2018
DOI: 10.1093/nar/gky1000
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15 years of GDR: New data and functionality in the Genome Database for Rosaceae

Abstract: The Genome Database for Rosaceae (GDR, https://www.rosaceae.org) is an integrated web-based community database resource providing access to publicly available genomics, genetics and breeding data and data-mining tools to facilitate basic, translational and applied research in Rosaceae. The volume of data in GDR has increased greatly over the last 5 years. The GDR now houses multiple versions of whole genome assembly and annotation data from 14 species, made available by recent advances in sequencing technology… Show more

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Cited by 354 publications
(264 citation statements)
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“…With the exception of Brassicales and Cucumis sativus (Cucurbitaceae), group Q UGTs can be found throughout the rosids (Vitales, malvids and fabids), suggesting that group Q was present in the common ancestor of Malvales ( T. cacao ) and Brassicales in the malvids, but was lost in Brassicales (Figure ). In addition, group Q UGTs are absent in the syntenic chromosomal regions of A. thaliana , but present in those of other rosids ( V. vinifera , E. grandis and R. chinensis ), providing further support to the loss of group Q UGTs in Brassicales (Figure ; the syntenic relationships among different chromosomal regions were reported in Amborella Genome Project, ; Proost et al ., ; Hibrand Saint‐Oyant et al ., ; Jung et al ., ). Similarly, two group Q UGTs in Musa acuminata (Zingiberales) share an ancestry with the other angiosperm group Q UGTs.…”
Section: Discussionmentioning
confidence: 97%
“…With the exception of Brassicales and Cucumis sativus (Cucurbitaceae), group Q UGTs can be found throughout the rosids (Vitales, malvids and fabids), suggesting that group Q was present in the common ancestor of Malvales ( T. cacao ) and Brassicales in the malvids, but was lost in Brassicales (Figure ). In addition, group Q UGTs are absent in the syntenic chromosomal regions of A. thaliana , but present in those of other rosids ( V. vinifera , E. grandis and R. chinensis ), providing further support to the loss of group Q UGTs in Brassicales (Figure ; the syntenic relationships among different chromosomal regions were reported in Amborella Genome Project, ; Proost et al ., ; Hibrand Saint‐Oyant et al ., ; Jung et al ., ). Similarly, two group Q UGTs in Musa acuminata (Zingiberales) share an ancestry with the other angiosperm group Q UGTs.…”
Section: Discussionmentioning
confidence: 97%
“…Gene ontology terms (GOs) were retrieved from the Genome Database for Rosaceae (GDR, Jung et al . 2019).…”
Section: Methodsmentioning
confidence: 99%
“…The research provides us with a comprehensive knowledge of RALF-like genes in seven Rosaceae species. The peach (Prunus persica) genome (v2.0.a1) [22], apple (Malus × domestica) genome (HFTH1 Whole Genome v1.0) [23], wild strawberry (Fragaria vesca) genome (v4.0.a1) [24], cultivated strawberry (Fragaria × ananassa) genome (v1.0.a1) [25], European pear (Pyrus communis) genome (v1.0) [26], sweet cherry (Prunus avium) genome (v1.0.a1) [27], and related annotation files were downloaded from GDR database [28].The genome and related annotation files of Japanese apricot (Prunus mume) (v1.0) [29] were retrieved from NCBI (https://www.ncbi.nlm.nih.gov/). The Arabidopsis RALF-like proteins were downloaded from the Phytozome database [30] using "RALF" as the keyword, and the RALF genes reported in another research were added [4].…”
mentioning
confidence: 99%
“…The research provides us with a comprehensive knowledge of RALF-like genes in seven Rosaceae species. The peach (Prunus persica) genome (v2.0.a1) [22], apple (Malus × domestica) genome (HFTH1 Whole Genome v1.0) [23], wild strawberry (Fragaria vesca) genome (v4.0.a1) [24], cultivated strawberry (Fragaria × ananassa) genome (v1.0.a1) [25], European pear (Pyrus communis) genome (v1.0) [26], sweet cherry (Prunus avium) genome (v1.0.a1) [27], and related annotation files were downloaded from GDR database [28].…”
mentioning
confidence: 99%