OrchidBase 4.0: a database for orchid genomics and molecular biology
Abstract Background The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic infor...
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| Format: | Article |
| Language: | English |
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BMC
2021-08-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-021-03140-0 |
| _version_ | 1818363322749157376 |
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| author | Yu-Yun Hsiao Chih-Hsiung Fu Sau-Yee Ho Chung-I Li You-Yi Chen Wan-Lin Wu Jeen-Shing Wang Di-Yang Zhang Wen-Qi Hu Xia Yu Wei-Hong Sun Zhuang Zhou Ke-Wei Liu Laiqiang Huang Si-Ren Lan Hong-Hwa Chen Wei-Sheng Wu Zhong-Jian Liu Wen-Chieh Tsai |
| author_facet | Yu-Yun Hsiao Chih-Hsiung Fu Sau-Yee Ho Chung-I Li You-Yi Chen Wan-Lin Wu Jeen-Shing Wang Di-Yang Zhang Wen-Qi Hu Xia Yu Wei-Hong Sun Zhuang Zhou Ke-Wei Liu Laiqiang Huang Si-Ren Lan Hong-Hwa Chen Wei-Sheng Wu Zhong-Jian Liu Wen-Chieh Tsai |
| author_sort | Yu-Yun Hsiao |
| collection | DOAJ |
| description | Abstract Background The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. Description Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. Conclusions OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/ |
| first_indexed | 2024-12-13T21:46:38Z |
| format | Article |
| id | doaj.art-89a7d504e5a24b66b073e29c7340c5ff |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-13T21:46:38Z |
| publishDate | 2021-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-89a7d504e5a24b66b073e29c7340c5ff2022-12-21T23:30:23ZengBMCBMC Plant Biology1471-22292021-08-0121111110.1186/s12870-021-03140-0OrchidBase 4.0: a database for orchid genomics and molecular biologyYu-Yun Hsiao0Chih-Hsiung Fu1Sau-Yee Ho2Chung-I Li3You-Yi Chen4Wan-Lin Wu5Jeen-Shing Wang6Di-Yang Zhang7Wen-Qi Hu8Xia Yu9Wei-Hong Sun10Zhuang Zhou11Ke-Wei Liu12Laiqiang Huang13Si-Ren Lan14Hong-Hwa Chen15Wei-Sheng Wu16Zhong-Jian Liu17Wen-Chieh Tsai18Orchid Research and Development Center, National Cheng Kung UniversityOrchid Research and Development Center, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityDepartment of Statistics, National Cheng Kung UniversityDepartment of Life Sciences, National Cheng Kung UniversityOrchid Research and Development Center, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversitySchool of Life Sciences, Tsinghua UniversitySchool of Life Sciences, Tsinghua UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityOrchid Research and Development Center, National Cheng Kung UniversityDepartment of Electrical Engineering, National Cheng Kung UniversityKey Lab of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry UniversityOrchid Research and Development Center, National Cheng Kung UniversityAbstract Background The Orchid family is the largest families of the monocotyledons and an economically important ornamental plant worldwide. Given the pivotal role of this plant to humans, botanical researchers and breeding communities should have access to valuable genomic and transcriptomic information of this plant. Previously, we established OrchidBase, which contains expressed sequence tags (ESTs) from different tissues and developmental stages of Phalaenopsis as well as biotic and abiotic stress-treated Phalaenopsis. The database includes floral transcriptomic sequences from 10 orchid species across all the five subfamilies of Orchidaceae. Description Recently, the whole-genome sequences of Apostasia shenzhenica, Dendrobium catenatum, and Phalaenopsis equestris were de novo assembled and analyzed. These datasets were used to develop OrchidBase 4.0, including genomic and transcriptomic data for these three orchid species. OrchidBase 4.0 offers information for gene annotation, gene expression with fragments per kilobase of transcript per millions mapped reads (FPKM), KEGG pathways and BLAST search. In addition, assembled genome sequences and location of genes and miRNAs could be visualized by the genome browser. The online resources in OrchidBase 4.0 can be accessed by browsing or using BLAST. Users can also download the assembled scaffold sequences and the predicted gene and protein sequences of these three orchid species. Conclusions OrchidBase 4.0 is the first database that contain the whole-genome sequences and annotations of multiple orchid species. OrchidBase 4.0 is available at http://orchidbase.itps.ncku.edu.tw/https://doi.org/10.1186/s12870-021-03140-0OrchidWhole-genome sequencesApostasia shenzhenicaDendrobium catenatumPhalaenopsis equestrisDatabase |
| spellingShingle | Yu-Yun Hsiao Chih-Hsiung Fu Sau-Yee Ho Chung-I Li You-Yi Chen Wan-Lin Wu Jeen-Shing Wang Di-Yang Zhang Wen-Qi Hu Xia Yu Wei-Hong Sun Zhuang Zhou Ke-Wei Liu Laiqiang Huang Si-Ren Lan Hong-Hwa Chen Wei-Sheng Wu Zhong-Jian Liu Wen-Chieh Tsai OrchidBase 4.0: a database for orchid genomics and molecular biology BMC Plant Biology Orchid Whole-genome sequences Apostasia shenzhenica Dendrobium catenatum Phalaenopsis equestris Database |
| title | OrchidBase 4.0: a database for orchid genomics and molecular biology |
| title_full | OrchidBase 4.0: a database for orchid genomics and molecular biology |
| title_fullStr | OrchidBase 4.0: a database for orchid genomics and molecular biology |
| title_full_unstemmed | OrchidBase 4.0: a database for orchid genomics and molecular biology |
| title_short | OrchidBase 4.0: a database for orchid genomics and molecular biology |
| title_sort | orchidbase 4 0 a database for orchid genomics and molecular biology |
| topic | Orchid Whole-genome sequences Apostasia shenzhenica Dendrobium catenatum Phalaenopsis equestris Database |
| url | https://doi.org/10.1186/s12870-021-03140-0 |
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