해조류에는 항산화, 항염증에 효과적인 다양한 생리 활성 화합물이 풍부하게 함유되어 있으며, 장에 유익한 섬유질이 다량 포함되어 있다. 이러한 특징들로 인하여 해조류는 기능성 식품 제조뿐만 아니라, 약리학, 의학적 응용 분야 등 다양한 산업 분야에서 중요한 자원으로 인식되고 있으며, 특히 해조류 발효 기술은 이러한 산업들에 다양한 방법으로 활용될 수 있다. 해조류는 새로운 생리 활성 화합물의 중요한 공급원으로 인정받고 있지만, 육상 식물 바이오매스에 비해 발전이 부족한 상태이다. 해조류를 산업적으로 사용하기 위해 이용되는 해조류 화합물 추출 기술에는 세포벽 처리의 어려움으로 인해 수율이 낮거나 비용 효율성이 떨어지는 등의 문제가 있으나, 최근에는 유산균과 효모종의 미생물을 이용하여 새로운 해조류 발효 제품을 만들어내는 기술이 발전하고 있다. 이러한 해조류 발효 제품은 기능성 식품 및 건강기능식품 시장에서 중요한 역할을 할 수 있으며, 소비자들에게 더 매력적인 제품을 제공할 수 있다. 해조류 발효는 해양 자원의 부가가치를 높이는 중요한 방법 중 하나로, 이를 통해 폴리페놀 함량, 항산화 활성, 생리활성 화합물의 생체 이용률을 증가시키고, 해조류의 감칠맛을 개선하여 소비자들의 만족도를 높일 수 있다. 또한, 해조류 발효는 대량의 양식 바이오매스를 보존할 수 있는 지속 가능한 가공 방법이며, 독성 화학 물질을 생략하여 자연스러운 추출 방법을 제공할 수 있다. 해조류 발효 기술은 아직 많은 연구가 필요하지만, 해조류 산업의 확대와 함께 미래에 매우 중요한 역할을 할 것으로 전망된다.

The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454 and Illumina/Solexa systems, along with bioinformation analysis technologies of whole-genome de novoassembly, expression profiling, DNA variation discovery, and genotyping. One of the advantages of the NGS systems is the cost-effectiveness to obtain the result of high-throughput DNA sequencing for genome, RNAnome, and miRNAnome studies. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data and for resequencing the samples with a reference genome DNA sequence. To construct high-quality contig consensus sequences, each DNA fragment read length is important to obtain de novo assembly with long reading sequences of the Roche/454 system. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2× and 30×depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly, as hybrid assembly for novel genome sequencing would be cost-effective. In some cases, Illumina/Solexa data are used to construct scaffolds through de novo assembly with high coverage depth and large diverse fragment mate paired-end information,even though they are already participating in assembly and have made many contigs. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. MAQ and CLC software are useful to both single nucleotide polymorphism discovery and genotyping through a comparison of resequencing data to a reference genome. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples, such as control and exposed tissue. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20× and 50× coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively,is effective to create novel expressed reference sequences. However, only an average 30× coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference expressed sequence tag sequence. In an in silicomethod, conserved miRNA and novel miRNA discovery is available on massive miRNAnome data in any species. Particularly, the discovered target genes of miRNA could be robust to approach genome biology study.

To characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

The NGS technologies of genome DNA structure, expression profiling and epigenome elements have been used widely as approaches in the expertise of genome biology and genetics. The application to genome study has been particularly developed with the introduction of the next-generation DNA sequencer (NGS) Roche/454, Illumina/Solexa and PacBio systems along with bioinformation analysis technologies of whole-genome de novo assembly, expression profiling, DNA variation discovery, and genotyping. One of the advantages of the NGS systems is the cost-effectiveness to obtain the result of high-throughput DNA sequencing for genome, RNAnome, and miRNAnome studies. Both massive whole-genome shotgun paired-end sequencing and mate paired-end sequencing data are important steps for constructing de novo assembly of novel genome sequencing data and for resequencing the samples with a reference genome DNA sequence. To construct high-quality contig consensus sequences, each DNA fragment read length is important to obtain de novo assembly with long reading sequences of the Roche/454 and PacBio systems. It is necessary to have DNA sequence information from a multiplatform NGS with at least 2x and 30x depth sequence of genome coverage using Roche/454 and Illumina/Solexa, respectively, for effective an way of de novo assembly, as hybrid assembly for novel genome sequencing would be cost-effective. In some cases, Illumina/Solexa data are used to construct scaffolds through de novo assembly with high coverage depth and large diverse fragment mate paired-end information, even though they are already participating in assembly and have made many contigs. Massive short-length reading data from the Illumina/Solexa system is enough to discover DNA variation, resulting in reducing the cost of DNA sequencing. MAQ and CLC software are useful to both SNP discovery and genotyping through a comparison of resequencing data to a reference genome. Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples, such as control and exposed tissue. The long read sequence data of PacBio are more powerful to find full length cDNA sequence through de novo assembly in any whole-genome sequenced species. An average 30x coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference EST sequence. In an in silico method, conserved miRNA and novel miRNA discovery is available on massive miRNAnome data in any species. Particularly, the discovered target genes of miRNA could be robust to approach genome biology study.

Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yielding rice variety derived from a three-way cross between indica and japonica. Tongil contributed to staple food self-sufficiency of Korea, an achievement that was termed the ‘Korean Green Revolution’. In this study, we analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated from Tongil rice. Three parental accessions, two indica and one japonica types, of Tongil rice were also sequenced for approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare; the average SNP frequency of Tongil was 5.77 per kb. Genome composition based on the SNP data by comparing with the three parental genome sequences on sliding window of Nipponbare genome sequence revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent, different from the theoretical expectation in a three-way cross, i.e., 75% indica and 25% japonica parental origins on average. Copy number of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, yield-related QTLs or gene locations, and polymorphic transposon insertions were also comparatively analyzed between Tongil and parents using sequence-based tools. The results indicated that each genetic factor was transferred from parents into Tongil in proportion to the whole-genome composition. The Tongil rice is the first successful superior cultivar derived from indica × japonica hybridization in Korea. Defining of genome structure demonstrates that the Tongil genome is composed mostly of the indica genome with a small proportion of japonica genome introgression. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.

Whole-genome expression profile data are useful to approach genome system biology with quantification of expressed RNAs from a whole-genome transcriptome, depending on the tissue samples, such as control and exposed tissue. The hybrid mRNA sequences from Rohce/454 and Illumina/Solexa are more powerful to find novel genes through de novo assembly in any whole-genome sequenced species. The 20x and 50x coverage of the estimated transcriptome sequences using Roche/454 and Illumina/Solexa, respectively, is effective to create novel expressed reference sequences. However, only an average 30x coverage of a transcriptome with short read sequences of Illumina/Solexa is enough to check expression quantification, compared to the reference EST sequence. In any NGS application, the transcriptome expression information would be more useful than complete genome information research with the lowest sequencing budget for biologists to better understand gene regulation of related genetic phenotypes with the in silico method. The study of target genes related to specific traits including disease resists is available pathway analysis through comparing RNA sequencing among the genotypes.

Resequencing data is actively used for searching QTL or analyzing genetic diversity in the crops. However, the complexity of genome, caused by genome duplication, limits the utility of genome-wide association studies and linkage analyses to identify genes that regulate agronomically valuable traits. Here, we propose a comparative genomics approach based on core or common variation-based recombination blocks (CRB) using single nucleotide variation (SNV) density information. We found that the soybean genomes are assembled with long and distinct CRBs as large as 10Mb. CRB-based comparative genomics enabled us to accurately identify recombination blocks at the whole-chromosome level. We identified the Ih locus that determines the yellow hilum color in soybeans using CRB-based mapping with representative indel markers. These results suggest that the CRB-based comparison method is a promising platform for molecular breeding and map-based cloning.