Chromosome-level genome assembly of Japanese chestnut (<i>Castanea crenata</i> Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Shirasawa, Kenta; Nishio, Sogo; Terakami, Shingo; Botta, Roberto; Marinoni, Daniela Torello; Isobe, Sachiko

doi:10.1093/dnares/dsab016

Cited by 15 publications

(14 citation statements)

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“…Compared to the genome assembly of the Japanese chestnut cultivar 'Ginyose' (Shirasawa et al, 2021), the contig N50 of the genome assembly of cultivar 'Tsukuba' improved from 1.59 Mb to 6.36 Mb, and the cumulative length of these two assemblies also confirmed the continuity of the genome of cultivar 'Tsukuba' (Figure S5). There were also more sequences anchored to the pseudochromosomes in the genome assembly of cultivar 'Tsukuba'.…”

Section: Discussionmentioning

confidence: 69%

“…A total of 421.37 Mb of the sequence was annotated as repetitive sequences in the genome assembly of cultivar 'Tsukuba', which was similar to the genome assembly of cultivar 'Ginyose' (Shirasawa et al, 2021). The two Japanese chestnut genome assemblies exhibit a repetitive rate similar to that of the genome assembly of Chinese chestnut (431.41 Mb,55.74%;437.75 Mb,64.38%;423.16 Mb,53.49%;442.76 Mb,64.43%) described by Sun et al (Sun et al, 2020) and Hu et al (Hu et al, 2022), but slightly different from that found in research by Wang et al (366.84 Mb,53.24%) (Wang et al, 2020b) and Xing et al (390 Mb,49.69%) (Xing et al, 2019).…”

Section: Annotation and Evolutionary History Of The Japanese Chestnut...mentioning

confidence: 99%

“…and American chestnut ( C. dentate Borkh.). Both Japanese chestnut and Chinese chestnut are blight-resistant, in contrast to European chestnut and American chestnut ( Shirasawa et al., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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Chromosome-level genome assembly provides new insights into Japanese chestnut (Castanea crenata) genomes

et al. 2022

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Japanese chestnut (Castanea crenata Sieb. et Zucc) is an economically and ecologically important chestnut species in East Asia. Here, we presented a high-quality chromosome-level reference genome of the Japanese chestnut cultivar ‘Tsukuba’ by combining Nanopore long reads and Hi-C sequencing. The final assembly has a size of 718.30 Mb and consists of 12 pseudochromosomes ranging from 41.03 to 92.03 Mb, with a BUSCO complete gene percentage of 97.6%. A total of 421.37 Mb repetitive sequences and 46,744 gene models encoding 46,463 proteins were predicted in the genome. Genome evolution analysis showed that Japanese chestnut is closely related to Chinese chestnut and these species shared a common ancestor ~6.5 million years ago. This high-quality Japanese chestnut genome represents an important resource for the chestnut genomics community and will improve our understanding of chestnut biology and evolution.

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Section: Discussionmentioning

confidence: 69%

Section: Annotation and Evolutionary History Of The Japanese Chestnut...mentioning

confidence: 99%

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Chromosome-level genome assembly provides new insights into Japanese chestnut (Castanea crenata) genomes

et al. 2022

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“…Screening individual trees within a breeding population and identifying the genetic basis of important traits should become faster, possibly reducing the number of BC needed in traditional breeding programs. The de novo transcriptome assembly provided a significant contribution, however, future studies can now rely on genomes of C. mollissima ( Xing et al, 2019 ; Staton et al, 2020 ), C. crenata ( Shirasawa et al, 2021 ), and C. dentata ( Sandercock et al, 2022 ).…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

European and American chestnuts: An overview of the main threats and control efforts

et al. 2022

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Chestnuts are multipurpose trees significant for the economy and wildlife. These trees are currently found around the globe, demonstrating their genetic adaptation to different environmental conditions. Several biotic and abiotic stresses have challenged these species, contributing to the decline of European chestnut production and the functional extinction of the American chestnut. Several efforts started over the last century to understand the cellular, molecular, and genetic interactions behind all chestnut biotic and abiotic interactions. Most efforts have been toward breeding for the primary diseases, chestnut blight and ink disease caused by the pathogens, Cryphonectria parasitica and Phytophthora cinnamomi, respectively. In Europe and North America, researchers have been using the Asian chestnut species, which co-evolved with the pathogens, to introgress resistance genes into the susceptible species. Breeding woody trees has several limitations which can be mostly related to the long life cycles of these species and the big genome landscapes. Consequently, it takes decades to improve traits of interest, such as resistance to pathogens. Currently, the availability of genome sequences and next-generation sequencing techniques may provide new tools to help overcome most of the problems tree breeding is still facing. This review summarizes European and American chestnut’s main biotic stresses and discusses breeding and biotechnological efforts developed over the last decades, having ink disease and chestnut blight as the main focus. Climate change is a rising concern, and in this context, the adaptation of chestnuts to adverse environmental conditions is of extreme importance for chestnut production. Therefore, we also discuss the abiotic challenges on European chestnuts, where the response to abiotic stress at the genetic and molecular level has been explored.

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“…As a proof of concept, MYBs encoded in the recently sequenced Castanea crenata genome [65] were investigated. The predicted peptide sequences were screened with default parameters and resulted in the identification of 136 MYBs (Fig.…”

Section: Discovery Of Mybs In the Castanea Crenata Genome Sequencementioning

confidence: 99%

Automatic identification and annotation of MYB gene family members in plants

Pucker

2021

Preprint

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Background: MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies. Results: A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator. Conclusions: This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.

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Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Cited by 15 publications

References 20 publications

Chromosome-level genome assembly provides new insights into Japanese chestnut (Castanea crenata) genomes

Chromosome-level genome assembly provides new insights into Japanese chestnut (Castanea crenata) genomes

European and American chestnuts: An overview of the main threats and control efforts

Automatic identification and annotation of MYB gene family members in plants

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