The complete chloroplast genome sequence of Hemerocallis fulva

Abstract Hemerocallis fulva L. is a traditional Chinese medicine. The flowers of H. fulva are used in ethnic medicine to treat various diseases, including certain central nervous system diseases. In this study, we characterized the complete chloroplast genome of H. fulva. It is 156,059 bp in length and encodes 87 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenomic analysis showed that the H. fulva and species of Anemarrhena asphodeloides Bunge, Liriope muscari, and Liriope spicata were clustered together. This chloroplast genome sequencing offers genetic background for conservation and phylogenetic studies.

Hemerocallis fulva L.belongs to the Liliaceae family, which is widely used in folk emotional health improvement drugs in East Asia (China, Japan) and North America (Lin et al. 2011). Its flower has antioxidation (Lin et al. 2011), antibacterial (Sarg et al. 1990), antitumor (Cichewicz et al. 2004), and sleep improvement effects (Uezu 1998). Because of H. fulva flower is rich of hyperin (Guo et al. 2013), it is a promising antidepressant drug (Zheng et al. 2012).
However, as a result of long-cultivation and interspecific hybrids, there is confusion in the classification of the genus Hemerocallis based on phenotypic characterization. For example, wild Hemerocallis always showed a single flower color, whereas modern hybrid horticultural varieties always showed a more complex color distribution pattern (Cui et al. 2019). To provide a scientific classification way to Hemerocallis L., we conducted a chloroplast genome research and a phylogenetic analysis of H. fulva.
Genomic DNA was extracted from fresh leaves of a seedling of H. fulva from Huazhong Medicinal Botanical Garden, Institute of Chinese Medicinal Materials, Hubei Academy of Agricultural Sciences (Hubei, China, N30.180978, E109.756823). Genomic DNA was extracted with plant genomic DNA kit (Tiangen Biotech, China) and sequenced by using the Hiseq 2500 platform (Illumina, San Diego, CA). The chloroplast genome was assembled from the raw sequence data by using NOVOPlasty (v.2.7.2) with the seed sequence of rbcL from Arabidopsis thaliana (Dierckxsens et al. 2017). By using Bowtie 2 (v.2.0.1) (Langmead et al. 2009) to map all the original reads to the assembly, the correctness of the assembly is verified under the default settings. The annotation of the chloroplast genome was originally performed using CPGAVAS2 ) and then edited using Apollo (Misra and Harris 2006). The genome sequence and annotations have been deposited in GenBank with accession number MT806177.

Disclosure statement
No potential conflict of interest was reported by the author(s).

Data availability statement
The data that support the findings of this study are openly available in NCBI at https://www.ncbi.nlm.nih.gov/, the accession number is MT806177, and raw sequencing data used in this study have been deposited in SRA with accession number SRR12506380.