The complete chloroplast genomes of Allium sacculiferum, A. thunbergii, and A. taquetii (Amaryllidaceae) from Korea

Abstract

The genus Allium comprises some of the most commonly consumed food crops worldwide. The chloroplast genomes of A. sacculiferum, A. thunbergii, and A. taquetii are 152,444, 153,459, and 154,056 bp circular molecular genomes, respectively. The annotation results revealed the presence of 132 (89 protein-coding, 35 tRNA, and eight rRNA), 132 (86 protein-coding, 38 tRNA, and eight rRNA), and 132 (86 protein-coding, 38 tRNA, and eight rRNA) genes with 36.78%, 36.83%, and 36.88% total GC content in each genome, respectively. The chloroplast genome of each Allium species contains an 81,254, 82,473, and 83,068 bp LSC region, an 18,176, 18,006, and 17,958 bp SSC region, and a pair of 26,507, 26,490, and 26,515 bp IR regions, respectively. Phylogenetic analysis based on the 21 complete chloroplast genomes indicates that A. sacculiferum is closely related to A. koreanum; A. thunbergii and A taquetii are closely related to A. hookeri. This study shows that the three Allium species are Korean crop wild relatives that may be used to develop new Allium varieties in the future.

Keywords:

• Crop wild relatives
• phylogenetic analysis
• Allium sacculiferum
• Allium thunbergii
• Allium taquetii

Author contributions

Kyeong Min Kim: methodology, data analysis, software, and writing; Chung Youl Park: conceptualization, methodology, and software; Da Hyun Lee: sample preparing and acquisition of data; Young Ho Jung: sample preparing and acquisition of data; Hyeon Min Kim: sample preparation and acquisition of data; Chae Sun Na: supervision of the project, conceptualization, methodology, writing, revision, and editing.

Ethics statement

Seed collection was performed in accordance with the guidelines and regulations provided by the Baekdudaegan National Arboretum. There are no ethical issues or other conflicts of interest in this study.

Disclosure statement

There are no potential conflicts of interest to disclose.

Data availability statement

The genome sequence data of Allium sacculiferum, A. thunbergii, and A. taquetii that support the findings of this study are openly available in the GenBank of NCBI at https://www.ncbi.nlm.nih.gov/, under accession nos. OP755306, OP755308, and OP755307, respectively. The BioProject, SRA, and Bio-Sample numbers for A. sacculiferum are PRJNA822879, SRR18707531, and SAMN27281643, respectively; for A. thunbergii are PRJNA822879, SRR18707530, and SAMN27281644, respectively; and for A. taquetii are PRJNA822879, SRR18707529, and SAMN27281645, respectively.

Additional information

Funding

This study was supported by the R&D Program for Forest Science Technology [Project No. 2021400B10-2225-CA02], which is under the aegis of the Korea Forest Service.