The aim of this study was to identify the endogenous retrovirus (ERV) sequences in a bovine genome. We subjected bovine genomic DNA to PCR with degenerate or ovine ERV (OERV) family-specific primers that aimed to amplify the retroviral pro/pol region. Sequence analysis of 113 clones obtained by PCR revealed that 69 were of retroviral origin. On the basis of the OERV classification system, these clones from degenerate PCR could be divided into the ␤3, ␥4, and ␥9 families. PCR with OERV family-specific primers revealed an additional ERV that was classified into the bovine endogenous retrovirus (BERV) ␥7 family. In conclusion, here we report the results of a genome scale study of the BERV. Our study shows that the ERV family expansion in cattle may be somewhat limited, while more diverse family members of ERVs have been reported from other artiodactyls, such as pigs and sheep.The endogenous retroviruses (ERVs) in mammals are classified into the retroviral ␤ (B-/D-type) and ␥ (C-type) genera (3,20). To date, analyses of the ERVs in the genomes of several mammals, including humans, pigs, and sheep, have revealed the presence of multiple different families (1,2,4,5,7,10,11,13,15,16,17,19). For example, in the sheep genome, 12 different ovine ERV (OERV) families were detected. These were classified into three ␤ families (␤1 to ␤3) and nine ␥ families (␥1 to ␥9) (11). However, except for one pro/pol sequence from murine leukemia virus-related retrovirus (MLVRT1-BoEV) (19), no other sequence information regarding ERVs residing in the cattle genome is available.It is known that human ERVs (HERVs) comprise approximately 8% of the human genome (6). Thus, the identification of the ERVs in the bovine genome will be helpful for the annotation of the bovine genome; it will also improve our understanding of ERVs. We searched the bovine genome for the conserved pro/pol nucleotide sequences of ERVs by PCR using degenerate primers, which contain the active site motifs DTGA of protease (PR) protein and YMDD or YVDD of reverse transcriptase (RT) protein (7,10,11,18). Since we found that all ERV clones obtained by degenerate PCR were closely related to three specific OERV families, we also subjected the bovine genome to PCR using OERV family-specific primers.Degenerate PCR amplification of BERV sequences. We isolated the genomic DNA from one Korean Yellow native female cow (Bos taurus) by a simple lysis method (14). The template DNA was subjected to PCR using Taq polymerase and six pairs of degenerate primers previously used for suc-

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We performed RH mapping of 38 transcripts including 7 previously mapped markers selected from full-length enriched cDNA libraries of pigs to determine their locations within the porcine genome and mapped them to 13 chromosomes. The chromosomes with the largest number of mapped transcripts were Sus scrofa chromosome (SSC) 1 with 6, and 5 transcripts were mapped to SSC6 and 9 each. The average retention frequency of the amplified products was 31%, ranging from 74% for SSC9 to 12% for SSC17. The evolutionary conservation of syntenic structures for the chromosomal regions linked to the 38 genes was confirmed using 86 previously mapped genes surrounding them, indicating that the general syntenic structures of chromosomes were conserved among cattle, humans and pigs except for the presence of additional chromosomal breakages in humans and bovine due to an increase in chromosome numbers. The mapping information of 31 new genes can be used to more finely analyze the pig genome or could be used as functional gene markers for porcine QTL mapping.

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Sequences from the clones of full-length enriched cDNA libraries serve as valuable resources for functional genomics related studies, genome annotation and SNP discovery. We analyzed 7,392 high-quality chromatograms (Phred value ≥30) obtained from sequencing the 5' ends of clones derived from full-length enriched cDNA libraries of Korean native pigs including brainstem, liver, cerebellum, neocortex and spleen libraries. In addition, 50,000 EST sequence trace files obtained from GenBank were combined with our sequences to identify cSNPs in silico. The process generated 11,324 contigs, of which 2,895 contigs contained at least one SNP and among them 610 contigs had a minimum of one sequence from Korean native pigs. Of 610 contigs, we randomly selected 262 contigs and performed in silico analysis for the identification of cSNPs. From the results, we identified 1,531 putative coding single nucleotide polymorphisms (cSNPs) and the SNP detection frequency was one SNP per 465 bp. A large-scale sequencing result of clones from full-length enriched cDNA libraries and identified cSNPs will serve as a useful resource to functional genomics related projects such as a pig HapMap project in the near future.