHC was exemplified by the finding that the genes for the tumor necrosis factors a and 3 (TNFa and TNFf, respectively) are linked to the HLA genes (6) and map close to the H-2D region in mouse (7).Clusters of overlapping cosmid clones have been isolated from the subregions of the class II loci (3) and fro...

Little is known as to why a large number of human diseases are influenced by the maijor histocompatibility complex. In some cases, a direct involvement of the products of the polymorphic class I and class H, as well as the less variable products of the class m, genes has been proposed. During characterization of the class HI region for the presence of additional loci, we have located a duplicated locus encoding the major heat shock protein HSP70 between the complement and tumor necrosis factor genes. The HSP70 loci are 12 kilobases apart and lie 92 kilobases telomeric of the C2 gene. As HSP70 proteins have been linked with a protective role during and after cellular stress, and HSP70 analogues are often presented as antigens in bacterial and protozoal infections, this finding may have major implications with regard to the major histocompatibility complex and associated diseases.