Background: Section Camellia is the most diverse group in the genus Camellia L., and this group of plants has a long history of cultivation in China as popular ornamental flowers and oil plants. Sect. Camellia plants present diverse morphological variations and complexity among species, resulting in uncertainty in the classification of species, which has resulted in a degree of inconvenience and confusion in the use of plant resources and research. Methods: Here, We sequenced and assembled the chloroplast genomes of 6 sect. Camellia and performed comparative chloroplast genome analysis and phylogenetic studies combined with 15 existing sect. Camellia plants. Results: The chloroplast genome of 21 species in sect. Camellia species were quadripartite with length of 156,587–157,068 bp base pairs (bp), and a highly conserved and moderately differentiated chloroplast genome arrangement. The 21 sect. Camellia chloroplast genomes were similar to those of angiosperms, with high consistency in gene number, gene content and gene structure. After the annotation process, we identified a total of 132 genes, specifically 87 sequences coding for proteins (CDS), 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The ycf1 gene in 21 species of the sect. Camellia was present only in the small single-copy/inverted repeat of a (SSC/IRa) region. Sequence variation was greater in the large single-copy (LSC) region than in the IR region, and the majority of the protein-coding genes presented high codon preferences. The chloroplast genomes of 21 plant species exhibit relatively conserved SC (single copy region)/IR (inverted repeat region) boundaries. We detected a total of 2975 single sequence repeats (SSRs) as well as 833 dispersed nuclear elements (INEs). Among these SSRs, A/T repeats and AT/AT repeats dominated, while among INEs, forward repeats and palindromic repeats predominated. Codon usage frequencies were largely similar, with 30 high-frequency codons detected. Comparative analysis revealed five hotspot regions (rps16, psaJ, rpl33, rps8, and rpl16) and two gene intervals (atpH-atpI and petD-rpoA) in the cp genome, which can be used as potential molecular markers. In addition, the phylogenetic tree constructed from the chloroplast genome revealed that these 21 species and Camellia oleifera aggregated into a single branch, which was further subdivided into two evolutionarily independent sub-branches. Conclusions: It was confirmed that sect. Camellia and C. oleifera Abel are closely related in Camellia genus. These findings will enhance our knowledge of the sect. Camellia of plants, deepen our understanding of their genetic characteristics and phylogenetic pathways, and provide strong support for the scientific development and rational utilization of the plant resources of the sect. Camellia.

Sect. Tuberculata Chang in the genus Camellia (Theaceae Mirb.) is named after the “tubercle-like projections on the surface of the capsule and ovary”. Due to complex morphological variations in these taxon and insufficient field investigations, the interspecies relationships are unclear, the species’ definitions are vague, and the names are confusing. This is not conducive to the conservation and study of these species. Therefore, herein, we systematically explore the taxonomic status of five sect. Tuberculata species using morphological, pollen morphological, and molecular phylogenetic methods. The results showed that (1) the morphological characteristics of the flower, fruit, and leaves of C. anlungensis and C. leyeensis are similar. Furthermore, the pollen characteristics and pollen wall ornamentation show that there is no significant difference between the two species; (2) there are significant differences between C. acutiperulata and C. anlungensis in terms of leaf shape (elliptic vs. obovate), calyx characteristics (sepal apex pointed vs. sepal oblong), and fruit shape (subglobose folds with shallow verruculose vs. flat folds and verruculose protuberances with pronounced internal cleavage); (3) C. pyxidiacea and C. rubituberculata differ in flower color (white or light color vs. red) and fruit verrucae (obviously deeply cleft vs. shallowly uncracked); (4) a phylogenetic tree based on the chloroplast genome shows that C. anlungensis and C. leyeensis form a single clade (BS = 100%, PP = 1.0) and are on a different branch, with C. acutiperulata on clade II (BS = 100%, PP = 1.0), and C. pyxidiacea and C. rubituberculata clustered on different branches of clade I (BS = 99%, PP = 1.00). Considering the above results together, we propose that C. leyeensis should be treated as a homonym of C. anlungensis, and C. acutiperulata, C. pyxidiacea, and C. rubituberculata should be considered as separate species. Clarifying the taxonomic status of these five species not only advances our understanding of the significance and complexity of the systematic classification of the genus Camellia but also has important implications for diversity conservation and population genetics.

Sect. Tuberculate Chang belongs to the genus Camellia, which is an endemic group in China and has high research value. However, the phenotypic patterns of this taxon are complex and diverse, and the phenotypic variation in key traits is still unclear. In this study, a total of 212 samples from 18 populations of sect. Tuberculate plants were studied for 30 phenotypic traits of flowers, fruits, and leaves using analysis of variance, correlation analysis, principal component analysis, and cluster analysis. The results showed the following. (1) The plants in sect. Tuberculate were rich in phenotypic trait variation and possessed rich phenotypic diversity. The differentiation of phenotypic traits mainly came from among populations, with leaves (66.804%) being the largest and flowers (53.476%) being the smallest. Qualitative traits (70.264%) were greater than quantitative traits (57.608%). (2) Correlation analyses showed close and complex relationships among the phenotypic traits of flowers, fruits, and leaves. (3) The cumulative contribution of the first 10 principal components was up to 73.49%, which screened out 12 major traits contributing to the phenotypic differences in plants of sect. Tuberculate. (4) Q-type analysis showed that they were classified into 18 taxa at a Euclidean distance of 7.5 and 11 taxa at a Euclidean distance of 10. The 18 populations were not fully clustered according to the geographic distance of the plants, and there was an overlap between some of the populations. In summary, the degree of variation in phenotypic traits among populations of sect. Tuberculate plants is high, which is affected by the climatic environment. The 12 major phenotypic traits screened can be used as the basis for the classification of sect. Tuberculate plants. There are trait overlaps among some populations, which may be affected by the stochastic influence of the geographic climate and gene flow. This study will provide important references for interspecific identification, classification system construction, genetic mechanism, germplasm resource conservation, and exploitation of plants in sect. Tuberculate.

Geodorum eulophioides is a unique and endangered species belonging to the Orchidaceae family in China. It has great potential as an ornamental horticultural plant. However, little is known about its genetic diversity and reasons for being endangered due to its narrow distribution and few populations in the wild. To effectively evaluate and conserve available resources, the genetic diversity and population structure of G. eulophioides were analyzed in this study. A total of 94 individuals from 10 natural populations were studied using site-specific amplified fragment sequencing (SLAF-seq). Based on the 76,340 SNPs detected by SLAF-seq, genetic diversity analysis was performed and markers associated with environmental variables were determined. The results showed that the level of genetic diversity in the 10 natural populations studied was low, with PIC values ranging from 0.1874 to 0.2156. FIS values ranged from −0.2376 to 0.2658, with excess and deficiency in heterozygotes. FST values ranged from 0.0482 to 0.3144, with genetic variation among populations. AMOVA results showed that the genetic variation among populations accounted for 21.35% of the total variation, and the remaining genetic variation among individuals within populations was 78.65%. The results of the population structure analysis showed that 94 individuals were classified into three major groups and two subgroups. Environmental association analysis using Bayenv2 and LFMM yielded thirty and eighteen putative adaptive loci, respectively, and five specific functional genes were annotated. In summary, this study provides further insight into the genetic structure of G. eulophioides and provides a reference for protection and restoration.

Sect. Tuberculata, as one of the endemic plant groups in China, belongs to the genus Camellia of the Theaceae family and possesses significant economic and ecological value. Nevertheless, the characteristics of habitat distribution and the major eco-environmental variables affecting its suitability are poorly understood. In this study, using 65 occurrence records, along with 60 environmental factors, historical, present and future suitable habitats were estimated using MaxEnt modeling, and the important environmental variables affecting the geographical distribution of sect. Tuberculata were analyzed. The results indicate that the size of the its potential habitat area in the current climate was 1.05 × 10⁵ km², and the highly suitable habitats were located in Guizhou, central-southern Sichuan, the Wuling Mountains in Chongqing, the Panjiang Basin, and southwestern Hunan. The highest probability of presence for it occurs at mean diurnal range (bio2) ≤ 7.83 °C, basic saturation (s_bs) ≤ 53.36%, temperature annual range (bio7) ≤ 27.49 °C, −7.75 °C < mean temperature of driest quarter (bio9) < 7.75 °C, annual UV-B seasonality (uvb2) ≤ 1.31 × 10⁵ W/m², and mean UV-B of highest month (uvb3) ≤ 5089.61 W/m². In particular, bio2 is its most important environmental factor. During the historical period, the potential habitat area for sect. Tuberculata was severely fragmented; in contrast, the current period has a more concentrated habitat area. In the three future periods, the potential habitat area will change by varying degrees, depending on the aggressiveness of emissions reductions, and the increase in the potential habitat area was the largest in the SSP2.6 (Low-concentration greenhouse gas emissions) scenario. Although the SSP8.5 (High-concentration greenhouse gas emissions) scenario indicated an expansion in its habitat in the short term, its growth and development would be adversely affected in the long term. In the centroid analysis, the centroid of its potential habitat will shift from lower to higher latitudes in the northwest direction. The findings of our study will aid efforts to uncover its originsand geographic differentiation, conservation of unique germplasms, and forestry development and utilization.

Sect. Tuberculata in the genus Camellia, is named after the "tubercle-like projections on the surface of the capsule and ovary". Due to complex morphological variations in these taxon and insufficient field investigations, the interspecific relationships are unclear, the species definitions are vague, and the names are confusing. This is not conducive to the conservation and study of these species. Therefore, herein, we systematically explored the taxonomic status of five sect. Tuberculata species using morphological, pollen morphology, and molecular phylogenetic methods. The result showed that (1) morphological characteristics for the flower, fruit, and leaves of C. anlungensis and C. leyeensis were similar. Furthermore, the pollen characteristics and pollen wall ornamentation showed that it was no significant difference between the two species. (2) there were significant differences between C. acutiperulata and C. anlungensis in terms of leaf shape (elliptic vs. obovate), calyx characteristics (sepal apex pointed vs. sepal oblong), and fruit shape (subglobose folds with shallow verruculose vs. flat folds and verruculose protuberances with pronounced internal cleavage). (3) C. pyxidiacea and C. rubituberculata differed in flower color (white or few light vs. red), fruit verrucae (obviously deeply cleft vs. shallowly uncracked). (4) a phylogenetic tree based on the chloroplast genome showed that C. anlungensis and C. leyeensis form a single clade (BS = 100%, PP = 1.0) and were on a different branch with C. acutiperulata in clade II, (BS = 100%, PP = 1.0); C. pyxidiacea and C. rubituberculata were clustered on different branches of clade I (BS = 99%, PP = 1.00). Integrated above results, we consider that C. leyeensis should be treated as a homonym of C. anlungensis; C. acutiperulata, C. pyxidiacea, C. rubituberculata respectively as a separate species. Clarifying the taxonomic status of these five species not only advances our understanding of the significance and complexity of the systematic classification of the genus Camellia but also has important implications for diversity conservation and population genetics.