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No.	タイトル	出版年月	著者	誌名	巻号頁	掲載種別	単著・共著区分	DOI1	ISSN	URL1	URL2	出版者・発行元	概要
1	A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don	2024/11/05	Takeshi Fujino Katsushi Yamaguchi Toshiyuki T. Yokoyama Toshiya Hamanaka Yoritaka Harazono Hiroaki Kamada Wataru Kobayashi Tokuko Ujino-Ihara Kentaro Uchiyama Asako Matsumoto Ayako Izuno Yoshihiko Tsumura Atsushi Toyoda Shuji Shigenobu Yoshinari Moriguchi Saneyoshi Ueno Masahiro Kasahara	BMC Genomics	25/ 1	研究論文（学術雑誌）		10.1186/s12864-024-10929-4		URL	URL_2	Springer Science and Business Media LLC	Abstract Background The Japanese cedar (Cryptomeria japonica D. Don) is one of the most important Japanese forest trees, occupying approximately 44% of artificial forests and planted in East Asia, the Azores Archipelago, and certain islands in the Indian Ocean. Although the huge genome of the species (ca. 9 Gbp) with abundant repeat elements may have represented an obstacle for genetic analysis, this species is easily propagated by cutting, flowered by gibberellic acid, transformed by Agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica recommend it as a model conifer species for which reference genome sequences are necessary. Results Herein, we report the first chromosome-level assembly of C. japonica (2n = 22) using third-generation selfed progeny (estimated homozygosity rate = 0.96). Young leaf tissue was used to extract high molecular weight DNA (> 50 kb) for HiFi PacBio long-read sequencing and to construct an Hi-C/Omni-C library for Illumina short-read sequencing. The 29× and 26× genome coverage of HiFi and Illumina reads, respectively, for de novo assembly yielded 2,651 contigs (9.1 Gbp, N50 contig size 12.0 Mbp). Hi-C analysis mapped 97% of the nucleotides on 11 chromosomes. The assembly was verified through comparison with a consensus linkage map comprising 7,781 markers. BUSCO analysis identified ∼ 91% conserved genes. Conclusions Annotations of genes and comparisons of repeat elements with other Cupressaceae and Pinaceae species provide a fundamental resource for conifer research.
2	Odd-Paired is Involved in Morphological Divergence of Snail-Feeding Beetles	2024/06/01	Junji Konuma Tomochika Fujisawa Tomoaki Nishiyama Masahiro Kasahara Tomoko F Shibata Masafumi Nozawa Shuji Shigenobu Atsushi Toyoda Mitsuyasu Hasebe Teiji Sota	Molecular Biology and Evolution	41, msae110-msae110	研究論文（学術雑誌）		10.1093/molbev/msae110
3	Efficient selection of a biallelic and nonchimeric gene-edited tree using Oxford Nanopore Technologies sequencing	2023/12/25	Ryosuke Sato Yoshihiko Nanasato Naoki Takata Soichiro Nagano Eitaro Fukatsu Takeshi Fujino Katushi Yamaguchi Yoshinari Moriguchi Shuji Shigenobu Yutaka Suzuki Masahiro Kasahara Saneyoshi Ueno	Tree Physiology		研究論文（学術雑誌）		10.1093/treephys/tpad158		URL		Oxford University Press (OUP)	Abstract The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 nuclease (Cas9) system is a versatile and essential biotechnological tool in the life sciences that allows efficient genome editing. When generating gene-edited trees, T0-generation plants are often used for subsequent analysis because of the time that is required to obtain the desired mutants via crossing. However, T0-generation plants exhibit various unexpected mutations, which emphasizes the need to identify mutants with expected mutation patterns. The two critical checkpoints in this process are to confirm the expected mutation patterns in both alleles and to exclude somatic chimeric plants. In this study, we generated gene-edited Cryptomeria japonica plants and established a method to determine chimerism and mutation patterns using fragment analysis and Oxford Nanopore Technologies (ONT)-based amplicon sequencing. In the first screening, fragment analysis, i.e., indel detection via amplicon analysis (IDAA), was used to predict indel mutation patterns in both alleles and to discriminate somatic chimeric plants in 188 candidate mutants. In the second screening, we precisely determined the mutation patterns and chimerism in the mutants using ONT-based amplicon sequencing, where confirmation of both alleles can be achieved using allele-specific markers flanking the single guide RNA (sgRNA) target site. In the present study, a bioinformatic analysis procedure was developed and provided for the rapid and accurate determination of DNA mutation patterns using ONT-based amplicon sequencing. As ONT amplicon sequencing has a low running cost compared with other long-read analysis methods, such as PacBio, it is a powerful tool in plant genetics and biotechnology to select gene-edited plants with expected indel patterns in the T0-generation.
4	Somatic mutation rates scale with time not growth rate in long-lived tropical trees	2023/10/09	Akiko Satake Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Na’iem Sapto Indrioko Widiyatno Susilo Purnomo Almudena Mollá–Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara	eLife		研究論文（学術雑誌）		10.7554/elife.88456.2					<jats:p>The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation.</jats:p> <jats:p>The significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.</jats:p>
5	A single-nucleotide substitution of CjTKPR1 determines pollen production in the gymnosperm plant Cryptomeria japonica.	2023/08	Hiroyuki Kakui Tokuko Ujino-Ihara Yoichi Hasegawa Eriko Tsurisaki Norihiro Futamura Junji Iwai Yuumi Higuchi Takeshi Fujino Yutaka Suzuki Masahiro Kasahara Katsushi Yamaguchi Shuji Shigenobu Masahiro Otani Masaru Nakano Masaaki Nameta Shinsuke Shibata Saneyoshi Ueno Yoshinari Moriguchi	PNAS nexus	2/ 8, pgad236	研究論文（学術雑誌）		10.1093/pnasnexus/pgad236					Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades. The MALE STERILITY 4 (MS4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TETRAKETIDE α-PYRONE REDUCTASE 1 (TKPR1) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution ("T" to "C" at 244-nt position) of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plants not only for Japanese cedar but also for broader plant species.
6	The molecular clock in long-lived tropical trees is independent of growth rate	2023/06/06	Ryosuke Imai Takeshi Fujino Sou Tomimoto Kayoko Ohta Mohammad Na’iem Sapto Indrioko Widiyatno Susilo Purnomo Almudena Mollá-Morales Viktoria Nizhynska Naoki Tani Yoshihisa Suyama Eriko Sasaki Masahiro Kasahara Akiko Satake					10.7554/elife.88456.1				eLife Sciences Publications, Ltd	The rates and patterns of somatic mutations in wild plants, as well as how they relate to longevity, are largely unknown1–3. Here, we examined the somatic mutation landscapes of slow- and fast-growing tropical species in central Borneo, Indonesia. Using newly-constructed genomes, we identified an average of 480 mutations in the slow-growing species (265-year-old, 44.1 m in height), which was five times greater than that observed in the fast-growing species (66-year-old, 43.9 m). The number of somatic mutations increased linearly with branch length. The somatic mutation rate per meter was higher in the slow-growing species, yet the rate per year remained constant across both species. The mutational spectra exhibited a dominance of spontaneous mutations, specifically cytosine-to-thymine substitutions at CpG sites. An analysis of nucleotide substitutions at both the intra- and inter-individual level revealed that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. We developed a model to evaluate the relative contribution of cell division on mutational processes, and postulate that cell-division independent mutagenesis predominates. These findings deepen our understanding of mutational processes underlying the generation of genetic diversity in a tropical ecosystem.
7	スギ (Cryptomeria japonica D. Don) の全ゲノム配列の決定	2023/05/30	藤野健山口勝司横山稔之濵中俊哉原薗陛正鎌田寛彬小林航伊原徳子内山憲太郎松本麻子伊津野彩子津村義彦豊田敦重信秀治森口喜成上野真義笠原雅弘	日本森林学会大会発表データベース	134, 371			10.11519/jfsc.134.0_371				日本森林学会	スギ (Cryptomeria japonica D. Don) はゲノムサイズが約 11 Gbp と巨大であり、ゲノム中に占める反復配列の割合も多いことから長らくゲノム配列の決定が困難であった。我々は 3 度の自殖を経たスギの 1 個体（国東3 S3-3）から抽出した長鎖 DNA をもとに PacBio HiFi ライブラリを作成し de novo アセンブリすることで合計 9.1 Gbp から成る 2,651 個のコンティグを得た。さらに同個体から作成した Omni-C ライブラリに基づく解析でコンティグを全 11 本の染色体上に配置することに成功した。アセンブリ配列を 7,781 個のマーカーから構成された遺伝学的地図と比較し高い整合性が見られたことからアセンブリの正確性が検証された。ゲノムアセンブリに対して RNA-seq, Iso-seq および ESTs (Futamura et al., 2008) から成る transcript 配列と OrthoDB v10 に対する相同性とに基づく遺伝子予測を行い、約 5 万 5 千個の遺伝子セットを得た。この遺伝子セットは BUSCO による評価で 91.4% という針葉樹では最高水準の完全性を得た。染色体レベルでのスギゲノム配列の解読はポジショナルクローニングなどの分子育種の基盤を提供する。
8	スギ (Cryptomeria japonica D. Don) の全ゲノム配列の決定	2023/05/30	藤野健, 山口勝司, 横山稔之, 濵中俊哉, 原薗陛正, 鎌田寛彬, 小林航, 伊原徳子, 内山憲太郎, 松本麻子, 伊津野彩子, 津村義彦, 豊田敦, 重信秀治, 森口喜成, 上野真義, 笠原雅弘	日本森林学会大会発表データベース	134/ 0, 371					URL		日本森林学会	<p>スギ (Cryptomeria japonica D. Don) はゲノムサイズが約 11 Gbp と巨大であり、ゲノム中に占める反復配列の割合も多いことから長らくゲノム配列の決定が困難であった。我々は 3 度の自殖を経たスギの 1 個体（国東3 S3-3）から抽出した長鎖 DNA をもとに PacBio HiFi ライブラリを作成し de novo アセンブリすることで合計 9.1 Gbp から成る 2,651 個のコンティグを得た。さらに同個体から作成した Omni-C ライブラリに基づく解析でコンティグを全 11 本の染色体上に配置することに成功した。アセンブリ配列を 7,781 個のマーカーから構成された遺伝学的地図と比較し高い整合性が見られたことからアセンブリの正確性が検証された。ゲノムアセンブリに対して RNA-seq, Iso-seq および ESTs (Futamura et al., 2008) から成る transcript 配列と OrthoDB v10 に対する相同性とに基づく遺伝子予測を行い、約 5 万 5 千個の遺伝子セットを得た。この遺伝子セットは BUSCO による評価で 91.4% という針葉樹では最高水準の完全性を得た。染色体レベルでのスギゲノム配列の解読はポジショナルクローニングなどの分子育種の基盤を提供する。</p>
9	スギゲノム参照配列を用いた雄性不稔遺伝子（MS3）候補遺伝子の同定	2023/05/30	上野真義, 長谷川陽一, 鶴田燃海, 伊原徳子, 宮澤真一, 角井宏行, 岩井淳治, 平山聡子, 藤野健, 山口勝司, 鈴木穣, 豊田敦, 重信秀治, 笠原雅弘, 森口喜成	日本森林学会大会発表データベース	134/ 0, 372					URL		日本森林学会	<p> 無花粉スギは、花粉を飛散しないため花粉症対策に有効である。無花粉スギでは花粉形成に関連する遺伝子（雄性不稔遺伝子）に異常があるため成熟した花粉を作ることができない。現在までに4つの雄性不稔遺伝子が同定され、そのうちの2つの遺伝子（MS1およびMS4）は塩基配列の欠失および置換により機能を失ったと推定されている。本研究では、スギの参照ゲノム配列（藤野ら、本大会）を活用することで、雄性不稔遺伝子MS3を同定した。161個体の戻し交配家系での連鎖解析の結果、MS3遺伝子座を1.25 cMの範囲に絞り込んだところ、chr1（第1染色体）の3.98 Mbpの範囲に存在する77個の遺伝子に絞り込まれた。原因遺伝子が雄花で発現する遺伝子で、有害な突然変異を持つと仮定しRNA-Seq法で探索した結果、MS3の無花粉スギ系統でアミノ酸置換によりタンパク質の正常な機能が阻害されると推定される1個の遺伝子を見出した。この遺伝子は相同性検索の結果、シロイヌナズナのアシルCoA合成酵素（ACOS5）との類似性が高く、シロイヌナズナの変異体は雄性不稔を示すことから、MS3の原因遺伝子として可能性が高いと考えられた。</p>
10	A divergent <scp>RWP‐RK</scp> transcription factor determines mating type in heterothallic Closterium	2023/01/09	Hiroyuki Sekimoto Ayumi Komiya Natsumi Tsuyuki Junko Kawai Naho Kanda Ryo Ootsuki Yutaka Suzuki Atsushi Toyoda Asao Fujiyama Masahiro Kasahara Jun Abe Yuki Tsuchikane Tomoaki Nishiyama	New Phytologist		研究論文（学術雑誌）		10.1111/nph.18662	0028-646X	URL	URL_2	Wiley
11	LPMX: a pure rootless composable container system	2022/12	Xu Yang Masahiro Kasahara	BMC Bioinformatics	23/ 1	研究論文（学術雑誌）		10.1186/s12859-022-04649-3				Springer Science and Business Media {LLC}
12	アルゴリズムの頂が持つ力はいかに？ -ゲノコン2021 開催記録-	2022/06/15	清水佳奈坂本一憲笠原雅弘	情報処理	63/ 7, none		共著	10.20729/00218439		URL		[出版社不明]
13	機能証明実験による無花粉スギMS4原因遺伝子の同定	2022/05/30	角井宏行, 伊原徳子, 長谷川陽一, 二村典宏, 岩井淳治, 樋口有未, 藤野健, 鈴木穣, 笠原雅弘, 山口勝司, 重信秀治, 大谷真広, 中野優, 上野真義, 森口喜成	日本森林学会大会発表データベース	133/ 0, 12					URL		日本森林学会	<p>スギの無花粉形質を制御する遺伝子座の1つ、MS4 (MALE STERILITY 4)は、潜性ホモ接合(ms4/ms4)で無花粉形質を示す。我々はこれまでに分離集団を用いた連鎖解析によりその遺伝子座を明らかにしてきた(Moriguchi et al. TGG 2016; Hasegawa et al. PLoS ONE 2018)。MS4の原因遺伝子の同定を目的に、MS4座のさらなる絞り込みを行い、RNA-seqによって雄花で発現する遺伝子を探索したところ、シロイヌナズナおよびイネで花粉発達に必須の遺伝子である TKPR1 (TETRAKETIDE α-PYRONE REDUCTASE 1) が含まれていることがわかった。スギCjTKPR1の野生型と変異型のアミノ酸配列を比較したところ、わずか1塩基置換に起因する1アミノ酸置換のみが検出された。この1塩基置換が無花粉スギMS4の原因変異であるかどうかを明らかにする目的で、無花粉のシロイヌナズナTKPR1変異体にCjTKPR1の野生型配列もしくは1塩基置換した変異配列を導入し、花粉生産が補完されるかを解析した。その結果、CjTKPR1の野生型配列を導入した個体は花粉生産が回復した一方で、変異型配列を導入した個体は無花粉のままであったことから、CjTKPR1の1塩基置換が無花粉スギMS4の原因変異であると考えられた。</p>
14	LPMX: a pure rootless composable container system	2022/03	Yang, Xu, Kasahara, Masahiro	BMC BIOINFORMATICS	23/ 1			10.1186/s12859-022-04649-3	1471-2105
15	Single-nucleotide substitution determines pollen production in Japanese cedar	2022/03/20	Hiroyuki Kakui Tokuko Ujino-Ihara Yoichi Hasegawa Eriko Tsurisaki Norihiro Futamura Junji Iwai Yuumi Higuchi Takeshi Fujino Yutaka Suzuki Masahiro Kasahara Katsushi Yamaguchi Shuji Shigenobu Masahiro Otani Masaru Nakano Saneyoshi Ueno Yoshinari Moriguchi	bioRxiv		研究論文（学術雑誌）		10.1101/2022.03.17.484665		URL
16	無花粉スギMS4の原因はCjTKPR1の1塩基置換変異である	2022	角井宏行伊原徳子長谷川陽一釣崎恵里子二村典宏岩井淳治樋口有未藤野健鈴木穣笠原雅弘山口勝司重信秀治大谷真広中野優上野真義森口喜成	育種学研究	24				1344-7629
17	Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don)	2021/01	Hasegawa, Yoichi, Ueno, Saneyoshi, Wei, Fu-Jin, Matsumoto, Asako, Uchiyama, Kentaro, Ujino-Ihara, Tokuko, Hakamata, Tetsuji, Fujino, Takeshi, Kasahara, Masahiro, Bino, Takahiro, Yamaguchi, Katsushi, Shigenobu, Shuji, Tsumura, Yoshihiko, Moriguchi, Yoshinari	SCIENTIFIC REPORTS	11/ 1			10.1038/s41598-020-80688-1	2045-2322
18	Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don).	2021/01/15	Yoichi Hasegawa Saneyoshi Ueno Fu-Jin Wei Asako Matsumoto Kentaro Uchiyama Tokuko Ujino-Ihara Tetsuji Hakamata Takeshi Fujino Masahiro Kasahara Takahiro Bino Katsushi Yamaguchi Shuji Shigenobu Yoshihiko Tsumura Yoshinari Moriguchi	Scientific reports	11/ 1, 1496-1496	研究論文（学術雑誌）		10.1038/s41598-020-80688-1		URL			Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) in Cryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterile C. japonica to reduce the pollinosis caused by pollen dispersal from artificial C. japonica forests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with the ms1. All nine breeding materials with the allele ms1 had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene of MS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials of C. japonica with the allele ms1 adapted to the unique environment of each region of the Japanese archipelago.
19	Long-read sequencing for non-small-cell lung cancer genomes	2020/09	Sakamoto, Yoshitaka, Xu, Liu, Seki, Masahide, Yokoyama, Toshiyuki T., Kasahara, Masahiro, Kashima, Yukie, Ohashi, Akihiro, Shimada, Yoko, Motoi, Noriko, Tsuchihara, Katsuya, Kobayashi, Susumu S., Kohno, Takashi, Shiraishi, Yuichi, Suzuki, Ayako, Suzuki, Yutaka	GENOME RESEARCH	30/ 9, 1243-1257			10.1101/gr.261941.120	1088-9051
20	Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don.	2020/09/29	Hasegawa Yoichi,Ueno Saneyoshi,Wei Fu-Jin,Matsumoto Asako,Ujino-Ihara Tokuko,Uchiyama Kentaro,Moriguchi Yoshinari,Kasahara Masahiro,Fujino Takeshi,Shigenobu Shuji,Yamaguchi Katsushi,Bino Takahiro,Hakamata Tetsuji	BMC research notes	13/ 1, 457			10.1186/s13104-020-05296-8	1756-0500				Due to the allergic nature of the pollen of Cryptomeria japonica, the most important Japanese forestry conifer, a pollen-free cultivar is preferred. Mutant trees detected in nature have been used to produce a pollen-free cultivar. In order to reduce the time and cost needed for production and breeding, we aimed to develop simple diagnostic molecular markers for mutant alleles of the causative gene MALE STERILITY 1 (MS1) in C. japonica to rapidly identify pollen-free mutants.We developed PCR and LAMP markers to detect mutant alleles and to present experimental options depending on available laboratory equipment. LAMP markers were developed for field stations, where PCR machines are unavailable. The LAMP method only needs heat-blocks or a water bath to perform the isothermal amplification and assay results can be read by the naked eye. Because the causative mutations were deletions, we developed two kinds of PCR markers, amplified length polymorphism (ALP) and allele specific PCR (ASP) markers. These assays can be visualized using capillary or agarose gel electrophoresis.
21	Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don.	2020/09/29	Yoichi Hasegawa Saneyoshi Ueno Fu-Jin Wei Asako Matsumoto Tokuko Ujino-Ihara Kentaro Uchiyama Yoshinari Moriguchi Masahiro Kasahara Takeshi Fujino Shuji Shigenobu Katsushi Yamaguchi Takahiro Bino Tetsuji Hakamata	BMC research notes	13/ 1, 457-457	研究論文（学術雑誌）		10.1186/s13104-020-05296-8		URL			OBJECTIVE: Due to the allergic nature of the pollen of Cryptomeria japonica, the most important Japanese forestry conifer, a pollen-free cultivar is preferred. Mutant trees detected in nature have been used to produce a pollen-free cultivar. In order to reduce the time and cost needed for production and breeding, we aimed to develop simple diagnostic molecular markers for mutant alleles of the causative gene MALE STERILITY 1 (MS1) in C. japonica to rapidly identify pollen-free mutants. RESULTS: We developed PCR and LAMP markers to detect mutant alleles and to present experimental options depending on available laboratory equipment. LAMP markers were developed for field stations, where PCR machines are unavailable. The LAMP method only needs heat-blocks or a water bath to perform the isothermal amplification and assay results can be read by the naked eye. Because the causative mutations were deletions, we developed two kinds of PCR markers, amplified length polymorphism (ALP) and allele specific PCR (ASP) markers. These assays can be visualized using capillary or agarose gel electrophoresis.
22	Long-read sequencing for non-small-cell lung cancer genomes	2020/09/04	Yoshitaka Sakamoto Liu Xu Masahide Seki Toshiyuki T. Yokoyama Masahiro Kasahara Yukie Kashima Akihiro Ohashi Yoko Shimada Noriko Motoi Katsuya Tsuchihara Susumu S. Kobayashi Takashi Kohno Yuichi Shiraishi Ayako Suzuki Yutaka Suzuki	Genome Research	30/ 9, 1243-1257	研究論文（学術雑誌）		10.1101/gr.261941.120				Cold Spring Harbor Laboratory	Here, we report the application of a long-read sequencer, PromethION, for analyzing human cancer genomes. We first conducted whole-genome sequencing on lung cancer cell lines. We found that it is possible to genotype known cancerous mutations, such as point mutations. We also found that long-read sequencing is particularly useful for precisely identifying and characterizing structural aberrations, such as large deletions, gene fusions, and other chromosomal rearrangements. In addition, we identified several medium-sized structural aberrations consisting of complex combinations of local duplications, inversions, and microdeletions. These complex mutations occurred even in key cancer-related genes, such as STK11, NF1, SMARCA4, and PTEN The biological relevance of those mutations was further revealed by epigenome, transcriptome, and protein analyses of the affected signaling pathways. Such structural aberrations were also found in clinical lung adenocarcinoma specimens. Those structural aberrations were unlikely to be reliably detected by conventional short-read sequencing. Therefore, long-read sequencing may contribute to understanding the molecular etiology of patients for whom causative cancerous mutations remain unknown and therapeutic strategies are elusive.
23	スギの雄性不稔候補遺伝子（MS1)の同定と遺伝的多様性解析	2020/05/25	上野真義, 長谷川陽一, 魏甫錦, 松本麻子, 内山憲太郎, 伊原徳子, 袴田哲司, 藤野健, 笠原雅弘, 尾納隆大, 山口勝司, 重信秀治, 津村義彦, 森口喜成	日本森林学会大会発表データベース	131/ 0, 128					URL		日本森林学会	<p>無花粉スギは、花粉を飛散しないため花粉症対策に利用されている。無花粉スギでは、変異型アレルがホモ接合となるため雄性不稔となるが、野生型アレルとのヘテロ接合体は正常な花粉発生を示すため、外観から判別できない。雄性不稔遺伝子を同定し、その多様性を明らかにすることで、無花粉スギ育種素材のマーカー選抜が容易になる。本研究では、雄花で発現する遺伝子を網羅的に解析し、雄性不稔の候補遺伝子を同定した。候補遺伝子は連鎖地図上のMS1から0 cMに位置し、無花粉スギ系統ではタンパク質のコード領域に変異（塩基の欠失）があるため、機能が失われると推定された。候補遺伝子のほぼ全長の塩基配列を雄性不稔系統と全国の天然林に由来するスギの合計83個体で解析したところ、雄性不稔を引き起こす変異には少なくとも2種類あることが明らかになった。これらの変異はいずれも広く分布する共通のハプロタイプから派生したものと推定された。さらにPCR法とLAMP法によるマーカー開発を行った。今後はゲノム編集により雄性不稔の原因遺伝子を確定させるとともに、マーカー選抜により多様な無花粉スギ育種素材の探索を行う予定である。</p>
24	Visualization tools for human structural variations identified by whole-genome sequencing.	2020/01	Toshiyuki T Yokoyama Masahiro Kasahara	Journal of human genetics	65/ 1, 49-60	研究論文（学術雑誌）		10.1038/s10038-019-0687-0	1435-232X,1434-5161	URL			Visualizing structural variations (SVs) is a critical step for finding associations between SVs and human traits or diseases. Given that there are many sequencing platforms used for SV identification and given that how best to visualize SVs together with other data, such as read alignments and annotations, depends on research goals, there are dozens of SV visualization tools designed for different research goals and sequencing platforms. Here, we provide a comprehensive survey of over 30 SV visualization tools to help users choose which tools to use. This review targets users who wish to visualize a set of SVs identified from the massively parallel sequencing reads of an individual human genome. We first categorize the ways in which SV visualization tools display SVs into ten major categories, which we denote as view modules. View modules allow readers to understand the features of each SV visualization tool quickly. Next, we introduce the features of individual SV visualization tools from several aspects, including whether SV views are integrated with annotations, whether long-read alignment is displayed, whether underlying data structures are graph-based, the type of SVs shown, whether auditing is possible, whether bird's eye view is available, sequencing platforms, and the number of samples. We hope that this review will serve as a guide for readers on the currently available SV visualization tools and lead to the development of new SV visualization tools in the near future.
25	ゲノム構造の差異を可視化するグラフゲノムブラウザ	2020	横山稔之, 坂本祥駿, 関真秀, 鈴木穣, 笠原雅弘	可視化情報学会誌	40/ 156, 14-18				09164731	URL		社団法人可視化情報学会	<p>ゲノムの個体間の差異に着目し、数学的なグラフ構造としてゲノムを可視化するためのツールであるグラフゲノムブラウザを開発した。ゲノム科学の研究において、遺伝情報の総体であるゲノムを可視化することは、その差異を検証し、解釈する上で重要である。このとき、複数のゲノムを数学的なグラフ構造で表現するグラフゲノムをデータ構造として用いることで、ゲノム間の様々な差異をより自然に表現することが可能となる。ここでは、グラフゲノムの可視化をするためのゲノムブラウザであるグラフゲノムブラウザとして、MoMI-Gを紹介する。このツールでは、差異の可視化に必要となる様々な情報を表現するための可視化モジュールを実装した。またこれを用いて、がん培養細胞において発見されている融合遺伝子の可視化を行った。グラフゲノムブラウザは、複雑な差異に対し、可視化を通した探索的な解析を可能にする。</p>
26	ゲノム構造の差異を可視化するグラフゲノムブラウザ	2020	横山稔之坂本祥駿関真秀鈴木穣笠原雅弘	可視化情報学会誌	40/ 156				0916-4731
27	MoMI-G: modular multi-scale integrated genome graph browser.	2019/11/05	Toshiyuki T Yokoyama Yoshitaka Sakamoto Masahide Seki Yutaka Suzuki Masahiro Kasahara	BMC bioinformatics	20/ 1, 548-548	研究論文（学術雑誌）		10.1186/s12859-019-3145-2		URL			BACKGROUND: Genome graph is an emerging approach for representing structural variants on genomes with branches. For example, representing structural variants of cancer genomes as a genome graph is more natural than representing such genomes as differences from the linear reference genome. While more and more structural variants are being identified by long-read sequencing, many of them are difficult to visualize using existing structural variants visualization tools. To this end, visualization method for large genome graphs such as human cancer genome graphs is demanded. RESULTS: We developed MOdular Multi-scale Integrated Genome graph browser, MoMI-G, a web-based genome graph browser that can visualize genome graphs with structural variants and supporting evidences such as read alignments, read depth, and annotations. This browser allows more intuitive recognition of large, nested, and potentially more complex structural variations. MoMI-G has view modules for different scales, which allow users to view the whole genome down to nucleotide-level alignments of long reads. Alignments spanning reference alleles and those spanning alternative alleles are shown in the same view. Users can customize the view, if they are not satisfied with the preset views. In addition, MoMI-G has Interval Card Deck, a feature for rapid manual inspection of hundreds of structural variants. Herein, we describe the utility of MoMI-G by using representative examples of large and nested structural variations found in two cell lines, LC-2/ad and CHM1. CONCLUSIONS: Users can inspect complex and large structural variations found by long-read analysis in large genomes such as human genomes more smoothly and more intuitively. In addition, users can easily filter out false positives by manually inspecting hundreds of identified structural variants with supporting long-read alignments and annotations in a short time. SOFTWARE AVAILABILITY: MoMI-G is freely available at https://github.com/MoMI-G/MoMI-G under the MIT license.
28	スギゲノムの解読と解析	2019/03	笠原雅弘	京都大学化学研究所スーパーコンピュータシステム研究成果報告書	2018, 83-83							京都大学化学研究所	平成30年度京都大学化学研究所スーパーコンピュータシステム利用報告書
29	ロングリードで挑むスギゲノム配列決定	2019	藤野健笠原雅弘山口勝司鈴木創魏甫錦内山憲太郎小澤太郎尾納隆大伊藤勇太重信秀治	日本森林学会大会発表データベース	130/ 0, 718			10.11519/jfsc.130.0_718		URL		日本森林学会	<p>スギのゲノムサイズは11Gbp程度と推定されており、ヒトの3倍以上の大きさを持つ。加えて、スギゲノムには反復配列が多数含まれ、このことがショットガン・シークエンシング法による配列決定を極めて困難にしている。一方、近年の一分子シークエンシング技術の発展によりリード長が増大し、またショートリードから擬似的な長鎖リードを作成する技術も登場してきたことでゲノムアセンブリ手法の幅は広がってきた。本発表では、スギのゲノムアセンブリの試みを通じて分かってきたスギのゲノム配列の特徴を紹介し、それを支えるシークエンシング技術や情報解析についても説明する。大きな問題点として、スギゲノム配列には数十kbにわたり反復配列が連続して並ぶような箇所が極めて頻繁に存在するため、PacBioリードと通常のゲノムアセンブリソフトウェアの組み合わせだけでは短いゲノム配列しか得られないという点が挙げられる。反復配列の問題を解決し、より長いゲノム配列を得るためのいくつかの戦略をシークエンシング技術およびソフトウェアの面から紹介し、スギゲノム配列の決定のための道筋を示したい。</p>
30	Introducing difference recurrence relations for faster semi-global alignment of long sequences	2018/02/19	Hajime Suzuki Masahiro Kasahara	BMC Bioinformatics	19/ Suppl 1, 45	研究論文（学術雑誌）		10.1186/s12859-018-2014-8	1471-2105			BioMed Central Ltd.	Background: The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long this situation hampers the use of the full SIMD width of modern processors. Results: We proposed a faster semi-global alignment algorithm, "difference recurrence relations," that runs more rapidly than the state-of-the-art algorithm by a factor of 2.1. Instead of calculating and storing all the values in a DP matrix directly, our algorithm computes and stores mainly the differences between the values of adjacent cells in the matrix. Although the SWG algorithm and our algorithm can output exactly the same result, our algorithm mainly involves 8-bit integer operations, enabling us to exploit the full width of SIMD operations (e.g., 32) on modern processors. We also developed a library, libgaba, so that developers can easily integrate our algorithm into alignment programs. Conclusions: Our novel algorithm and optimized library implementation will facilitate accelerating nucleotide long-read analysis algorithms that use pairwise alignment stages. The library is implemented in the C programming language and available at https://github.com/ocxtal/libgaba.
31	ナノポアシークエンサーが研究の常識を変える!ナノポアリードのアライメントツール	2018/01/01	鈴木創笠原雅弘	実験医学	36/ 1, 16‐20				0288-5514	URL
32	グラフゲノムブラウザ	2017/12	横山稔之坂本祥駿関真秀鈴木穣笠原雅弘	生命科学系学会合同年次大会	2017年度, [4AT27-1315)]							生命科学系学会合同年次大会運営事務局
33	Genome of the pitcher plant Cephalotus reveals genetic changes associated with carnivory	2017/03	Kenji Fukushima Xiaodong Fang David Alvarez-Ponce Huimin Cai Lorenzo Carretero-Paulet Cui Chen Tien-Hao Chang Kimberly M. Farr Tomomichi Fujita Yuji Hiwatashi Yoshikazu Hoshi Takamasa Imai Masahiro Kasahara Pablo Librado Likai Mao Hitoshi Mori Tomoaki Nishiyama Masafumi Nozawa Gergo Palfalvi Stephen T. Pollard Julio Rozas Alejandro Sanchez-Gracia David Sankoff Tomoko F. Shibata Shuji Shigenobu Naomi Sumikawa Taketoshi Uzawa Meiying Xie Chunfang Zheng David D. Pollock Victor A. Albert Shuaicheng Li Mitsuyasu Hasebe	NATURE ECOLOGY & EVOLUTION	1/ 3, 59	研究論文（学術雑誌）		10.1038/s41559-016-0059	2397-334X			NATURE PUBLISHING GROUP	Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption. Analysis of digestive fluid proteins from C. follicularis and three other carnivorous plants with independent carnivorous origins revealed repeated co-options of stress-responsive protein lineages coupled with convergent amino acid substitutions to acquire digestive physiology. These results imply constraints on the available routes to evolve plant carnivory.
34	グラフゲノムブラウザ	2017	横山稔之坂本祥駿関真秀鈴木穣笠原雅弘	日本生化学会大会(Web)	90th
35	Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes	2014/08	Mari Miyamoto Daisuke Motooka Kazuyoshi Gotoh Takamasa Imai Kazutoshi Yoshitake Naohisa Goto Tetsuya Iida Teruo Yasunaga Toshihiro Horii Kazuharu Arakawa Masahiro Kasahara Shota Nakamura	BMC GENOMICS	15, 699	研究論文（学術雑誌）		10.1186/1471-2164-15-699	1471-2164			BIOMED CENTRAL LTD	Background: The availability of diverse second- and third-generation sequencing technologies enables the rapid determination of the sequences of bacterial genomes. However, identifying the sequencing technology most suitable for producing a finished genome with multiple chromosomes remains a challenge. We evaluated the abilities of the following three second-generation sequencers: Roche 454 GS Junior (GS Jr), Life Technologies Ion PGM (Ion PGM), and Illumina MiSeq (MiSeq) and a third-generation sequencer, the Pacific Biosciences RS sequencer (PacBio), by sequencing and assembling the genome of Vibrio parahaemolyticus, which consists of a 5-Mb genome comprising two circular chromosomes. Results: We sequenced the genome of V. parahaemolyticus with GS Jr, Ion PGM, MiSeq, and PacBio and performed de novo assembly with several genome assemblers. Although GS Jr generated the longest mean read length of 418 bp among the second-generation sequencers, the maximum contig length of the best assembly from GS Jr was 165 kbp, and the number of contigs was 309. Single runs of Ion PGM and MiSeq produced data of considerably greater sequencing coverage, 279x and 1,927x, respectively. The optimized result for Ion PGM contained 61 contigs assembled from reads of 77x coverage, and the longest contig was 895 kbp in size. Those for MiSeq were 34 contigs, 58x coverage, and 733 kbp, respectively. These results suggest that higher coverage depth is unnecessary for a better assembly result. We observed that multiple rRNA coding regions were fragmented in the assemblies from the second-generation sequencers, whereas PacBio generated two exceptionally long contigs of 3,288,561 and 1,875,537 bps, each of which was from a single chromosome, with 73x coverage and mean read length 3,119 bp, allowing us to determine the absolute positions of all rRNA operons. Conclusions: PacBio outperformed the other sequencers in terms of the length of contigs and reconstructed the greatest portion of the genome, achieving a genome assembly of "finished grade" because of its long reads. It showed the potential to assemble more complex genomes with multiple chromosomes containing more repetitive sequences.
36	次世代ゲノムテクノロジーの登場とその未来 7.1分子リアルタイムDNAシークエンサーを用いた史上最高精度のゲノム配列解読	2013/09/10	笠原雅弘	実験医学	31/ 15, 2365-2370				0288-5514	URL
37	Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.	2013/09	Suetsugu Y Futahashi R Kanamori H Kadono-Okuda K Sasanuma S Narukawa J Ajimura M Jouraku A Namiki N Shimomura M Sezutsu H Osanai-Futahashi M Suzuki MG Daimon T Shinoda T Taniai K Asaoka K Niwa R Kawaoka S Katsuma S Tamura T Noda H Kasahara M Sugano S Suzuki Y Fujiwara H Kataoka H Arunkumar KP Tomar A Nagaraju J Goldsmith MR Feng Q Xia Q Yamamoto K Shimada T Mita K	G3 (Bethesda, Md.)	3/ 9, 1481-1492	研究論文（学術雑誌）		10.1534/g3.113.006239					The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.
38	Segmental duplications in the silkworm genome	2013/07	Qian Zhao Zhenglin Zhu Masahiro Kasahara Shinichi Morishita Ze Zhang	BMC GENOMICS	14, 521	研究論文（学術雑誌）		10.1186/1471-2164-14-521	1471-2164			BIOMED CENTRAL LTD	Background: Segmental duplications (SDs) or low-copy repeats play important roles in both gene and genome evolution. SDs have been extensively investigated in many organisms, however, there is no information about SDs in the silkworm, Bombyx mori. Result: In this study, we identified and annotated the SDs in the silkworm genome. Our results suggested that SDs constitute similar to 1.4% of the silkworm genome sequence (>= 1 kb in length and >= 90% in the identity of sequence); the number is similar to that in Drosophila melanogaster but smaller than mammalian organisms. Almost half (42%) of the SD sequences are not assigned to chromosomes, indicating that the SDs are challenges for the assembling of genome sequences. We also provided experimental validation of large duplications using qPCR. The analysis of SD content indicated that the genes related to immunity, detoxification, reproduction, and environmental signal recognition are significantly enriched in the silkworm SDs. Conclusion: Our results suggested that segmental duplications have been problematic for sequencing and assembling of the silkworm genome. SDs may have important biological significances in immunity, detoxification, reproduction, and environmental signal recognition in the silkworm. This study provides insight into the evolution of the silkworm genome and an invaluable resource for insect genomics research.
39	Cost-Effective Sequencing of Full-Length cDNA Clones Powered by a De Novo-Reference Hybrid Assembly	2010/05	Reginaldo M. Kuroshu Junichi Watanabe Sumio Sugano Shinichi Morishita Yutaka Suzuki Masahiro Kasahara	PLOS ONE	5/ 5, e10517	研究論文（学術雑誌）		10.1371/journal.pone.0010517	1932-6203			PUBLIC LIBRARY SCIENCE	Background: Sequencing full-length cDNA clones is important to determine gene structures including alternative splice forms, and provides valuable resources for experimental analyses to reveal the biological functions of coded proteins. However, previous approaches for sequencing cDNA clones were expensive or time-consuming, and therefore, a fast and efficient sequencing approach was demanded. Methodology: We developed a program, MuSICA 2, that assembles millions of short (36-nucleotide) reads collected from a single flow cell lane of Illumina Genome Analyzer to shotgun-sequence,800 human full-length cDNA clones. MuSICA 2 performs a hybrid assembly in which an external de novo assembler is run first and the result is then improved by reference alignment of shotgun reads. We compared the MuSICA 2 assembly with 200 pooled full-length cDNA clones finished independently by the conventional primer-walking using Sanger sequencers. The exon-intron structure of the coding sequence was correct for more than 95% of the clones with coding sequence annotation when we excluded cDNA clones insufficiently represented in the shotgun library due to PCR failure (42 out of 200 clones excluded), and the nucleotide-level accuracy of coding sequences of those correct clones was over 99.99%. We also applied MuSICA 2 to full-length cDNA clones from Toxoplasma gondii, to confirm that its ability was competent even for non-human species. Conclusions: The entire sequencing and shotgun assembly takes less than 1 week and the consumables cost only, similar to US$3 per clone, demonstrating a significant advantage over previous approaches.
40	動物の多細胞化と遺伝子族多様化の関連性:I.シグナル伝達系	2010	岩部直之隈啓一加藤和貴藤博幸佐々木剛廣瀬希菅裕宮田隆岡田雅人鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	生化学	ROMBUNNO.1P-1143				0037-1017	URL
41	動物の多細胞化と遺伝子族多様化の関連性:II.細胞接着因子と転写因子	2010	隈啓一岩部直之加藤和貴藤博幸佐々木剛菅裕宮田隆鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	生化学	ROMBUNNO.1P-1144				0037-1017	URL
42	Genome sequencing project of a choanoflagellate, Monosiga ovata: II. Divergence patterns of gene family members in the early evolution of animals	2009/12	Naoyuki Iwabe Keiichi Kuma Kazutaka Katoh Hiroyuki Toh Nozomi Hirose Go Sasaki Yusuke Murata Hiroshi Suga Takashi Miyata Yutaka Suzuki Masahiro Kasahara Tadasu Shin-I Kazuko Ohishi Hiroshi Kagoshima Atsushi Toyoda Yoko Kuroki Sumio Sugano Shinichi Morishita Yuji Kohara Asao Fujiyama	GENES & GENETIC SYSTEMS	84/ 6, 450-450				1341-7568			GENETICS SOC JAPAN
43	Genome sequencing project of a choanoflagellate, Monosiga ovata: I. Genome structure	2009/12	Keiichi Kuma Naoyuki Iwabe Kazutaka Katoh Hiroyuki Toh Nozomi Hirose Go Sasaki Hiroshi Suga Takashi Miyata Yutaka Suzuki Masahiro Kasahara Tadasu Shin-I Kazuko Ohishi Hiroshi Kagoshima Atsushi Toyoda Yoko Kuroki Sumio Sugano Shinichi Morishita Yuji Kohara Asao Fujiyama	GENES & GENETIC SYSTEMS	84/ 6, 449-449				1341-7568			GENETICS SOC JAPAN
44	立襟鞭毛虫Monosiga ovataゲノム計画:II.動物初期進化における遺伝子の多様化	2009/08/28	岩部直之隈啓一加藤和貴藤博幸廣瀬希佐々木剛村田友輔菅裕宮田隆鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	日本遺伝学会大会プログラム・予稿集	81st, 123					URL
45	立襟鞭毛虫Monosiga ovataゲノム計画:I.ゲノム概観	2009/08/28	隈啓一岩部直之加藤和貴藤博幸廣瀬希佐々木剛菅裕宮田隆鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	日本遺伝学会大会プログラム・予稿集	81st, 122					URL
46	Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites	2009/01	Shin Sasaki Cecilia C. Mello Atsuko Shimada Yoichiro Nakatani Shin-ichi Hashimoto Masako Ogawa Kouji Matsushima Sam Guoping Gu Masahiro Kasahara Budrul Ahsan Atsushi Sasaki Taro Saito Yutaka Suzuki Sumio Sugano Yuji Kohara Hiroyuki Takeda Andrew Fire Shinichi Morishita	SCIENCE	323/ 5912, 401-404	研究論文（学術雑誌）		10.1126/science.1163183	0036-8075			AMER ASSOC ADVANCEMENT SCIENCE	Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using medaka (Japanese killifish, Oryzias latipes), by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping similar to 37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive similar to 200-base pair (bp) periodic pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately +200, +400, and +600 bp, whereas the point mutation rate showed corresponding valleys. This similar to 200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, +200, +400, and +600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale.
47	The genome of a lepidopteran model insect, the silkworm Bombyx mori	2008/12	Qingyou Xia Jun Wang Zeyang Zhou Ruiqiang Li Wei Fan Daojun Cheng Tingcai Cheng Junjie Qin Jun Duan Hanfu Xu Qibin Li Ning Li Mingwei Wang Fangyin Dai Chun Liu Ying Lin Ping Zhao Huijie Zhang Shiping Liu Xingfu Zha Chunfeng Li Aichun Zhao Minhui Pan Guoqing Pan Yihong Shen Zhihong Gao Zilong Wang Genhong Wang Zhengli Wu Yong Hou Chunli Chai Quanyou Yu Ningjia He Ze Zhang Songgang Li Huanming Yang Cheng Lu Jian Wang Zhonghuai Xiang Kazuei Mita Masahiro Kasahara Yoichiro Nakatani Kimiko Yamamoto Hiroaki Abe Brudrul Ahsan Takaaki Dai-mon Koichiro Doi Tsuguru Fujii Haruhiko Fujiwara Asao Fujiyama Ryo Futahashi Shin-ichi Hashimoto Jun Ishibashi Masafumi Iwami Keiko Kadono-Okuda Hiroyuki Kanamori Hiroshi Kataoka Susumu Katsuma Shinpei Kawaoka Hideki Kawasaki Yuji Kohara Toshinori Kozaki Reginaldo M. Kuroshu Seigo Kuwazaki Kouji Matsushima Hiroshi Minami Yukinobu Nagayasu Tatsuro Nakagawa Junko Narukawa Junko Nohata Kazuko Ohishi Yukiteru Ono Mizuko Osanai-Futahashi Katsu-hisa Ozaki Wei Qu Ladislav Roller Shin Sasaki Takuji Sasaki Atsushi Seino Masaru Shimomura Michihiko Shimomura Tadasu Shin-I Tetsuro Shinoda Takahiro Shiotsuki Yoshitaka Suetsugu Sumio Sugano Makiko Suwa Yutaka Suzuki Shige-Haru Takiya Toshiki Tamura Hiromitsu Tanaka Yoshiaki Tanaka Kazushige Touhara Tomoyuki Yamada Minoru Yamakawa Naoki Yamanaka Hiroshi Yoshikawa Yang-Sheng Zhong Toru Shima-da Shinichi Morishita	INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY	38/ 12, 1036-1045	研究論文（学術雑誌）		10.1016/j.ibmb.2008.11.004	0965-1748			PERGAMON-ELSEVIER SCIENCE LTD	Bombyx mori, the domesticated silkworm, is a major insect model for research, and the first lepidopteran for which draft genome sequences became available in 2004. Two independent data sets from whole-genome shotgun sequencing were merged and assembled together with newly obtained fosmid- and BAC-end sequences. The remarkably improved new assembly is presented here. The 8.5-fold sequence coverage of an estimated 432 Mb genome was assembled into scaffolds with an N50 size of similar to 3.7 Mb; the largest scaffold was 14.5 million base pairs. With help of a high-density SNP linkage map, we anchored 87% of the scaffold sequences to all 28 chromosomes. A particular feature was the high repetitive sequence content estimated to be 43.6% and that consisted mainly of transposable elements. We predicted 14,623 gene models based on a CLEAN-based algorithm, a more accurate prediction than the previous gene models for this species. Over three thousand silkworm genes have no homologs in other insect or vertebrate genomes. Some insights into gene evolution and into characteristic biological processes are presented here and in other papers in this issue. The massive silk production correlates with the existence of specific IRNA clusters, and of several sericin genes assembled in a cluster. The silkworm's adaptation to feeding on mulberry leaves, which contain toxic alkaloids, is likely linked to the presence of new-type sucrase genes, apparently acquired from bacteria. The silkworm genome also revealed the cascade of genes involved in the juvenile hormone biosynthesis pathway, and a large number of cuticular protein genes. (C) 2008 Elsevier Ltd. All rights reserved.
48	超高速シーケンサーとバイオインフォマティクスクロマチン構造は遺伝的変異の主要因の1つである(Chromatin structure as a major determinant of natural genetic variation)	2008/11	森下真一佐々木伸 Mello Cecilia 島田敦子中谷洋一郎橋本真一 Ogawa Masako 松島綱治 Gu Sam Guoping 笠原雅弘 Ahsan Budrul 佐々木惇斉藤太郎鈴木穣菅野純夫小原雄治武田洋幸 Fire Andrew	日本生化学会大会・日本分子生物学会年会合同大会講演要旨集	81回・31回, 3S8-8							(公社)日本生化学会
49	メダカ高密度SNP連鎖地図の作成と組換えの雌雄差	2008/08/20	成瀬清神藤智子笠原雅弘佐々木伸森下真一小原雄治武田洋幸	日本動物学会大会予稿集	79th, 115					URL
50	ゲノムアセンブラと新型シークエンサーを使用したゲノムシークエンシングの未来	2008/05/01	笠原雅弘	実験医学	26/ 7, 1021-1032				0288-5514	URL
51	立襟鞭毛虫Monosiga ovataゲノムプロジェクト:II.動物の初期進化における遺伝子多様化	2008	岩部直之隈啓一加藤和貴藤博幸廣瀬希佐々木剛菅裕宮田隆鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	生化学	1P-0693				0037-1017	URL
52	立襟鞭毛虫Monosiga ovataゲノムプロジェクト:I.ゲノムの概観	2008	隈啓一岩部直之加藤和貴藤博幸廣瀬希菅裕宮田隆鈴木穣笠原雅弘新井理大石加寿子鹿児島浩豊田敦黒木陽子菅野純夫森下真一小原雄治藤山秋佐夫	生化学	1P-0692				0037-1017	URL
53	Prospects on the Bombyx genome analysis	2007/05	K. Mita M. Kasahara S. Sasaki Y. Nagayasu T. Yamada H. Kanamori N. Namiki M. Kitagawa H. Yamashita Y. Yasukochi K. Kadono-Okuda K. Yamamoto M. Ajimura G. Rvikumar M. Shimomura Y. Nagamura T. Shin-I H. Abe T. Shimada S. Morishita T. Sasaki	JOURNAL OF INSECT SCIENCE	7	（MISC）研究発表要旨（国際会議）			1536-2442			UNIV ARIZONA
54	Large-scale genome sequence processing	2006/01/01	Masahiro Kasahara Shinichi Morishita	Large-Scale Genome Sequence Processing	1-237	（MISC）その他記事		10.1142/P436				Imperial College Press	Efficient computer programs have made it possible to elucidate and analyze large-scale genomic sequences. Fundamental tasks, such as the assembly of numerous whole-genome shotgun fragments, the alignment of complementary DNA sequences with a long genome, and the design of gene-specific primers or oligomers, require efficient algorithms and state-of-the-art implementation techniques. This textbook emphasizes basic software implementation techniques for processing large-scale genome sequences and provides executable sample programs.
55	ゲノムから情報科学ゲノムアセンブラの開発その技術的・理論的背景	2005/12/15	森下真一笠原雅弘佐々木伸	蛋白質核酸酵素	50/ 16, 2255-2262				0039-9450	URL		共立出版
56	ゲノムアセンブラの開発--その技術的・理論的背景 (ゲノムから生命システムへ) -- (ゲノムから情報科学)	2005/12	森下真一笠原雅弘佐々木伸	蛋白質核酸酵素	50/ 16, 2255-2262				0039-9450			共立出版
57	Medaka genome sequencing and the vertebrate genome evolution	2005/12	Kiyoshi Naruse Yoichiro Nakatani Wei Qu Masahiro Kasahara Shin Sasaki Tomoyuki Yamada Ahsan Budrul Koichiro Doi Yukinobu Nagayasu Shin-ichi Hashimoto Takanori Narita Yoko Kuroki Atsushi Toyoda Tomoko Jindo Daisuke Kobayashi Tadasu Shin-I Yuji Kohara Asao Fujiyama Shin-ichi Morishita Hiroyuki Takeda	ZOOLOGICAL SCIENCE	22/ 12, 1511-1512				0289-0003			ZOOLOGICAL SOC JAPAN
58	Draft genome sequence of medaka (Orizias latides) and its usetip ful applications	2005/12	Masahiro Kasahara Shin Sasaki Yoichiro Nakatani Wei Qu Ahsan Budrul Tomoyuki Yamada Yukinobu Nagayasu Koichiro Doi Kiyoshi Naruse Takanori Narita Tadasu Shin-I Tomoko Jindo Shin-ichi Hashimoto Koji Matsushima Yoko Kuroki Asao Fujiyama Hiroyuki Takeda Shinichi Morishita Yuji Kohara	ZOOLOGICAL SCIENCE	22/ 12, 1395-1396				0289-0003			ZOOLOGICAL SOC JAPAN
59	Medaka genome sequencing and the comparative genomics of fishes	2005/12	Kiyoshi Naruse Yoichiro Nakatani Wei Qu Masahiro Kasahara Shin Sasaki Tomoyuki Yamada Ahsan Budrul Koichiro Doi Yukinobu Nagayasu Shin-ichi Hashimoto Takanori Narita Yoko Kuroki Atsushi Toyoda Tomoko Jindo Daisuke Kobayashi Tadasu Shin-I Yusuke Takehana Keita Tanaka Mitsuru Sakaizumi Yuji Kohara Asao Fujiyama Shin-ichi Morishita Hiroyuki Takeda	ZOOLOGICAL SCIENCE	22/ 12, 1378-1379				0289-0003			ZOOLOGICAL SOC JAPAN
60	Introduction to genome assembler	2005/12	Morishita S. Kasahara M. Sasaki S.	Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme	50/ 16 Suppl, 2255-2262	研究論文（学術雑誌）			0039-9450	URL
61	メダカのゲノム進化解析	2005/11/25	中谷洋一郎成瀬清 QU Wei 笠原雅弘佐々木伸永安佑希允 BUDRUL Ahsan 山田智之土井晃一郎成田貴則新井理橋本真一藤山秋佐夫小原雄治武田洋幸森下真一	日本分子生物学会年会講演要旨集	28th, 41					URL
62	The genome sequence of silkworm, Bombyx mori	2004/02	K Mita M Kasahara S Sasaki Y Nagayasu T Yamada H Kanamori N Namiki M Kitagawa H Yamashita Y Yasukochi K Kadono-Okuda K Yamamoto M Ajimura G Ravikumar M Shimomura Y Nagamura T Shin-I H Abe T Shimada S Morishita T Sasaki	DNA RESEARCH	11/ 1, 27-35	研究論文（学術雑誌）			1340-2838			UNIVERSAL ACADEMY PRESS INC	We performed threefold shotgun sequencing of the silkworm (Bombyx Mori) genome to obtain a draft sequence and establish a basic resource for comprehensive genome analysis. By using the newly developed RAMEN assembler, the sequence data derived from whole-genome shotgun (WGS) sequencing were assembled into 49,345 scaffolds that span a total length of 514 Mb including gaps and 387 Mb without gaps. Because the genome size of the silkworm is estimated to be 530 Mb, almost 97% of the genome has been organized in scaffolds, of which 75% has been sequenced. By carrying out a BLAST search for 50 characteristic Bombyx genes and 11,202 non-redundant expressed sequence tags (ESTs) in a Bombyx EST database against the WGS sequence data, we evaluated the validity of the sequence for elucidating the majority of silkworm genes. Analysis of the WGS data revealed that the silkworm genome contains many repetitive sequences with an average length of <500 bp. These repetitive sequences appear to have been derived from truncated transposons, which are interspersed at 2.5- to 3-kb intervals throughout the genome. This pattern suggests that silkworm may have an active mechanism that promotes removal of transposons from the genome. We also found evidence for insertions of mitochondrial DNA fragments at 9 sites. A search for Bombyx orthologs to Drosophila genes controlling sex determination in the WGS data revealed 11 Bombyx genes and suggested that the sex-determining systems differ profoundly between the two species.

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