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ANAgdb currently encompasses 10 publicly available genome assemblies across six species and 1 newly assembled genome (Amtr_2024) produced by our group, including Amborella trichopoda, Brasenia schreberi, Euryale ferox, Euryale ferox, Nuphar advena, Nymphaea colorata, and Nymphaea thermarum. These datasets represent all open-access genome assemblies in the ANA-grade.
Genome Information
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ANAgdb now includes a comprehensive collection of 167 RNA-Seq libraries from five ANA-grade species. This collection comprises data from various tissues, in-cluding 14 tissues from Amborella trichopoda, 7 from Brasenia schreberi, 2 from Euryale ferox, 7 from Nymphaea colorata, and 5 from Nymphaea thermarum. For each gene, the FPKM values are provided ...
Transcriptome Information
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ANAgdb has retrieved sRNA-seq datasets for A. trichopoda and N. colorata from public databases. Utilizing the established miRNA identification pipeline cen-tered around miRDeep-P2 (Kuang et al., 2018), we identified 186 miRNAs belong-ing to 109 families in A. trichopoda and 141 miRNAs belonging to 88 families in N. colorata.
miRNA Information
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ANAgdb provides the taxonomic information including 123 scientific names from Amborellales, Nymphaeales, and Austrobaileyales. Authority, reference, and link to Tropicos of each scientific name are also available.
Taxonomy Information
Citation
▶ ANAgdb: a multi-omics and taxonomy database for ANA-grade. Guo, Z.#, Luo, S.#, Wang, Q.#, Yang, Y., Bai, Y., Wei, J., Wang, D., Duan, Y.*, Yang, X.*, and Yang, Y.*. BMC Plant Biology. (2024)
▶ Genome
▷ Amborella trichopoda: Gap-less reference genome and distinct dominance of DTM (Mutator) transposons in Amborella trichocarpa. (unpublished)
▷ Amborella trichopoda: Amborella Genome, P., Albert, V.A., Barbazuk, W.B., dePamphilis, C.W., Der, J.P., Leebens-Mack, J., Ma, H., Palmer, J.D., Rounsley, S., Sankoff, D., et al. (2013). The amborella genome and the evolution of flowering plants. Science 342, 1241089.
▷ Brasenia schreberi: Lu, B., Shi, T., and Chen, J. Chromosome-level genome assembly of watershield (Brasenia schreberi).
▷ Euryale ferox: Data from NGDC.
▷ Euryale ferox: Yang, Y., Sun, P., Lv, L., Wang, D., Ru, D., Li, Y., Ma, T., Zhang, L., Shen, X., Meng, F., et al. (2020). Prickly waterlily and rigid hornwort genomes shed light on early angiosperm evolution. Nature Plants 6, 215-222.
▷ Nuphar advena: Data from NCBI.
▷ Nymphaea colorata: Zhang, L., Chen, F., Zhang, X., Li, Z., Zhao, Y., Lohaus, R., Chang, X., Dong, W., Ho, S.Y.W., Liu, X., et al. (2020). The water lily genome and the early evolution of flowering plants. Nature 577, 79-84.
▷ Nymphaea thermarum: Povilus, R.A., DaCosta, J.M., Grassa, C., Satyaki, P.R.V., Moeglein, M., Jaenisch, J., Xi, Z., Mathews, S., Gehring, M., Davis, C.C., et al. (2020). Water lily (Nymphaea thermarum) genome reveals variable genomic signatures of ancient vascular cambium losses. Proceedings of the National Academy of Sciences 117, 8649-8656.
Genome
ANAgdb currently encompasses 10 publicly available genome assemblies across six species and 1 newly assembled genome (Amtr_2024) produced by our group, including Amborella trichopoda, Brasenia schreberi, Euryale ferox, Euryale ferox, Nuphar advena, Nymphaea colorata, and Nymphaea thermarum. These datasets represent all open-access genome assemblies in the ANA-grade.
Genome Information
Transcriptome
ANAgdb now includes a comprehensive collection of 167 RNA-Seq libraries from five ANA-grade species. This collection comprises data from various tissues, in-cluding 14 tissues from Amborella trichopoda, 7 from Brasenia schreberi, 2 from Euryale ferox, 7 from Nymphaea colorata, and 5 from Nymphaea thermarum. For each gene, the FPKM values are provided for individual libraries and tissues, calculated using a combination of HISAT2 (Kim et al., 2019) and StringTie (Pertea et al., 2015).
Transcriptome Information
Tools
