Seong-Hyeuk Nam

GarlicESTdb: an online database and mining tool for garlic EST sequences

BackgroundAllium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.DescriptionGarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The GarlicESTdb web application is freely available at http://garlicdb.kribb.re.kr.ConclusionGarlicESTdb is the first incorporated online information database of EST sequences isolated from garlic that can be freely accessed and downloaded. It has many useful features for interactive mining of EST contigs and datasets from each library, including curation of annotated information, expression profiling, information retrieval, and summary of statistics of functional annotation. Consequently, the development of GarlicESTdb will provide a crucial contribution to biologists for data-mining and more efficient experimental studies.

Complete genome sequence of Halalkalicoccus jeotgali B3(T), an extremely halophilic archaeon.

Halalkalicoccus jeotgali B3(T), isolated from salt-fermented seafood from South Korea, is an extremely halophilic archaeon belonging to the family Halobacteriaceae. Here, we present the complete genome sequence of the type strain H. jeotgali B3(T) (3,698,650 bp, with a G+C content of 62.5%), which consists of one chromosome and six plasmids. This is the first complete genome sequence of the Halalkalicoccus species.

Novel mechanism of conjoined gene formation in the human genome

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.

Genome Sequence of Weissella cibaria KACC 11862

Weissella cibaria KACC 11862 is a Gram-positive, heterofermentative, Leuconostoc-like lactic acid bacterium that is widely distributed in Korean traditional foods such as kimchi. Here we report the draft genome sequence of the type strain, W. cibaria KACC 11862 (1,599 known genes, 80 RNA genes), which consists of 72 large contigs (>100 bp in size).

PESTAS: a web server for EST analysis and sequence mining

SUMMARY We have developed a web server for the high-throughput annotation of expressed sequence tags (ESTs) called pipeline for EST analysis service (PESTAS). PESTAS processes entire datasets with an automated pipeline of 13 analytic services, then deposits the data into the MySQL database and transforms it into three kinds of reports: preprocessing, assembling and annotation. All annotated information is provided to the scientist and can be downloaded through a web browser. To get more relevant functional annotation results, a curation function was introduced with which biologists can easily change the best-hit annotation information. We included a gene chip module that detects gene expression differences between libraries by comparing accession number counts from BLAST search results. PESTAS also provides access to the pathway information of KEGG, which is useful for mapping the relationships among networks of annotated enzymes, and is especially valuable for those researchers interested in biological pathways. AVAILABILITY PESTAS is available at http://pestas.kribb.re.kr/.

Genome Sequence of Lactobacillus farciminis KCTC 3681

Lactobacillus farciminis is one of the most prevalent lactic acid bacterial species present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of the type strain Lactobacillus farciminis KCTC 3681 (2,498,309 bp, with a G+C content of 36.4%), which consists of 5 scaffolds.

Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.

Although pioneering sequencing projects have shed light on the boxer and poodle genomes, a number of challenges need to be met before the sequencing and annotation of the dog genome can be considered complete. Here, we present the DNA sequence of the Jindo dog genome, sequenced to 45-fold average coverage using Illumina massively parallel sequencing technology. A comparison of the sequence to the reference boxer genome led to the identification of 4 675 437 single nucleotide polymorphisms (SNPs, including 3 346 058 novel SNPs), 71 642 indels and 8131 structural variations. Of these, 339 non-synonymous SNPs and 3 indels are located within coding sequences (CDS). In particular, 3 non-synonymous SNPs and a 26-bp deletion occur in the TCOF1 locus, implying that the difference observed in cranial facial morphology between Jindo and boxer dogs might be influenced by those variations. Through the annotation of the Jindo olfactory receptor gene family, we found 2 unique olfactory receptor genes and 236 olfactory receptor genes harbouring non-synonymous homozygous SNPs that are likely to affect smelling capability. In addition, we determined the DNA sequence of the Jindo dog mitochondrial genome and identified Jindo dog-specific mtDNA genotypes. This Jindo genome data upgrade our understanding of dog genomic architecture and will be a very valuable resource for investigating not only dog genetics and genomics but also human and dog disease genetics and comparative genomics.

Genome Sequence of Leuconostoc pseudomesenteroides KCTC 3652

We announce the genome sequence of one of the most prevalent lactic acid bacteria present during the manufacturing process of cane juice, the type strain Leuconostoc pseudomesenteroides KCTC 3652 (3,244,985 bp, with a G+C content of 38.3%), which consists of 1,160 large contigs (>100 bp in size). All of the contigs were assembled by the Newbler Assembler 2.3 software program (454 Life Sciences).

Draft Genome Sequence of Lactobacillus zeae KCTC 3804

We announce the draft genome sequence of the type strain Lactobacillus zeae KCTC 3804 (3,110,326 bp, with a G+C content of 47.8%), which is one of the most prevalent lactic acid bacteria present during the processing of raw cows milk. The genome consists of 113 large contigs (>100 bp). All of the contigs were assembled by Newbler Assembler 2.3 (454 Life Science).

Genome sequence of Leuconostoc argentinum KCTC 3773.

Leuconostoc argentinum is one of the most prevalent lactic acid bacteria present during the manufacturing process of kimchi, the best-known traditional Korean dish. Here, we present the draft genome sequence of type strain KCTC 3773 of Leuconostoc argentinum (1,720,683 bp, with a G+C content of 42.9%), which consists of 98 large contigs (>100 bp in size).