Nymphaea colorata

Introduction

REF

Colorata is a perennial aquatic herb. Rhizome hypertrophy.
Perennial tropical water lily with nearly rounded, serrated edges, greenish inlaid hazel patches, lilac backs, young lilac backs, overlapping ears, blue-purple flowers.
Floating leaf rounded or ovate, base curved, cordate or arrow-shaped, often without water leaf; Submerged leaves are thin and fragile.
Beautiful flowers that float or rise above the water; Sepal 4, proximal; Petals polywhorled, carpellary ring, adnate and semi-submerged in succulent cup receptacle, and partially united in lower part, extending upper part into style, stigma concave into stigma disc, ovule inverted, hanging in ovary wall.
Berry spongy, irregularly cracked, ripening below water surface; The seeds are hard and coated with gum.

Sequencing, Assembly, and Annotation

Assembly

To assemble the 49.8 Gb data composed of 5.5 million reads, we filtered the reads to remove organellar DNA, reads of poor quality or short length, and chimaeras. The contig-level assembly was performed on full PacBio long reads using the Canu package22. Canu v.1.3 was used for self-correction and assembly. We then polished the draft assembly using Arrow (https://github.com/PacificBiosciences/GenomicConsensus ). To increase the accuracy of the assembly, Illumina short reads were recruited for further polishing with the Pilon program (https://github.com/broadinstitute/pilon). The genome assembly quality was measured using BUSCO (Benchmarking Universal Single-Copy Orthologues)23 v.3.0. The paired-end reads from Hi-C were uniquely mapped onto the draft assembly contigs, which were grouped into chromosomes and scaffolded using the software Lachesis (https:// github.com/shendurelab/LACHESIS). Genscan (http://genes.mit.edu/GENSCAN.html) and Augustus24 were used to carry out de?novo predictions with gene model parameters trained from Arabidopsis thaliana. Furthermore, gene models were de?novo predicted using MAKER25. We then evaluated the genes by comparing MAKER results with the corresponding transcript evidence to select gene models that were the most consistent on the basis of an AED metric.

References

Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, Wang H, Chen X, Hu J, Liu Y, Qin Y, Wang K, Dong S, Liu Y, Zhang S, Yu X, Wu Q, Wang L, Yan X, Jiao Y, Kong H, Zhou X, Yu C, Chen Y, Li F, Wang J, Chen W, Chen X, Jia Q, Zhang C, Jiang Y, Zhang W, Liu G, Fu J, Chen F, Ma H, Van de Peer Y, Tang H. The water lily genome and the early evolution of flowering plants. Nature. 2020 Jan;577(7788):79-84. doi: 10.1038/s41586-019-1852-5. Epub 2019 Dec 18. PMID: 31853069; PMCID: PMC7015852.

Kingdom	Plantae
Phylum	Tracheophytes
Class	Angiosperms
Order	Nymphaeales
Family	Nymphaeaceae
Genus	Nymphaea
Species	N. nouchali
NCBI Taxonomy ID	210,225

Genome Size	409,930,971 n=806
Ave	508,599.22
Largest	44,612,865
N50	25,516,871 n=7
N60	25,082,955 n=9
N70	24,868,339 n=10
N80	23,035,089 n=12
N90	12,577,093 n=14
N100	3,011 n=806
N_count	62,600
Gaps	669

Taxonomy

Introduction

Sequencing, Assembly, and Annotation

Genome Statistics

Contacts

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