Characterization of swine short interspersed repetitive sequences

The sequence and analysis of a Chinese pig genome

Background

The pig is an economically important food source, amounting to approximately 40% of all meat consumed worldwide. Pigs also serve as an important model organism because of their similarity to humans at the anatomical, physiological and genetic level, making them very useful for studying a variety of human diseases. A pig strain of particular interest is the miniature pig, specifically the Wuzhishan pig (WZSP), as it has been extensively inbred. Its high level of homozygosity offers increased ease for selective breeding for specific traits and a more straightforward understanding of the genetic changes that underlie its biological characteristics. WZSP also serves as a promising means for applications in surgery, tissue engineering, and xenotransplantation. Here, we report the sequencing and analysis of an inbreeding WZSP genome.

Results

Our results reveal some unique genomic features, including a relatively high level of homozygosity in the diploid genome, an unusual distribution of heterozygosity, an over-representation of tRNA-derived transposable elements, a small amount of porcine endogenous retrovirus, and a lack of type C retroviruses. In addition, we carried out systematic research on gene evolution, together with a detailed investigation of the counterparts of human drug target genes.

Conclusion

Our results provide the opportunity to more clearly define the genomic character of pig, which could enhance our ability to create more useful pig models.

Nucleotide sequencing analysis of the swine 433-kb genomic segment located between the non-classical and classical SLA class I gene clusters

Genome analysis of the swine leukocyte antigen ( SLA) region is needed to obtain information on the MHC genomic sequence similarities and differences between the swine and human, given the possible use of swine organs for xenotransplantation. Here, the genomic sequences of a 433-kb segment located between the non-classical and classical SLA class I gene clusters were determined and analyzed for gene organization and contents of repetitive sequences. The genomic organization and diversity of this swine non-class I gene region was compared with the orthologous region of the human leukocyte antigen ( HLA) complex. The length of the fully sequenced SLA genomic segment was 433 kb compared with 595 kb in the corresponding HLA class I region. This 162-kb difference in size between the swine and human genomic segments can be explained by indel activity, and the greater variety and density of repetitive sequences within the human MHC. Twenty-one swine genes with strong sequence similarity to the corresponding human genes were identified, with the gene order from the centromere to telomere of HCR - SPR1 - SEEK1 - CDSN - STG - DPCR1 - KIAA1885 - TFIIH - DDR - IER3 - FLOT1 - TUBB - KIAA0170 - NRM - KIAA1949 - DDX16 - FLJ13158 - MRPS18B - FB19 - ABCFI - CAT56. The human SEEK1 and DPCR1 genes are pseudogenes in swine. We conclude that the swine non-class I gene region that we have sequenced is highly conserved and therefore homologous to the corresponding region located between the HLA-C and HLA-E genes in the human.

Wide distribution of short interspersed elements among eukaryotic genomes

Most short interspersed elements (SINEs) in eukaryotic genomes originate from tRNA and have internal promoters for RNA polymerase III. The promoter contains two boxes (A and B) spaced by approximately 33 bp. We used oligonucleotide primers specific to these boxes to detect SINEs in the genomic DNA by polymerase chain reaction (PCR). Appropriate DNA fragments were revealed by PCR in 30 out of 35 eukaryotic species suggesting the wide distribution of SINEs. The PCR products were used for hybridization screening of genomic libraries which resulted in identification of four novel SINE families. The application of this approach is illustrated by discovery of a SINE family in the genome of the bat Myotis daubentoni. Members of this SINE family termed VES have an additional B-like box, a putative polyadenylation signal and RNA polymerase III terminator.

Establishment and characterization of a porcine kidney cell line, FS-L3, which forms unique multicellular domes in serum-free culture

A stable porcine kidney epithelial cell line, FS-L3, was established and maintained in Eagle's minimum essential medium containing 0.295% tryptose phosphate broth, 0.5% Bacto Peptone, and 10 mM N, N-Bis (2-hydroxyethyl)-2-aminoethanesulfonic acid without any serum. The mode of chromosomes is 37 to 38. The FS-L3 cells formed fluid-filled, multicellular, three-dimensional domes on a single monolayer. The number of domes increased markedly after further cultivation. The origin of this cell line was confirmed as porcine by hybridization using PRE-1, which can be detected as a specific sequence in the porcine genome. It was also found that FS-L3 cells were free from possible adventitious viruses and mycoplasmas.

Molecular evidence from retroposons that whales form a clade within even-toed ungulates

The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.

A swine SINE (PRE-1 sequence) distribution in swine-related animal species and its phylogenetic analysis in swine genome

The distribution of PRE-1 sequence (a swine SINE) among the animal species related to Sus scrofa, i.e. Phacochoerus aethiopicus and Tayassu tajacu, was examined by dot-blot analysis using PRE-1 sequences as a probe. This revealed that Phacochoerus aethiopicus and Tayassu tajacu contained PRE-1 sequences, amounts of which in their genomes are almost the same as that in the swine genome, indicating that these species separated after PRE-1 sequences proliferated to diversify in the genome. In order to estimate the time when the PRE-1 started to diversify in the swine genome, PRE-1 sequences were extracted from GenBank DNA database by homology analysis using the PRE-1 consensus sequence as a probe. The 22 PRE-1 sequences obtained were aligned and their phylogenetic relation was calculated by the neighbour-joining method. The result of the calculation combined with the mutation rate of the pseudogenes (r = 4.6 x 10(-9)) indicated that the PRE-1 sequence diversified at least 43.2 million years ago. Taken together, the period of time since the separation of the three species, Sus scrofa, Phacochoerus aethiopicus and Tayassu tajacu, is currently estimated to be less than 43.2 million years.

Accelerated evolution in inhibitor domains of porcine elafin family members

Through the analysis of the porcine gene encoding the elastase inhibitor elafin, we demonstrated that there are at least three closely related members of the elafin family, and their genes have arisen by accelerated evolution. A porcine genomic DNA library was screened with a previously cloned human elafin cDNA probe, and several positive clones were obtained that can be distinguished by a combination of restriction enzymes. Sequence analysis of these clones revealed the presence of three homologous members whose genes, all consisting of three exons and two introns, are almost identical except the exon 2 sequences encoding the inhibitor domain called "WAP motif"; the intron sequences are related to each other with sequence similarities of 93-98%, whereas the exon 2 sequences exhibited only 60-77% similarities among the three members. The extreme divergence in the exon 2 sequences compared to the highly conserved intron sequences may be generated by accelerated mutations confined in a short stretch of the genes following recent duplication events of a single ancestral gene. An RNase protection assay indicated that the messages of the elafin family members are abundantly expressed in the trachea and intestine, suggesting that the most likely selective forces for the accelerated evolution are extrinsic proteinases produced by invasive microorganisms.

Survey on swine SINEs (PRE-1) as candidates for SSCP markers in genetic linkage analysis

Of 310 random cosmid clones, 216 were positive for PRE-1 sequences by Southern hybridization. Thirty nine sub-fragments positive for the PRE-1 sequences were cloned from independent cosmid clones, and sequenced, with 17 complete PRE-1 elements found. Seven PRE-1 loci were amplified by polymerase chain reaction using genomic DNA of 12 unrelated pigs as template. The amplified fragments were then subjected to an analysis of single strand conformation polymorphism, with all the loci being polymorphic.

Porcine SINE-associated microsatellite markers: evidence for new artiodactyl SINEs

Approximately 24% (170/710) of porcine (dG-dT)n.(dC-dA)n microsatellites isolated in our laboratory are associated with a previously described porcine Short Interdispersed Element (SINE) termed PRE-1 SINE. Another 5.6% (40/710) of the microsatellites were adjacent to two previously unidentified SINE sequences, which we have designated ARE-1P (Artiodactyl Repetitive Element-1 Porcine) and ARE-2P. The ARE repeats were also found in bovine microsatellite and genomic sequences in the GenBank database. Genotypic information was obtained from 68.9% of primers where at least one primer sequence was obtained from the PRE-1 SINE and 66.6% of primer pairs designed from the ARE SINEs. The use of primers derived from SINEs significantly increases the number of primer pairs available for genetic linkage studies in swine.

Integrating the porcine physical and linkage map using cosmid-derived markers

An essential part in the development of informative linkage maps is to include genetic markers that have been anchored by physical mapping. Here a set of 18 porcine cosmid-derived genetic markers are reported that have been mapped by linkage analysis, and that also have been physically localized by fluorescence in situ hybridization (FISH). Three different strategies were used to establish polymorphic markers from the cosmid clones. Firstly, dinucleotide microsatellite loci were derived by sequencing cosmid subclones containing (CA)n repeats. Secondly, variable SINE 3' poly(A) tracts (SINEVA) were identified by direct SINE-PCR amplification of cosmid clones. Thirdly, the cosmids were used in Southern blot hybridization to detect restriction fragment length polymorphisms (RFLPs). Compared with the most recent consensus compilation of the porcine gene map, the present assignment of markers to chromosomes 2p, 3, 4, 10, 12q, and 16 represents the first loci mapped to these chromosomes, for which linkage as well as in situ data are now available.

Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons

Using labeled transcripts generated in vitro from squid total genomic DNA as a probe, we isolated and characterized a SINE that is present in the squid genome. The squid SINE appears to be derived from a tRNA(Lys). When the consensus sequences of five different SINEs with a tRNA(Lys)-like structure from distantly related species, including squid, were aligned, we found in the tRNA-unrelated region two sequence motifs that were almost identical among these five SINEs. This observation suggests a common evolutionary origin for these SINEs and/or some function(s) for these motifs. Similar sequences were unexpectedly found to be present in sequences complementary to the U5 regions of several mammalian retroviruses whose primer is a tRNA(Lys). On the basis of these findings, we present a model for the generation of SINEs. We propose that they are derived from a "strong-stop DNA" with a primer tRNA(Lys) that is an intermediate in the reverse transcription of certain retroviruses. Our model suggests that a certain group of SINEs may have been generated by horizontal transmission, although it is not clear whether information was transmitted via a similar retrovirus or via an RNA or DNA of a SINE.

Variable SINE 3' poly(A) sequences: an abundant class of genetic markers in the pig genome

Previous studies on human DNA have shown that the 3' poly(A) tracts of Alu elements may display considerable genetic polymorphism. To explore whether this marker type is generally applicable in mammalian genomes, I analyzed porcine SINEs. A database screening revealed 17 porcine sequences with significant homology to a previously identified pig SINE. The occurrence in the database suggested a SINE frequency of one copy every 12 kb of pig DNA. All SINEs contained a 3' poly(A) tract with an average of 12 uninterrupted adenines. The repetitive regions were analyzed for polymorphism by locus-specific PCR amplification. Allelic length variation (two to five alleles among 10 pigs) was found at 8 out of 10 loci investigated, in most cases probably because of varying number of iterated adenine residues. There was a positive relationship between repeat length and the degree of polymorphism. Stable Mendelian inheritance was documented in 200 meioses each at four loci. The high genomic frequency of SINEs implies that a potentially informative marker may be found near any gene or in any cosmid clone. These SINE 3' poly(A) polymorphisms, termed SINEVA [SINE variable poly(A)s], thus provide an abundant and useful class of genetic marker in mammalian genomes.