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The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant.
Jia, Minlong; Wang, Jie; Cao, Dongmei; Jiang, Congrong; Li, Wei; Tembrock, Luke R; Xing, Guoming; Li, Sen; Wu, Zhiqiang.
Afiliação
  • Jia M; College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China.
  • Wang J; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
  • Cao D; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6000-6999, Australia.
  • Jiang C; Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
  • Li W; College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China. caodm787@163.com.
  • Tembrock LR; College of Horticulture, Shanxi Agricultural University, Taiyuan, 030031, China.
  • Xing G; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
  • Li S; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
  • Wu Z; Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80525, USA.
BMC Plant Biol ; 24(1): 44, 2024 Jan 11.
Article em En | MEDLINE | ID: mdl-38200455
ABSTRACT

BACKGROUND:

Hemerocallis citrina Baroni (Huang hua cai in Chinese) is a perennial herbaceous plant grown for its flower buds that are eaten fresh or dried and is known as the vegetarian three treasures. The nuclear genome of H. citrina has been reported, but the intraspecific variation of the plastome (plastid genome) has not yet been studied. Therefore, the panplastome of this species collected from diverse locations is reported here for the first time.

RESULTS:

In this study, 65 H. citrina samples were resequenced, de novo assembled, and aligned with the published plastome of H. citrina to resolve the H. citrina panplastome. The sizes of the 65 newly assembled complete plastomes of H. citrina ranged from 156,048 bp to 156,263 bp, and the total GC content ranged from 37.31 to 37.34%. The structure of the complete plastomes showed a typical tetrameric structure, including a large single copy (LSC), a small single copy (SSC), and a pair of inverted repeat regions (IRA and IRB). Many nucleotide variants were identified between plastomes, among which the variants in the intergenic spacer region were the most abundant, with the highest number of variants concentrated in the LSC region. Based on the phylogenetic tree constructed using the ML method, population structure analysis, and principal component analysis (PCA), the panplastome data were subdivided into five genetic clusters. The C5 genetic cluster was mostly represented by samples from Qidong, Hunan Province, while samples from Shanxi and Shaanxi Provinces were classified into the C4 genetic cluster. The greatest genetic diversity was found in the C1 genetic cluster, and the greatest genetic distance between any two clusters was found between the C4 and C5 clusters.

CONCLUSION:

The resolution of the panplastome and the analysis of the population structure of H. citrina plastomes provide important data for future breeding projects and germplasm preservation.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Hemerocallis Tipo de estudo: Health_economic_evaluation / Prognostic_studies Idioma: En Revista: BMC Plant Biol Assunto da revista: BOTANICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Hemerocallis Tipo de estudo: Health_economic_evaluation / Prognostic_studies Idioma: En Revista: BMC Plant Biol Assunto da revista: BOTANICA Ano de publicação: 2024 Tipo de documento: Article País de afiliação: China