The pan-plastome of Hemerocallis citrina reveals new insights into the genetic diversity and cultivation history of an economically important food plant.

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.

Response of gas-exchange characteristics and chlorophyll fluorescence to acute sulfur dioxide exposure in landscape plants.

To explore the toxicity and action mechanism of acute sulfur dioxide (SO2) on urban landscape plants, a simulated SO2 stress environment by using fumigation chamber involving increasing SO2 concentration (0, 25, 50, 100, 200 mg m-3) was carried out among three species. After 72 h of exposure, SO2-induced oxidative damage indicated by electrolyte leakage increased with higher dose of SO2. Meanwhile, SO2 decreased the contents of chlorophyll a, chlorophyll b and carotenoid and increased the contents of sulfur. Net photosynthetic rate (Pn) decreased as a result of stomatal closure when SO2 dose was lower than 50 mg m-3, out of this range, non-stomatal limitation play a dominant role in the decline of Pn. Simultaneous measurements of chlorophyll fluorescence imaging (CFI) also revealed that the maximal quantum efficiency of PSII photochemistry in dark-adapted state (Fv/Fm) and the realized operating efficiency of PSII photochemistry (Fq'/Fm') was reduced by SO2 in a dose-dependent manner. In addition, the maximum quantum efficiency of PSII photochemistry in light-adapted state (Fv'/Fm') and the PSII efficiency factor (Fq'/Fv') decreased when exposure to SO2. These results implied that acute SO2 exposure induced photoinhibition of PSII reaction centers in landscape plants. Our study also indicated that different urban landscape plant species resist differently to SO2: Euonymus kiautschovicus > Ligustrum vicaryi > Syringa oblata according to gas-exchange characteristics and chlorophyll fluorescence responses.

The pan-plastome of Prunus mume: insights into Prunus diversity, phylogeny, and domestication history.

Backgrounds: Prunus mume in the Rosaceae and commonly referred to as mei or Chinese plum is widely used as a traditional ornamental flowering plant and fruit tree in China. Although some population and genetic analyses have been conducted for this species, no extensive comparisons of genetic variation from plastomes have yet been investigated. Methods: We de novo assembled a total of 322 complete P. mume plastomes in this study and did a series of comparative analyses to better resolve pan-plastomic patterns of P. mume. To determine the phylogeny and domestication history of this species, we reconstructed the phylogenetic tree of Prunus genus, and resolved the population structure of P. mume. We also examined the nucleotide variation of P. mume to find potential DNA barcodes. Results: The assembled plastomes exhibited a typical quadripartite structure and ranged from 157,871 bp to 158,213 bp in total size with a GC content ranging from 36.73 to 36.75%. A total of 112 unique genes were identified. Single nucleotide variants (SNVs) were the most common variants found among the plastomes, followed by nucleotide insertions/deletions (InDels), and block substitutions with the intergenic spacer (IGS) regions containing the greatest number of variants. From the pan-plastome data six well-supported genetic clusters were resolved using multiple different population structure analyses. The different cultivars were unevenly distributed among multiple clades. We also reconstructed a phylogeny for multiple species of Prunus to better understand genus level diversity and history from which a complex introgressive relationship between mei and other apricots/plums was resolved. Conclusion: This study constructed the pan-plastome of P. mume, which indicated the domestication of P. mume involved multiple genetic origins and possible matrilineal introgression from other species. The phylogenetic analysis in Prunus and the population structure of P. mume provide an important maternal history for Prunus and the groundwork for future studies on intergenomic sequence transfers, cytonuclear incompatibility, and conservation genetics.