著者

Kenta Shirasawa Daijiro Harada Hideki Hirakawa Sachiko Isobe Chittaranjan Kole

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20146, (Released:2021-04-06)

被引用文献数

19

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Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 300 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 88.7%, the average coverage of chromosome-level pseudomolecules was 72.9%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.

著者

Takashi Okubo Takahiro Tsukui Hiroko Maita Shinobu Okamoto Kenshiro Oshima Takatomo Fujisawa Akihiro Saito Hiroyuki Futamata Reiko Hattori Yumi Shimomura Shin Haruta Sho Morimoto Yong Wang Yoriko Sakai Masahira Hattori Shin-ichi Aizawa Kenji V. P. Nagashima Sachiko Masuda Tsutomu Hattori Akifumi Yamashita Zhihua Bao Masahito Hayatsu Hiromi Kajiya-Kanegae Ikuo Yoshinaga Kazunori Sakamoto Koki Toyota Mitsuteru Nakao Mitsuyo Kohara Mizue Anda Rieko Niwa Park Jung-Hwan Reiko Sameshima-Saito Shin-ichi Tokuda Sumiko Yamamoto Syuji Yamamoto Tadashi Yokoyama Tomoko Akutsu Yasukazu Nakamura Yuka Nakahira-Yanaka Yuko Takada Hoshino Hideki Hirakawa Hisayuki Mitsui Kimihiro Terasawa Manabu Itakura Shusei Sato Wakako Ikeda-Ohtsubo Natsuko Sakakura Eli Kaminuma Kiwamu Minamisawa

出版者

Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.1203230372, (Released:2012-03-28)

参考文献数

1

被引用文献数

37 53

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Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

著者

Katsuhiko Sumitomo Kenta Shirasawa Sachiko N. Isobe Hideki Hirakawa Akiho Harata Masato Kawabe Masafumi Yagi Masaaki Osaka Miyuki Kunihisa Fumiya Taniguchi

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20063, (Released:2021-03-25)

被引用文献数

6

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White rust caused by Puccinia horiana Henn. adversely affects chrysanthemum (Chrysanthemum morifolium Ramat.) production. The breeding of resistant varieties is effective in controlling the disease. Here we aimed to develop DNA markers for the strong resistance to P. horiana. We conducted a linkage analysis based on the genome-wide association study (GWAS) method. We employed a biparental population for the GWAS, wherein the single nucleotide polymorphism (SNP) allele frequency could be predicted. The population was derived from crosses between a strong resistant “Southern Pegasus” and a susceptible line. The GWAS used simplex and double-simplex SNP markers selected out of SNP candidates mined from ddRAD-Seq data of an F1 biparental population. These F1 individuals segregated in a 1:1 ratio of resistant to susceptible. Twenty-one simplex SNPs were significantly associated with P. horiana resistance in “Southern Pegasus” and generated one linkage group. These results show the presence of a single resistance gene in “Southern Pegasus”. We identified the nearest SNP marker located 2.2 cM from P. horiana resistance locus and demonstrated this SNP marker-resistance link using an independent population. This is the first report of an effective DNA marker linked to a gene for P. horiana resistance in chrysanthemum.

著者

Kenta Shirasawa Daijiro Harada Hideki Hirakawa Sachiko Isobe Chittaranjan Kole

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.71, no.2, pp.117-124, 2021 (Released:2021-05-20)

参考文献数

44

被引用文献数

19

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Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.

著者

Sachiko Isobe Kenta Shirasawa Hideki Hirakawa

出版者

The Japanese Society for Horticultural Science

雑誌

The Horticulture Journal (ISSN:21890102)

巻号頁・発行日

vol.89, no.2, pp.108-114, 2020 (Released:2020-04-06)

参考文献数

37

被引用文献数

3

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Next generation sequencing (NGS) is one of the most impactful technologies to appear in the 21st century, and has already brought important changes to agriculture, especially in the field of breeding. Construction of a reference genome is key to the advancement of genomic studies, and therefore, de novo whole genome assembly has been performed in various plants, including strawberry. Strawberry (Fragaria × ananassa) is an allo-octoploid species (2n = 8x = 56), which has four discriminable subgenomes. Because of its complex genome structure, de novo whole genome assembly in strawberry has been considered a difficult challenge. However, recent advances of NGS technologies have allowed the construction of chromosome-scale de novo whole genome assembly. In this manuscript, we review the recent advances in de novo whole genome sequencing in strawberry and other Fragaria species. The genome structure and domestication history in strawberry is one of the largest questions in genetic and genomic studies in strawberry. Therefore, the domestication history in strawberry is also be reviewed based on comparisons of genes and genome sequences across Fragaria species.

著者

Turgut Yigit Akyol Rieko Niwa Hideki Hirakawa Hayato Maruyama Takumi Sato Takae Suzuki Ayako Fukunaga Takashi Sato Shigenobu Yoshida Keitaro Tawaraya Masanori Saito Tatsuhiro Ezawa Shusei Sato

出版者

Japanese Society of Microbial Ecology · The Japanese Society of Soil Microbiology

雑誌

Microbes and Environments (ISSN:13426311)

巻号頁・発行日

pp.ME18109, (Released:2018-12-22)

被引用文献数

31

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Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.

著者

Naoki Yokotani Yoshinori Hasegawa Yusuke Kouzai Hideki Hirakawa Sachiko Isobe

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

vol.40, no.4, pp.273-282, 2023-12-25 (Released:2023-12-25)

参考文献数

51

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Salicylic acid (SA) is known to be involved in the immunity against Clavibacter michiganensis ssp. michiganensis (Cmm) that causes bacterial canker in tomato. To identify the candidate genes associated with SA-inducible Cmm resistance, transcriptome analysis was conducted via RNA sequencing in tomato plants treated with SA. SA treatment upregulated various defense-associated genes, such as PR and GST genes, in tomato cotyledons. A comparison of SA- and Cmm-responsive genes revealed that both SA treatment and Cmm infection commonly upregulated a large number of genes. Gene Ontology (GO) analysis indicated that the GO terms associated with plant immunity were over-represented in both SA- and Cmm-induced genes. The genes commonly downregulated by both SA treatment and Cmm infection were associated with the cell cycle and may be involved in growth and immunity trade-off through cell division. After SA treatment, several proteins that were predicted to play a role in immune signaling, such as resistance gene analogs, Ca2+ sensors, and WRKY transcription factors, were transcriptionally upregulated. The W-box element, which was targeted by WRKYs, was over-represented in the promoter regions of genes upregulated by both SA treatment and Cmm infection, supporting the speculation that WRKYs are important for the SA-mediated immunity against Cmm. Prediction of protein–protein interactions suggested that genes encoding receptor-like kinases and EF-hand proteins play an important role in immune signaling. Thus, various candidate genes involved in SA-inducible Cmm resistance were identified.

著者

Masako Ichikawa Norio Kato Erika Toda Masakazu Kashihara Yuji Ishida Yukoh Hiei Sachiko N. Isobe Kenta Shirasawa Hideki Hirakawa Takashi Okamoto Toshihiko Komari

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.3, pp.349-353, 2023 (Released:2023-07-27)

参考文献数

25

被引用文献数

1

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Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The natural mutation rate of 1.2 × 10–8 calculated using the variants in the seed-propagated plants was consistent with the values reported previously. The ratio of single nucleotide variants (SNVs) among the variants in the seed-propagated plants was 91.1%, which is higher than 56.1% previously reported, and not significantly different from those in the regenerants. Overall, the ratio of transitions to transversions of SNVs was lower in the regenerants as shown previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.