Wiley Acta Medica Okayama 1356-9597 31 5 2026 Transforming Life Science Through Chromosome�]Level Genome Assemblies e70145 EN Tetsuo Kon Department of Neurosciences and Developmental Biology, University of Vienna Kosuke Kataoka Graduate School of Engineering, Tokyo University of Agriculture and Technology Yi�]Jyun Luo Biodiversity Research Center, Academia Sinica Johannes Nicolaus Wibisana Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University Kouhei Toga Laboratory of BioDX, PtBio Co�]Creation Research Center, Genome Editing Innovation Center, Hiroshima University Narumi Uno Laboratory of Bioengineering, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences Yuki Monden Graduate School of Environmental, Life, Natural Science, and Technology, Okayama University Mayuko Hamada Ushimado Marine Institute, Okayama University Advances in long-read sequencing and Hi–C scaffolding have made chromosome-level genome assembly increasingly accessible to individual laboratories, shifting genome research from large consortium-led projects toward investigator-driven studies across diverse taxa. This transition allows researchers to select organisms based on biological questions rather than the prior availability of genomic resources. In this review, we summarize the core experimental and computational steps for generating, evaluating, and annotating chromosome-level assemblies, and examine how they have advanced research in non-model organisms and genetically complex systems. Representative case studies illustrate four major contributions: resolving structural variation and lineage-specific genome architecture, linking genome organization to phenotypic innovation and plasticity, reconstructing deep chromosome evolution and macrosynteny, and distinguishing homologous and homoeologous chromosomes in polyploid genomes. These examples show that chromosome-level assemblies provide more than complete reference sequences. They establish a continuous genomic coordinate system through which genes, regulatory elements, transposable element insertions, sequence variants, and cellular states can be interpreted within broader chromosomal, population, and evolutionary contexts. We describe this integrative perspective as �gglocal biology.�h Future progress will require pangenomic, population-scale, and haplotype-resolved resources integrated with multi-omics and functional analyses. Collectively, chromosome-level genomics is reshaping life science by embedding molecular functions within chromosomal and evolutionary contexts. No potential conflict of interest relevant to this article was reported.

Japanese Society of Breeding Acta Medica Okayama 1344-7610 75 3 2025 Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon, Cucumis melo L. 168 178 EN Katsunori Tanaka Faculty of Agriculture and Life Science, Hirosaki University Gentaro Shigita Graduate School of Environmental and Life Science, Okayama University Tran Phuong Dung Graduate School of Environmental and Life Science, Okayama University Phan Thi Phuong Nhi University of Agriculture and Forestry, Hue University Mami Takahashi Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Hidetaka Nishida Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Ryuji Ishikawa Faculty of Agriculture and Life Science, Hirosaki University Kenji Kato Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp. melo and the East Asian subsp. agrestis were characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence. In South Asia, in addition to the Europe/US and East Asian types, recombinant types between the two types were detected and accounted for 34.8% of South Asian melon. The finding of such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types. As to Momordica popular in South Asia, seed length was intermediate between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp. agrestis of the Ic type proved to be endemic to Africa, indicating its African origin. No potential conflict of interest relevant to this article was reported.

Oxford University Press (OUP) Acta Medica Okayama 0305-7364 135 7 2025 Molecular polymorphisms of the nuclear and chloroplast genomes among African melon germplasms reveal abundant and unique genetic diversity, especially in Sudan 1329 1343 EN Odirichi Nnennaya Imoh Graduate School of Environmental and Life Science, Okayama University Gentaro Shigita Graduate School of Environmental and Life Science, Okayama University Mitsuhiro Sugiyama Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) Tran Phuong Dung Graduate School of Environmental and Life Science, Okayama University Katsunori Tanaka Faculty of Agriculture and Life Science, Hirosaki University Mami Takahashi Graduate School of Environmental and Life Science, Okayama University Kazusa Nishimura Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Yuki Monden Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Hidetaka Nishida Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Mashaer Goda Plant Genetic Resources Conservation and Research Center, Agricultural Research Corporation Michel Pitrat INRAE, UR1052, Génétique et amélioration des fruits et légumes Kenji Kato Graduate School of Environmental, Life, Natural Science and Technology, Okayama University Background and Aims Africa is rich in wild species of Cucumis and is considered one of the places of origin of melon. However, our knowledge of African melon is limited, and genetic studies using melon germplasms with wide geographical coverage are required. Here, we analysed the genetic structure of African melons, with emphasis on Sudan.<br> Methods Ninety-seven accessions of African melon were examined along with 77 reference accessions representing Asian melon and major horticultural groups. Molecular polymorphisms in the nuclear and chloroplast genomes were investigated using 12 RAPD, 7 SSR and 3 SNP markers. Horticultural traits, including seed size, were measured for 46 accessions, mainly from Sudan.<br> Key Results African melons were divided into large and small seed-types based on seed length: large seed-type from Northern Africa and small seed-type from Western and Southern Africa. Both seed types are common in Sudan. Molecular genetic diversity in these geographical populations was as high as in India, the Asian centre of melon domestication. Large seed-types from Northern Africa were assigned to Pop4 by structure analysis and had Ib cytoplasm in common with Cantalupensis, Inodorus and Flexuosus. Small seed-types were highly diversified and geographically differentiated; specifically, Pop1 with Ia cytoplasm in Southern Africa and South Asia, Pop2 with Ia in East Asia, including Conomon and Makuwa, and Pop3 with Ia or Ic in Africa. Sudanese small seed-types were grouped in Pop3, while their cytoplasm type was a mixture of Ia and Ic. Sudanese Tibish had Ic cytoplasm, which was unique in Africa, common in Western Africa and Sudan, and also found in wild or feral types.<br> Conclusions Melon of Ic lineage, including Tibish, originated from wild melon in the �ewestern Sudan region�f, and independently of melon with Ia or Ib cytoplasm, which originated in Asia. This clearly indicates the polyphyletic origin of melon. No potential conflict of interest relevant to this article was reported.

Springer Science and Business Media LLC Acta Medica Okayama 0925-9864 71 3 2023 Analysis of genetic diversity and population structure in Cambodian melon landraces using molecular markers 1067 1083 EN Pervin Mst Naznin Graduate School of Environmental and Life Science, Okayama University Odirichi Nnennaya Imoh Graduate School of Environmental and Life Science, Okayama University Katsunori Tanaka Faculty of Agriculture and Life Science, Hirosaki University Ouch Sreynech Cambodian Agricultural Research and Development Institute Gentaro Shigita Department of Life Science Systems, Technical University of Munich Yon Sophea Cambodian Agricultural Research and Development Institute Sakhan Sophany Cambodian Agricultural Research and Development Institute Ouk Makara Plant Breeder, Retired Director of the Cambodian Agricultural Research and Development Institute Norihiko Tomooka Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO) Yuki Monden Graduate School of Environmental and Life Science, Okayama University Hidetaka Nishida Graduate School of Environmental and Life Science, Okayama University Kenji Kato Graduate School of Environmental and Life Science, Okayama University Genetic diversity of Cambodian melons was evaluated by the analysis of 12 random amplified polymorphic DNA (RAPD) and 7 simple sequence repeat (SSR) markers using 62 accessions of melon landraces and compared with 231 accessions from other areas for genetic characterization of Cambodian melons. Among 62 accessions, 56 accessions were morphologically classified as small-seed type with seed lengths shorter than 9 mm, as in the horticultural groups Conomon and Makuwa. Gene diversity of Cambodian melons was 0.228, which was equivalent to those of the groups Conomon and Makuwa and smaller than those of Vietnamese and Central Asian landraces. A phylogenetic tree constructed from a genetic distance matrix classified 293 accessions into three major clusters. Small-seed type accessions from East and Southeast Asia formed clusters I and II, which were distantly related with cluster III consisting of large-seed type melon from other areas. All Cambodian melons belonged to cluster I (except three accessions) along with those from Thailand, Myanmar, Yunnan (China), and Vietnam (�gDua thom�h in the northwest), thus indicating genetic similarity in these areas. In addition, the Cambodian melons were not differentiated among geographical populations. Conomon and Makuwa were classified into cluster II, together with melon groups from the plains of Vietnam. The presence of two groups of melons in Southeast Asia was also indicated by population structure and principal coordinate analysis. These results indicated a close genetic relationship between Cambodia and the neighboring countries, thus suggesting that Cambodian melons are not directly related to the establishment of Conomon and Makuwa. No potential conflict of interest relevant to this article was reported.

Japanese Society of Breeding Acta Medica Okayama 1344-7610 73 3 2023 Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection 269 277 EN Gentaro Shigita Graduate School of Environmental and Life Science, Okayama University Tran Phuong Dung Graduate School of Environmental and Life Science, Okayama University Mst. Naznin Pervin Graduate School of Environmental and Life Science, Okayama University Thanh-Thuy Duong Graduate School of Environmental and Life Science, Okayama University Odirich Nnennaya Imoh Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental and Life Science, Okayama University Hidetaka Nishida Graduate School of Environmental and Life Science, Okayama University Katsunori Tanaka Faculty of Agriculture and Life Science, Hirosaki University Mitsuhiro Sugiyama Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) Yoichi Kawazu Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO) Norihiko Tomooka Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO) Kenji Kato Graduate School of Environmental and Life Science, Okayama University Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset (�gcore collection�h) are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon. No potential conflict of interest relevant to this article was reported.

Frontiers Media SA Acta Medica Okayama 1664-462X 13 2022 Mapping of Nematode Resistance in Hexaploid Sweetpotato Using an Next-Generation Sequencing-Based Association Study 858747 EN Nozomi Obata Graduate School of Environmental and Life Science, Okayama University Hiroaki Tabuchi Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization Miyu Kurihara Faculty of Agriculture, Okayama University Eiji Yamamoto Graduate School of Agriculture, Meiji University Kenta Shirasawa Department of Frontier Research and Development, Kazusa DNA Research Institute Yuki Monden Graduate School of Environmental and Life Science, Okayama University The southern root-knot nematode (SRKN; Meloidogyne incognita) is a typical parasitic nematode that affects sweetpotato [Ipomoea batatas (L.) Lam.], causing a significant decrease in crop yield and commercial value. In Japan, the SRKN is classified into 10 races: SP1-SP5, SP6-1, SP6-2, and SP7-SP9, with the dominant race differing according to the cultivation area. Soil insecticides have previously been used to reduce the soil density of SRKNs; however, this practice is both costly and labor intensive. Therefore, the development of SRKN-resistant sweetpotato lines and cultivars is necessary. However, due to the complexity of polyploid inheritance and the highly heterogeneous genomic composition of sweetpotato, genetic information and research for this species are significantly lacking compared to those for other major diploid crop species. In this study, we utilized the recently developed genome-wide association approach, which uses multiple-dose markers to assess autopolyploid species. We performed an association analysis to investigate resistance toward SRKN-SP2, which is the major race in areas with high sweetpotato production in Japan. The segregation ratio of resistant and susceptible lines in the F-1 mapping population derived from the resistant "J-Red" and susceptible "Choshu" cultivars was fitted to 1: 3, suggesting that resistance to SP2 may be regulated by two loci present in the simplex. By aligning the double digest restriction-site associated DNA sequencing reads to the published Ipomoea trifida reference sequence, 46,982 single nucleotide polymorphisms (SNPs) were identified (sequencing depth > 200). The association study yielded its highest peak on chromosome 7 (Chr07) and second highest peak on chromosome 3 (Chr03), presenting as a single-dose in both loci. Selective DNA markers were developed to screen for resistant plants using the SNPs identified on Chr03 and Chr07. Our results showed that SRKN-SP2-resistant plants were selected with a probability of approximately 70% when combining the two selective DNA markers. This study serves as a model for the identification of genomic regions that control agricultural traits and the elucidation of their effects, and is expected to greatly advance marker-assisted breeding and association studies in polyploid crop species. No potential conflict of interest relevant to this article was reported.

MDPI Acta Medica Okayama 2223-7747 10 8 2021 Transcriptome Analysis Reveals Key Genes Involved in Weevil Resistance in the Hexaploid Sweetpotato 1535 EN Kanoko Nokihara Graduate School of Environmental and Life Science, Okayama University Yoshihiro Okada Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization Shinichiro Ohata Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental and Life Science, Okayama University Because weevils are the most damaging pests of sweetpotato, the development of cultivars resistant to weevil species is considered the most important aspect in sweetpotato breeding. However, the genes and the underlying molecular mechanisms related to weevil resistance are yet to be elucidated. In this study, we performed an RNA sequencing-based transcriptome analysis using the resistant Kyushu No. 166 (K166) and susceptible Tamayutaka cultivars. The weevil resistance test showed a significant difference between the two cultivars at 30 days after the inoculation, specifically in the weevil growth stage and the suppressed weevil pupation that was only observed in K166. Differential expression and gene ontology analyses revealed that the genes upregulated after inoculation in K166 were related to phosphorylation, metabolic, and cellular processes. Because the weevil resistance was considered to be related to the suppression of larval pupation, we investigated the juvenile hormone (JH)-related genes involved in the inhibition of insect metamorphosis. We found that the expression of some terpenoid-related genes, which are classified as plant-derived JHs, was significantly increased in K166. This is the first study involving a comprehensive gene expression analysis that provides new insights about the genes and mechanisms associated with weevil resistance in sweetpotato. No potential conflict of interest relevant to this article was reported.

Japanese Society of Breeding Acta Medica Okayama 1344-7610 70 2 2020 DNA markers based on retrotransposon insertion polymorphisms can detect short DNA fragments for strawberry cultivar identification 231 240 EN Chiharu Hirata Fukuoka Agriculture and Forestry Research Center Takamitsu Waki Tochigi Prefectural Agricultural Experiment Station Katsumi Shimomura Fukuoka Agriculture and Forestry Research Center Takuya Wada Fukuoka Agriculture and Forestry Research Center Seiya Tanaka Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Hidetoshi Ikegami Fukuoka Agriculture and Forestry Research Center Yousuke Uchimura Fukuoka Agriculture and Forestry Research Center Keita Hirashima Fukuoka Agriculture and Forestry Research Center Yoshiko Nakazawa Tochigi Prefectural Agricultural Experiment Station Kaori Okada Tochigi Prefectural Agricultural Experiment Station Kiyoshi Namai Tochigi Prefectural Agricultural Experiment Station Makoto Tahara Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental and Life Science, Okayama University In this study, DNA markers were developed for discrimination of strawberry (Fragaria �~ ananassa L.) cultivars based on retrotransposon insertion polymorphisms. We performed a comprehensive genomic search to identify retrotransposon insertion sites and subsequently selected one retrotransposon family, designated CL3, which provided reliable discrimination among strawberry cultivars. Through analyses of 75 strawberry cultivars, we developed eight cultivar-specific markers based on CL3 retrotransposon insertion sites. Used in combination with 10 additional polymorphic markers, we differentiated 35 strawberry cultivars commonly cultivated in Japan. In addition, we demonstrated that the retrotransposon-based markers were effective for PCR detection of DNA extracted from processed food materials, whereas a SSR marker was ineffective. These results indicated that the retrotransposon-based markers are useful for cultivar discrimination for processed food products, such as jams, in which DNA may be fragmented or degraded. No potential conflict of interest relevant to this article was reported.

Springer Acta Medica Okayama 1436-2228 2020 Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases EN Michiko Nemoto Graduate School of Environmental and Life Science, Okayama University Sayako Iwaki Graduate School of Environmental and Life Science, Okayama University Hisao Moriya Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental and Life Science, Okayama University Takashi Tamura Graduate School of Environmental and Life Science, Okayama University Kenji Inagaki Graduate School of Environmental and Life Science, Okayama University Shigeki Mayama Department of Biology, Tokyo Gakugei University Kiori Obuse Graduate School of Environmental and Life Science, Okayama University Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms. No potential conflict of interest relevant to this article was reported.

Oxford University Press Acta Medica Okayama 1340-2838 26 5 2019 Development of molecular markers associated with resistance to Meloidogyne incognita by performing quantitative trait locus analysis and genome-wide association study in sweetpotato 399 409 EN Rumi Sasai Graduate School of Environmental and Life Science, Okayama University Hiroaki Tabuchi Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization Kenta Shirasawa Kazusa DNA Research Institute Kazuki Kishimoto Graduate School of Environmental and Life Science, Okayama University Shusei Sato Graduate School of Life Science, Tohoku University Yoshihiro Okada Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization Akihide Kuramoto Graduate School of Agriculture, Kyoto University Akira Kobayashi Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization Sachiko Isobe Kazusa DNA Research Institute Makoto Tahara Graduate School of Environmental and Life Science, Okayama University Yuki Monden Graduate School of Environmental and Life Science, Okayama University The southern root-knot nematode, Meloidogyne incognita, is a pest that decreases yield and the quality of sweetpotato [Ipomoea batatas (L.) Lam.]. There is a demand to produce resistant cultivars and develop DNA markers to select this trait. However, sweetpotato is hexaploid, highly heterozygous, and has an enormous genome (similar to 3 Gb), which makes genetic linkage analysis difficult. In this study, a high-density linkage map was constructed based on retrotransposon insertion polymorphism, simple sequence repeat, and single nucleotide polymorphism markers. The markers were developed using F-1 progeny between J-Red, which exhibits resistance to multiple races of M. incognita, and Choshu, which is susceptible to multiple races of such pest. Quantitative trait locus (QTL) analysis and a genome-wide association study detected highly effective QTLs for resistance against three races, namely, SP1, SP4, and SP6-1, in the Ib01-6 J-Red linkage group. A polymerase chain reaction marker that can identify genotypes based on single nucleotide polymorphisms located in this QTL region can discriminate resistance from susceptibility in the F-1 progeny at a rate of 70%. Thus, this marker could be helpful in selecting sweetpotato cultivars that are resistant to multiple races of M. incognita. No potential conflict of interest relevant to this article was reported.

Oxford University Press Acta Medica Okayama 1340-2838 2014 Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform EN Yuki Monden Ayaka Yamamoto Akiko Shindo Makoto Tahara In many crop species, DNA fingerprinting is required for the precise identification of cultivars to protect the rights of breeders. Many families of retrotransposons have multiple copies throughout the eukaryotic genome and their integrated copies are inherited genetically. Thus, their insertion polymorphisms among cultivars are useful for DNA fingerprinting. In this study, we conducted a DNA fingerprinting based on the insertion polymorphisms of active retrotransposon families (Rtsp-1 and LIb) in sweet potato. Using 38 cultivars, we identified 2024 insertion sites in the two families with an Illumina MiSeq sequencing platform. Of these insertion sites, 91.4% appeared to be polymorphic among the cultivars and 376 cultivar-specific insertion sites were identified, which were converted directly into cultivar-specific sequence-characterized amplified region (SCAR) markers. A phylogenetic tree was constructed using these insertion sites, which corresponded well with known pedigree information, thereby indicating their suitability for genetic diversity studies. Thus, the genome-wide comparative analysis of active retrotransposon insertion sites using the bench-top MiSeq sequencing platform is highly effective for DNA fingerprinting without any requirement for whole genome sequence information. This approach may facilitate the development of practical polymerase chain reaction-based cultivar diagnostic system and could also be applied to the determination of genetic relationships. No potential conflict of interest relevant to this article was reported.

NRC Research Press Acta Medica Okayama 57 5 2014 Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site 245 252 EN Yuki Monden Nobuyuki Fujii Kentaro Yamaguchi Kazuho Ikeo Yoshiko Nakazawa Takamitsu Waki Keita Hirashima Yosuke Uchimura Makoto Tahara Retrotransposons have been used frequently for the development of molecular markers by using their insertion polymorphisms among cultivars, because multiple copies of these elements are dispersed throughout the genome and inserted copies are inherited genetically. Although a large number of long terminal repeat (LTR) retrotransposon families exist in the higher eukaryotic genomes, the identification of families that show high insertion polymorphism has been challenging. Here, we performed an efficient screening of these retrotransposon families using an Illumina HiSeq2000 sequencing platform with comprehensive LTR library construction based on the primer binding site (PBS), which is located adjacent to the 5�Œ LTR and has a motif that is universal and conserved among LTR retrotransposon families. The paired-end sequencing library of the fragments containing a large number of LTR sequences and their insertion sites was sequenced for seven strawberry (Fragaria �~ ananassa Duchesne) cultivars and one diploid wild species (Fragaria vesca L.). Among them, we screened 24 families with a �gunique�h insertion site that appeared only in one cultivar and not in any others, assuming that this type of insertion should have occurred quite recently. Finally, we confirmed experimentally the selected LTR families showed high insertion polymorphisms among closely related cultivars. No potential conflict of interest relevant to this article was reported.

Elsevier B.V. Acta Medica Okayama 0168-1656 185 2014 A rapid and enhanced DNA detection method for crop cultivar discrimination 57 62 EN Yuki Monden Kazuto Takasaki Satoshi Futo Kousuke Niwa Mitsuo Kawase Hiroto Akitake Makoto Tahara In many crops species, the development of a rapid and precise cultivar discrimination system has been required for plant breeding and patent protection of plant cultivars and agricultural products. Here, we successfully evaluated strawberry cultivars via a novel method, namely, the single tag hybridization (STH) chromatographic printed array strip (PAS) using the PCR products of eight genomic regions. In a previous study, we showed that genotyping of eight genomic regions derived from FaRE1 retrotransposon insertion site enabled to discriminate 32 strawberry cultivars precisely, however, this method required agarose/acrylamide gel electrophoresis, thus has the difficulty for practical application. In contrast, novel DNA detection method in this study has some great advantages over standard DNA detection methods, including agarose/acrylamide gel electrophoresis, because it produces signals for DNA detection with dramatically higher sensitivity in a shorter time without any preparation or staining of a gel. Moreover, this method enables the visualization of multiplex signals simultaneously in a single reaction using several independent amplification products. We expect that this novel method will become a rapid and convenient cultivar screening assay for practical purposes, and will be widely applied to various situations, including laboratory research, and on-site inspection of plant cultivars and agricultural products. No potential conflict of interest relevant to this article was reported.

‰ªŽR‘åŠw”_Šw•” Acta Medica Okayama 2186-7755 103 2014 Characterization of a novel retrotransposon TriRe‒1 using nullisomic-tetrasomic lines of hexaploid wheat 21 30 EN Yuki Monden Takeru Takai Makoto Tahara �@Retrotransposons constitute the large fraction (�`80%) of the wheat genome where numerous and diverse retrotransposon families exist, where especially the long terminal repeat (LTR) retrotransposon family is known to be predominant. Thus, they have been considered to contribute to the genome expansion, sequence diversification and the genome structure alternation in the wheat genome. In addition, the insertion polymorphism of the LTR retrotransposon family among the cultivars has been known to be quite useful for the genetic analysis such as the linkage mapping and the phylogenetic studies. Here, we report the characteristics of a novel active LTR retrotransposon family TriRe‒1, which belongs to the Ty1‒copia group in the hexaploid wheat (Triticum aestivum L.) genome. This retroelement appears to encode all proteins required for the transposition and showed high insertion polymorphism among the hexaploid wheat cultivars, suggesting its potential of transpositional activity with at least recent transposition during wheat evolution. We studied the chromosomal localization of the TriRe‒1 insertion site based on the genome-wide comparative analysis using the nullisomic-tetrasomic lines of the cultivar Chinese Spring. The results showed that although the majority of the TriRe‒1 insertion sites exist across the homoeologous chromosomes of A, B or D genomes, a higher number of insertions in the B genome was detected compared to A or D genome, suggesting a specific amplification in the history of B genome progenitors. In conclusion, a novel LTR retrotransposon TriRe‒1 should be valuable for the development of molecular markers based on insertion polymorphism among the cultivars, and also the genome-specific TriRe‒1 insertion site can be utilized to study evolutional history of wheat genomes. No potential conflict of interest relevant to this article was reported.