• Korean Journal of Agricultural Science
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• v.43 no.1
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• pp.1-13
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• 2016

Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.

• Journal of Plant Biotechnology
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• v.48 no.3
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• pp.139-147
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• 2021

Since whole-genome duplication (WGD) of diploid Chrysanthemum nankingense and de novo assembly whole-genome of C. seticuspe have been obtained, they have afforded to perceive the diversity evolution and gene discovery in the improved investigation of chrysanthemum breeding. The robust tools of high-throughput identification and analysis of gene function and expression produce their vast importance in chrysanthemum genomics. However, the gigantic genome size and heterozygosity are also mentioned as the major obstacles preventing the chrysanthemum breeding practices and functional genomics analysis. Nonetheless, some of technological contemporaries provide scientific efficient and promising solutions to diminish the drawbacks and investigate the high proficient methods for generous phenotyping data obtaining and system progress in future perspectives. This review provides valuable strategies for a broad overview about the high-throughput identification, and molecular analysis of gene function and expression in chrysanthemum. We also contribute the efficient proposition about specific protocols for considering chrysanthemum genes. In further perspective, the proper high-throughput identification will continue to advance rapidly and advertise the next generation in chrysanthemum breeding.

• Journal of Genetic Medicine
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• v.1 no.1
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• pp.27-31
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• 1997

Steroid 21 hydroxylase deficiency is a major cause of congenital adrenal hyperplasia (CAH) and is caused by genetic impairment of the gene (CYP21B). In the human genome, CYP21B is located within the MHC class III region on the short arm of chromosome 6. Most of the genes in this region are highly polymorphic and crowded. Also the CYP21B gene is accompanied by its pseudogene (CYP21A) and tandemly arranged with two genes of fourth component of complement. This highly complex gene cluster in this area may predispose genetic instability of CYP21, i.e. mutations. In this study, tried to investigate the frequency of duplication and deletion of CYP21 and patterns of the genetic alterations of these genes.We also compared the genetic alteration in normal subjects with those of the CAH patients. The results showed that 15% of the normal korean population have duplication or deletion of CYP21. There was one normal subject with heterozygous deletion of CYP21B. Of the 5 CAH patients examined, 2 were found to show abnormal patterns. One was a large-scale gene conversion and the other a gene conversion associated with deletion involving both CYP21B and C4 locus II gene. Through this study, we carne to the conclusion that the duplication or even deletion of CYP21 and C4 might be quite a common event in the Korean population and these rearrangements must be regarded as polymorphisms. It could contribute to a high incidencs of CAH by providing a genetic pool of instable CYP21.

• Fisheries and Aquatic Sciences
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• v.14 no.4
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• pp.303-310
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• 2011

We characterized a cytoplasmic actin gene locus in greenling Hexagrammos otakii (Scorpaeniformes). Genomic clones isolated from the greenling DNA library contained two homologous cytoplasmic actin gene copies (HObact2.1 and HObact2.2) in a tail-to-head orientation. Their gene structure is characterized by six translated exons and one non-translated exon. Exon-intron organization and the nucleotide sequences of the two actin gene isoforms are very similar. However, only the HObact2.1 isoform contains microsatellite-like, dinucleotide repeats in the 5'-flanking region (named HOms2002) and intron 1 following the non-translated exon 1 (named HOms769). One microsatellite locus (HOms769) was highly polymorphic while the other (HOms2002) was not. Based on bioinformatic analysis, different transcription factor binding motifs are related to stress and immune responses in the two actin isoforms. Semiquantitative and real-time reverse transcription-PCR assays showed that both isoform transcripts were detectable ubiquitously in all the tissues examined. However, the basal expression levels of each isoform varied across tissues. Overall, the two isoforms showed a similar, but not identical, expression pattern. Our data suggest that the cytoplasmic actin genes may be the result of a recent duplication event in the greenling genome, which has not experienced significant subfunctionalization in their housekeeping roles.

• Biomolecules & Therapeutics
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• v.25 no.1
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• pp.57-68
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• 2017

Seven transmembrane receptors (7TMRs), also known as G protein-coupled receptors, are popular targets of drug development, particularly 7TMR systems that are activated by peptide ligands. Although many pharmaceutical drugs have been discovered via conventional bulk analysis techniques the increasing availability of structural and evolutionary data are facilitating change to rational, targeted drug design. This article discusses the appeal of neuropeptide-7TMR systems as drug targets and provides an overview of concepts in the evolution of vertebrate genomes and gene families. Subsequently, methods that use evolutionary concepts and comparative analysis techniques to aid in gene discovery, gene function identification, and novel drug design are provided along with case study examples.

• The KIPS Transactions:PartA
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• v.16A no.3
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• pp.143-152
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• 2009

One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the "gene clusters" on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

• The Plant Pathology Journal
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• v.34 no.5
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• pp.435-444
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• 2018

Receptor-like proteins (RLPs) are involved in plant development and disease resistance. Only some of the RLPs in tomato (Solanum lycopersicum L.) have been functionally characterized though 176 genes encoding RLPs, which have been identified in the tomato genome. To further understand the role of RLPs in tomato, we performed genome-guided classification and transcriptome analysis of these genes. Phylogenic comparisons revealed that the tomato RLP members could be divided into eight subgroups and that the genes evolved independently compared to similar genes in Arabidopsis. Based on location and physical clustering analyses, we conclude that tomato RLPs likely expanded primarily through tandem duplication events. According to tissue specific RNA-seq data, 71 RLPs were expressed in at least one of the following tissues: root, leaf, bud, flower, or fruit. Several genes had expression patterns that were tissue specific. In addition, tomato RLP expression profiles after infection with different pathogens showed distinguish gene regulations according to disease induction and resistance response as well as infection by bacteria and virus. Notably, Some RLPs were highly and/or unique expressed in susceptible tomato to pathogen, suggesting that the RLP could be involved in disease response, possibly as a host-susceptibility factor. Our study could provide an important clues for further investigations into the function of tomato RLPs involved in developmental and response to pathogens.

• Journal of Plant Biotechnology
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• v.2 no.2
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• pp.101-108
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• 2000

The liverwort Pellia borealis is a diploid, monoecious, allopolypliod species (n=18) that as it was postulated, originated after hybridization and duplication of chromosome sets of two cryptic species: Pellia epiphylta-species N (n=9) and Pellia epiphylla-species 5 (n=9). Our recent results have supported the allopolyploid origin of P.borealis. We have shown that the nuclear genome of P.borealis consists of two nuclear genomes: one derived from P.epiphylla-species N and the other from P.epiphylla-species 5. In this paper we show the origin of chloroplast and mitochondrial genomes in an allopolyploid species P.borealis. To our knowledge there is no information concerning the way of mitochondria and chloroplast inheritance in Brophyta. Using an allopolyploid species of p. borealis as a model species we have decided to look into chloroplast and mitochondrial genomes of P.borealis, P.epiphylla-species N and P.epiphylla-species S for nucleotide sequences that would allow us to differentiate between both cryptic species and to identify the origin of organelle genomes in the alloploid species. We have amplified and sequenced a chloroplast $tRNA^{Leu}$ gene (anticodon UAA) containing an intron that has shown to be highly variable in a nucleotide sequence and used for plant population genetics. Unfortunately these sequences were identical in all three liverwort species tested. The analysis of the nucleotide sequence of chloroplast, an intron containing $tRNA^{Gly}$ (anticodon UCC) genes, gave expected results: the intron nucleotide sequence was identical in the case of both P.borealis and P.epiphyllaspecies N, while the sequence obtained from P.epiphyllasperies S was different in several nucleotide positions. These results were confirmed by the nucleotide sequence of another chloroplast molecular marker the chloroplast, an intron-contaning $tRNA^{Lys}$ gene (anticodon UUU). We have also sequenced mitochondrial, an intron-containing $tRNA^{Ser}$ gene (anticodon GCU) in all three liverwort species. In this case we found that, as in the case of the chloroplast genome, P.borealis mitochondrial genome was inherited from P.epiphylla-species N. On the basis of our results we claim that both organelle genomes of P.borealis derived from P.epiphylla-species N.

• Molecules and Cells
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• v.23 no.2
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• pp.182-191
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• 2007

The complete mitochondrial genome of a troglobite millipede Antrokoreana gracilipes (Verhoeff, 1938) (Dipolopoda, Juliformia, Julida) was sequenced and characterized. The genome (14,747 bp) contains 37 genes (2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-encoding genes) and two large non-coding regions (225 bp and 31 bp), as previously reported for two diplopods, Narceus annularus (order Spirobolida) and Thyropygus sp. (order Spirostreptida). The A + T content of the genome is 62.1%, and four tRNAs ($tRNA^{Ser(AGN)}$, $tRNA^{Cys}$, $tRNA^{Ile}$ and $tRNA^{Met}$) have unusual and unstable secondary structures. Whereas Narceus and Thyropygus have identical gene arrangements, the $tRNA^{Thr}$ and $tRNA^{Trp}$ of Antrokoreana differ from them in their orientations and/or positions. This suggests that the Spirobolida and Spirostreptida are more closely related to each other than to the Dipolopoda. Three scenarios are proposed to account for the unique gene arrangement of Antrokoreana. The data also imply that the Duplication and Nonrandom Loss (DNL) model is applicable to the order Julida. Bayesian inference (BI) and maximum likelihood (ML) analyses using amino acid sequences deduced from the 12 mitochondrial protein-encoding genes (excluding ATP8) support the view that the three juliformian members are monophyletic (BI 100%; ML 100%), that Thyropygus (Spirostreptida) and Narceus (Spirobolida) are clustered together (BI 100%; ML 83%), and that Antrokoreana (Julida) is a sister of the two. However, due to conflict with previous reports using cladistic approaches based on morphological characteristics, further studies are needed to confirm the close relationship between Spirostreptida and Spirobolida.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.28-28
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• 2022

This paper presents the first genome assemblies of Philippine mangoes that provide valuable reference for varietal improvement and genomic studies on mango and related fruit crops. WE sequenced whole genomes of3 species, Mangifera odorata (Huani), Mangifera altissima (Paho), and Mangifera indica 'Carabao' (Sweet Elena). 'Carabao' is the major export variety of the Philippines; Paho is identified as vulnerable by the IUCN Red List of Threatened Species; Huani has fruit sap acrid which is the primary defense mechanism against insects and birds. We used Falcon, a diploid aware -de novo assembler to assemble SMRT generated long-read sequences. Falcon-unzip was employed to phase the output assembly producing larger contig sets (primary contigs) and shorter contigs corresponding to haplotypes (haplotigs). Assembly statistics were generated by comparing the assembly to a reference genome, Tommy Atkins, using Quality Assessment Tool (QUAST). Moreover, the extent of duplication and completeness of gene content was measured using Benchmarking Universal Single-Copy Orthologs (BUSCO). Draft assemblies with high duplications were processed using Purge Haplotigs and Purge Dups to lessen duplications with minimal impact on genome completeness. De novo assemblies of Huani, Paho and 'Carabao' were then generated with primary contig sizes of 463.64 Mb, 508.95 Mb and 401.51 Mb respectively. These draft assemblies of Huani, Paho and 'Carabao' showed 96.90%, 95.17% and 99.07% complete BUSCOs respectively which is comparable to 'Tommy Atkins' genome (98.6%). Using two mango transcriptome data (pooled RNA-seq from different mango varieties and tissues), 91-96% or 24-30 million reads were successfully mapped back for each generated assembly indicating high degree of completeness. The results obtained demonstrated the highly contiguous, phased, and near complete genome assembly of three Philippine mango species for structural and functional annotation of gene units, especially those with economic importance.