Camellia nitidissima, a rare and endangered shrub is narrowly distributed in South China and North Vietnam occurring in forest understory. Their light tolerance mechanism is unclear. We measured photosynthesis and related parameters on 2-years-old cuttings growing at 10, 30, 50 and 100% sunlight. Our research question was: At what light level are C. nitidissima cuttings responding most favorably, and what is the eco-physiological basis for their response to light? We hypothesized that as a forest understory growth of C. nitidissima would respond most favorably at low to intermediate light by optimizing photosynthetic activity, and high light will affect photosynthetic functions due to photoinhibition, damage of photosynthetic apparatus and concomitant enzyme activity. With increasing light, the maximum net photosynthetic rate (PNmax) and apparent quantum yield (AQY) decreased, while the light compensation point increased, and light saturation point first increased followed by a decrease. The PNmax and AQY under 50 and 100% sunlight were significantly lower than that under 10 and 30% sunlight. The chlorophyll fluorescence parameters Fm, Fv, Fv/Fm all decreased under high light (> 50%). The contents of chlorophyll a (Chla), chlorophyll b (Chlb), and carotenoid (Car) decreased with increasing light. Relative conductivity, malondialdehyde (MDA) and proline contents in leaves were significantly increased in high light but we found no significant difference in these indices at 10 and 30% sunlight. We conclude that C. nitidissima is a shade adapted plant with poor adaptability to high light (> 50%). The novelty of this research is the demonstration of the eco-physiological basis of its light tolerance (conversely, shade adaptation) mechanisms indicated by decreased photosynthetic activity, chlorophyll fluorescence, Chla, Chlb and Car contents and concomitant increase in relative conductivity, MDA and proline contents at high light causing photoinhibition. For artificial propagation of C. nitidissima we recommend growing cuttings below 30% sunlight. For in situ conservation of this valuable, rare and endangered shrub it is necessary to protect its natural habitats.

Background: Heteroplexis Chang is an endangered genus endemic to China with important ecological and medicinal value. However, due to the lack of genetic data, our conservation strategies have repeatedly been delayed by controversial phylogenetic (molecular) relationships within the genera. In this study, we reported three new Heteroplexis chloroplast (cp.) genomes (H. vernonioides, H. impressinervia and H. microcephala) to clarify phylogenetic relationships between species allocated in this genus and other related Compositae. Results: All three new cp. genomes were highly conserved, showing the classic four regions. Size ranged from 152,984 − 153,221 bp and contained 130 genes (85 protein-coding genes, 37 tRNA, eight rRNA) and two pseudogenes. By comparative genomic and phylogenetic analyses, we found a large-scale inversion of the entire large single-copy (LSC) region in H. vernonioides, H. impressinervia and H. microcephala, being experimentally verified by PCR. The inverted repeat (IR) regions showed high similarity within the five Heteroplexis plastomes, showing small-size contractions. Phylogenetic analyses did not support the monophyly of Heteroplexis genus, whereas clustered the five species within two differentiated clades within Aster genus. These phylogenetic analyses suggested that the five Heteroplexis species might be subsumed into the Aster genus. Conclusion: Our results enrich the data on the cp. genomes of the genus Heteroplexis, providing valuable genetic resources for future studies on the taxonomy, phylogeny, and evolution of Aster genus.

Garcinia paucinervis is an evergreen tree with high medicinal value. Due to its vulnerable reproductive capacity coupled with excessive logging by humans, G. paucinervis has become an endangered species. In order to protect this species effectively, we drew the complete chloroplast genome of G. paucinervis and performed a series of comparative analyses on G. paucinervis and its neighbouring species. The chloroplast genome size of G. paucinervis is 157702 bp. In the chloroplast genome, we identified 130 genes, 56 RNA editing sites in the protein-coding genes, as well as 241 simple sequence repeats (SSRs) and 49 complex repetitive sequences. Comparative analysis identified some high divergent sequences in the intergenic spacers, which can be used as candidate markers for phylogenetic study. From an adaptive evolution point of view, a branch-site model analysis identified positively selected sites in 5 genes, most of which are involved in ribosome biogenesis, protein synthesis and other developmental processes. The detected codon substitutions may be associated with the evolution of G. paucinervis to adapt to the extreme habitat in karst. In addition, the result of the phylogenetic analysis supports the previous phylogenomic studies of taxa within the rosids clade. The ML tree revealed that G. mangostana was a sister to G. gummi-gutta, and they formed a diverging lineage to G. paucinervis in Garcinia. The above information is of great significance for us to understand the evolution of G. paucinervis chloroplast and lays the foundations for future studies in species conservation.

Though the karst regions in south and southwest China are plant diversity hotspots, our understanding of the phylogeography and evolutionary history of the plants there remains limited. The genus Heteroplexis (Asteraceae) is one of the typical representative plants isolated by karst habitat islands, and is also an endangered and endemic plant to China. In this study, species-level phylogeographic analysis of the genus Heteroplexis was conducted using restriction site-associated DNA sequencing (RADseq). The genetic structure showed a clear phylogeographic structure consistent with the current species boundaries in the H. microcephala, H. incana, H. vernonioides, H. sericophylla, and H. impressinervia. The significant global (R = 0.37, P < 0.01) and regional (R = 0.650.95, P < 0.05) isolation by distance (IBD) signals among species indicate strong geographic isolation in the karst mountains, which may result in chronically restricted gene flow and increased genetic drift and differentiation. Furthermore, the phylogeographic structure of Heteroplexis suggested a southward migration since the last glacial period. Demographic analysis revealed the karst mountains as a refuge for Heteroplexis species. Finally, both Treemix and ABBA-BABA statistic detected significant historical gene flow between species. Significant historical gene flow and long-term stability of effective population size (Ne) together explain the high genome-wide genetic diversity among species (π = 0.05370.0838). However, the recent collapse of Ne, widespread inbreeding within populations, and restricted contemporary gene flow suggest that Heteroplexis species are probably facing a high risk of genetic diversity loss. Our results help to understand the evolutionary history of karst plants and guide conservation.

Keteleeria davidiana var. calcarea is an endangered tree with considerable economic potential that used as timber wood for furniture and house construction. However, the natural population of K. davidiana var. calcarea is very fragmented, which is the cause for its low genetic diversity. In this study, we report the complete chloroplast genome of K. davidiana var. calcarea using Illumina sequencing. The chloroplast genome size is 117,670 bp in length, harboring a pair of very short inverted repeats (IRs) of 262 bp separated by a large single copy (LSC) sequence of 64,634 bp and a small single copy (SSC) sequence of 53,078 bp. The chloroplast genome K. davidiana var. calcarea contains 113 genes (74 protein genes, 35 tRNA genes, and 4 rRNA genes) and the overall GC content is 38.6%. The maximum likelihood phylogenetic analysis shows that K. davidiana var. calcarea is clustered with K. davidiana in genus Keteleeria. This complete chloroplast genome will help us to understand the evolution of K. davidiana var. calcarea and lays the foundations for future studies in this species conservation.

Liquidambar formosana (Hamamelidaceae) is a tertiary relic species widely distributed in subtropical areas, and is a common endemic broad-leaved tree species in south China. Here, we report and describe for the first time the complete chloroplast genome of L. formosana based on Illumina double-ended sequencing data. The complete plastid genome was 160,425 bp, which contained inverted repeats (IR) of 26,266 bp separated by a large single-copy (LSC) and a small single-copy (SSC) of 88,971 bp and 18,922 bp, respectively. The cpDNA contains 132 genes, comprising 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the plastome is 37.9%. The phylogenetic analysis of 18 selected chloroplast genomes demonstrated that L. formosana was close to the species Sinowilsonia henryi.