AI Article Synopsis
- Orchids are diverse species with unique floral structures, making them significant both economically and culturally.
- The newly updated OrchidBase 6.0 includes whole-genome sequences and transcriptomes for three Cymbidium species, enhancing research resources for the plant science community.
- New analytical methods were created to improve orchid genome analysis, supporting the growing needs for data management and research in orchid genetics.
Article Abstract
Background: Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study.
Description: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version of OrchidBase 6.0. Furthermore, four new analytical methods, namely regulation, updated transcriptome, advanced BLAST, and domain search, were developed for orchid genome analyses.
Conclusion: OrchidBase 6.0 extended genetic information to that of eight orchid species and created new tools for an expanded community curation in response to the ever-increasing volume and complexity of data.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11697506 | PMC |
| http://dx.doi.org/10.1186/s12870-024-06024-1 | DOI Listing |
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- New analytical methods were created to improve orchid genome analysis, supporting the growing needs for data management and research in orchid genetics.
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