For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.

Leuconostoc citreum is one of the most prevalent lactic acid bacteria during the manufacturing process of kimchi, the best-known Korean traditional dish. We have determined the complete genome sequence of L. citreum KM20. It consists of a 1.80-Mb chromosome and four circular plasmids and reveals genes likely involved in kimchi fermentation and its probiotic effects.Kimchi is a popular fermented Korean food made from a variety of vegetables with assorted, often spicy seasonings such as hot pepper (Capsicum annuum var. annuum). The vegetables of choice for this traditional health food are most commonly a Korean cabbage called baechu or napa cabbage (Brassica rapa subsp. pekinensis) and/or an East Asian giant white radish called mu (Raphanus sativus var. niger). Analyses of the kimchi microflora, both culture based and metagenomic, indicated that Leuconostoc citreum is a dominant microbe during the early and mid-phases of kimchi fermentation (2, 4), and thus it can be useful as a starter culture (2). A strain of L. citreum, designated KM20, that can suppress the growth of pathogenic microorganisms such as Bacillus cereus, Listeria monocytogenes, Micrococcus luteus, Pseudomonas aeruginosa, and Salmonella enterica serovar Typhimurium and is cytotoxic to HT-29 cells was isolated from baechu kimchi fermented at 10°C (data not shown).The complete genome sequence of this strain was determined by the conventional whole-genome shotgun strategy. Genomic libraries harboring 1.2-kb, 2-kb, and 40-kb fragments were constructed, and a total of ϳ56,000 chromatograms (16.3-fold coverage) were produced, either by an ABI 3730xl model genetic analyzer or RISA-384. Basecalling, fragment assembly, contig editing, and primer design were performed using Phred/ Phrap/Consed software packages. Gap closure was carried out by primer walking on gap-spanning clones or PCR products. Physical gaps were closed by combinatorial PCR and custom primer walking on the amplified products. Misassemblies due to repetitive sequences were checked in terms of mate information and were corrected manually using Consed. The final error rate was estimated to be less than 1 bp per 900,000 bp (1.98 bp errors throughout the entire genome). Putative protein-coding genes, predicted by Yacop software (5), were assigned functions by a hierarchical information transfer from the best hits received from searches of public protein databases such as TIGRFAMs, UniProt, COG, KEGG, NCBI-NR, and Pfam, with the aid of AutoFACT (3).The L. citreum KM20 genome is composed of one circular chromosome of 1,796,284 bp (39.0% GϩC content) and four circular plasmids (pLCK1, 38,713 bp; pLCK2, 31,463 bp; pLCK3, 17,971 bp; and pLCK4, 12,183 bp) with slightly lower GϩC contents. The entire genome contains 1,820 proteincoding genes, i.e., 1,702 genes on the chromosome and 49, 36, 29, and 13 genes on each plasmid, respectively, as well as four rRNA operons and 69 tRNA genes on the chromosome. No complete prophages were found, but several phage-related genes were identified, including one sit...

Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.

We sequenced a 208-kb BAC clone spanning the bovine prion protein (PRNP) locus, and compared the genomic structure with that of human. As a result, we determined the precise breakpoint between the two syntenic genomes, located on the 5' UTR of the PRNP gene, and discovered two highly repetitive sequences near the breakpoint. Further analysis demonstrated that the genomic structure of three genes, PRNP, PRND, and RASSF2, within the syntenic region of the bovine genome is highly conserved in order and orientation. The PRNT locus was not found in bovine but is conserved in several primates, including human. Moreover, we confirmed that the bovine RASSF2 is composed of 10 exons, as is the human gene, showing some difference from a previous report. Our findings may provide useful clues for understanding the evolutional process in the PRNP locus and also the mechanism that allows TSE from cattle to infect humans.

We captured the whole human exome by hybridization using synthesized oligonucleotides, based on a high-density microarray design, and we sequenced those captured human exons using high-throughput sequencing on a Genome Sequencer FLX instrument. Of the uniquely mapped reads, 71% fell within target regions, and these corresponded to coverage of 94% of human genes, 87% of exons, and 70% of the total base-pair length of the CCDS set. Our study provides strong evidence for the practical usefulness of this method on a genome-wide scale, showing the resequenced whole human exome database with 501 microRNAs and 307 novel SNPs.