TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome

Koshimizu, Shizuka; Nakamura, Yoshitomo; Nishitani, Chikako; Kobayashi, Mariko; Ohyanagi, Hajime; Yamamoto, Takatsugu; Yano, Kentarô

doi:10.1038/s41598-019-55287-4

Cited by 11 publications

(7 citation statements)

References 42 publications

(46 reference statements)

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“…The predicted genes in the genomes of the Japanese pear (PPY_r1.0), apple (GDDH13, v1.1), 4 Chinese white pear (Dangshan Suli, v1.1), 6 European pear (Bartlett DH, v2.0), 5 and the transcriptome of Japanese pear (Ppyrifolia_protein_v1.0). 10 …”

Section: Results and Data Descriptionmentioning

confidence: 99%

“…Two presets of Augustus and SNAP for Arabidopsis were used as training data for ab initio prediction. In addition, peptide sequences of apple (GDDH13, v1.1), 4 European pear (Bartlett DH, v2.0), 5 and Chinese white pear (Dangshan Suli, v1.1) 6 registered in the Genome Database for Rosaceae (GDR), 17 as well as transcriptome data for Japanese pear (Ppyrifolia_protein_v1.0), 10 were also employed in the prediction based on the protein homology evidence. Short gene sequences of <300 bases, as well as genes predicted with an annotation edit distance (AED) of >0.5 which threshold is proposed as good annotations in the MAKER protocol, were removed to facilitate selection of high-confidence genes.…”

Section: Methodsmentioning

confidence: 99%

“…In apple 4 and European pear, 5 doubled-haploid lines were developed to reduce the genome complexities to simplify the de novo genome sequencing analysis. However, neither doubled-haploid lines nor genome sequence data are available for Japanese pear, despite the publication of transcriptome data 10 and genetic maps. 11 , 12 …”

Section: Introductionmentioning

confidence: 99%

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Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

2021

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Aim We analyzed the genome sequence of a Japanese pear (Pyrus pyrifolia) to facilitate its genetics and genomics as well as breeding programs, in which a variety ′Nijisseiki′ with superior flesh texture has been used as a parent for most Japanese pear cultivars. Methods and results De novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6 Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 high-confidence protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of genome-wide duplication was observed, consistent with related species. Conclusion and Perspective This is the first chromosome-scale genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

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Section: Results and Data Descriptionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

2021

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“…A reference transcriptome of Chinese pear ( Pyrus pyrifolia ) was constructed by utilizing PacBio, 454, and Sanger sequencing, and it is stored in the database TRANSNAP ( http://plantomics.mind.meiji.ac.jp/nashi/ ) (Koshimizu et al, 2019 ). The database also includes gene functional annotation performed by BLASTP (Altschul et al, 1990 ), KAAS (Moriya et al, 2007 ), and InterProScan (Jones et al, 2014 ).…”

Section: Computational Databases For Rosaceae Speciesmentioning

confidence: 99%

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Xiao

Mount

et al. 2021

Front. Plant Sci.

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Rosaceae, a large plant family of more than 3,000 species, consists of many economically important fruit and ornamental crops, including peach, apple, strawberry, raspberry, cherry, and rose. These horticultural crops are not only important economic drivers in many regions of the world, but also major sources of human nutrition. Additionally, due to the diversity of fruit types in Rosaceae, this plant family offers excellent opportunities for investigations into fleshy fruit diversity, evolution, and development. With the development of high-throughput sequencing technologies and computational tools, an increasing number of high-quality genomes and transcriptomes of Rosaceae species have become available and will greatly facilitate Rosaceae research and breeding. This review summarizes major genomic resources and genome research progress in Rosaceae, highlights important databases, and suggests areas for further improvement. The availability of these big data resources will greatly accelerate research progress and enhance the agricultural productivity of Rosaceae.

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“…To simplify genomic analysis, doubled-haploid lines were developed to reduce the genome complexities in materials used for genome sequencing 5,6 . However, neither doubled-haploid lines nor genome sequence data are available for Japanese pear, despite the publication of transcriptome data 10 and genetic maps 11,12 .…”

Section: Introductionmentioning

confidence: 99%

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

Shirasawa

Itai

Isobe

2020

Preprint

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AimThe Japanese pear (P. pyrifolia) variety ‘Nijisseiki’ is valued for its superior flesh texture, which has led to its use as a breeding parent for most Japanese pear cultivars. However, in the absence of genomic resources for Japanese pear, the parents of the ‘Nijisseiki’ cultivar remain unknown, as does the genetic basis of its favorable texture. The genomes of pear and related species are complex due to ancestral whole genome duplication and high heterozygosity, and long-sequencing technology was used to address this.Methods and ResultsDe novo assembly of long sequence reads covered 136× of the Japanese pear genome and generated 503.9 Mb contigs consisting of 114 sequences with an N50 value of 7.6□Mb. Contigs were assigned to Japanese pear genetic maps to establish 17 chromosome-scale sequences. In total, 44,876 protein-encoding genes were predicted, 84.3% of which were supported by predicted genes and transcriptome data from Japanese pear relatives. As expected, evidence of whole genome duplication was observed, consistent with related species.Conclusion and PerspectiveThis is the first genome sequence analysis reported for Japanese pear, and this resource will support breeding programs and provide new insights into the physiology and evolutionary history of Japanese pear.

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TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome

Cited by 11 publications

References 42 publications

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

An Atlas of Genomic Resources for Studying Rosaceae Fruits and Ornamentals

Chromosome-scale genome assembly of Japanese pear (Pyrus pyrifolia) variety ‘Nijisseiki’

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