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realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)

With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensiv...

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Autores principales: Chen, Fei, Zhang, Jiawei, Chen, Junhao, Li, Xiaojiang, Dong, Wei, Hu, Jian, Lin, Meigui, Liu, Yanhui, Li, Guowei, Wang, Zhengjia, Zhang, Liangsheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051438/
https://www.ncbi.nlm.nih.gov/pubmed/30020436
http://dx.doi.org/10.1093/database/bay072
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author Chen, Fei
Zhang, Jiawei
Chen, Junhao
Li, Xiaojiang
Dong, Wei
Hu, Jian
Lin, Meigui
Liu, Yanhui
Li, Guowei
Wang, Zhengjia
Zhang, Liangsheng
author_facet Chen, Fei
Zhang, Jiawei
Chen, Junhao
Li, Xiaojiang
Dong, Wei
Hu, Jian
Lin, Meigui
Liu, Yanhui
Li, Guowei
Wang, Zhengjia
Zhang, Liangsheng
author_sort Chen, Fei
collection PubMed
description With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development. Database URL: http://realdb.algaegenome.org/
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spelling pubmed-60514382018-07-23 realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta) Chen, Fei Zhang, Jiawei Chen, Junhao Li, Xiaojiang Dong, Wei Hu, Jian Lin, Meigui Liu, Yanhui Li, Guowei Wang, Zhengjia Zhang, Liangsheng Database (Oxford) Original Article With over 6000 species in seven classes, red algae (Rhodophyta) have diverse economic, ecological, experimental and evolutionary values. However, red algae are usually absent or rare in comparative analyses because genomic information of this phylum is often under-represented in various comprehensive genome databases. To improve the accessibility to the ome data and omics tools for red algae, we provided 10 genomes and 27 transcriptomes representing all seven classes of Rhodophyta. Three genomes and 18 transcriptomes were de novo assembled and annotated in this project. User-friendly BLAST suit, Jbrowse tools and search system were developed for online analyses. Detailed introductions to red algae taxonomy and the sequencing status are also provided. In conclusion, realDB (realDB.algaegenome.org) provides a platform covering the most genome and transcriptome data for red algae and a suite of tools for online analyses, and will attract both red algal biologists and those working on plant ecology, evolution and development. Database URL: http://realdb.algaegenome.org/ Oxford University Press 2018-07-17 /pmc/articles/PMC6051438/ /pubmed/30020436 http://dx.doi.org/10.1093/database/bay072 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Chen, Fei
Zhang, Jiawei
Chen, Junhao
Li, Xiaojiang
Dong, Wei
Hu, Jian
Lin, Meigui
Liu, Yanhui
Li, Guowei
Wang, Zhengjia
Zhang, Liangsheng
realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title_full realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title_fullStr realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title_full_unstemmed realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title_short realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta)
title_sort realdb: a genome and transcriptome resource for the red algae (phylum rhodophyta)
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6051438/
https://www.ncbi.nlm.nih.gov/pubmed/30020436
http://dx.doi.org/10.1093/database/bay072
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