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Advancements in bioinformatics and genomics have heightened the significance of cytotaxonomy and morphology as fields of study. The quantification of various characters forms the basis of morphological investigations. However, due to variations among characters across different taxa, manual measurements are commonly employed. Yet, existing measurem...
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... terms of verification results for Length, Size, and Angle (Table S1), the relative standard deviation of measurements generally ranged from 0% to 2%. The angle measurements exhibited relatively small relative deviations, while the area measurements showed larger relative deviations, ranging from below 0.5% to between 1.5% and 2%. ...Context 2
... 1D&E presents a visual comparison of the photos before and after correction. Table 1 displays the results of measuring the length and angle of the ruler. Before the correction, the average value of the five "10 mm" measurement segments was 10.25 ± 0.2559 mm, while after correction, it improved to 10.09 ± 0.1581 mm. ...Context 3
... tools help mitigate color deviation and numerical deviation caused by the image acquisition process, ensuring improved measurement accuracy. Table 1 demonstrates the significant improvement in measurement precision achieved through image correction, reducing errors caused by photography. MATO also features a cursor zoom function that enhances the accuracy of fixed points during measurements, reducing errors resulting from imprecise point selection when measuring morphological features such as length and area. ...Context 4
... assess the precision of the measurements, we conducted five repetitions of selected samples for length, size, and angle measurements. We calculated the standard deviation and relative standard deviation to evaluate the measurement consistency and precision (Table S1). As counting and color data represent discontinuous traits and do not directly reflect measurement precision, they were not included in the analysis. ...Context 5
... terms of verification results for Length, Size, and Angle (Table S1), the relative standard deviation of measurements generally ranged from 0% to 2%. The angle measurements exhibited relatively small relative deviations, while the area measurements showed larger relative deviations, ranging from below 0.5% to between 1.5% and 2%. ...Context 6
... 1D&E presents a visual comparison of the photos before and after correction. Table 1 displays the results of measuring the length and angle of the ruler. Before the correction, the average value of the five "10 mm" measurement segments was 10.25 ± 0.2559 mm, while after correction, it improved to 10.09 ± 0.1581 mm. ...Context 7
... tools help mitigate color deviation and numerical deviation caused by the image acquisition process, ensuring improved measurement accuracy. Table 1 demonstrates the significant improvement in measurement precision achieved through image correction, reducing errors caused by photography. MATO also features a cursor zoom function that enhances the accuracy of fixed points during measurements, reducing errors resulting from imprecise point selection when measuring morphological features such as length and area. ...Context 8
... assess the precision of the measurements, we conducted five repetitions of selected samples for length, size, and angle measurements. We calculated the standard deviation and relative standard deviation to evaluate the measurement consistency and precision (Table S1). As counting and color data represent discontinuous traits and do not directly reflect measurement precision, they were not included in the analysis. ...Citations
... Stomatal index: number of stomata per unit area/(number of stomata per unit area + number of epidermal cells in the same unit area) × 100%. The above measurement processes were carried out in MATO v4.2 software [36]. (2) Scanning electron microscope observation: The silica gel-dried basal leaves were washed with distilled water and then treated with different concentrations of ethanol for gradient dehydration (15%, 30%, 50%, 70%, 85%, 95% I, 95% II, 100% I, 100% II), with each concentration being processed for 1 min. ...
... Then, ten morphologically intact fruits of each species were randomly selected for observation under a stereomicroscope (SMZ25, Nikon Corp., Tokyo, Japan), and then the dorsal and commissure views of fruits of each species were observed, photographed and preserved. Finally, the length and width values of ten fruits of each species were measured using MATO v4.2 software [36], and we then calculated the mean values. (2) Observation of anatomical characteristics of fruits. ...
... Then, we randomly selected twenty pollen of each species to observe and photograph their shape and the equatorial and polar views under a light microscope (Olympus-BX51) at 10 × 100 magnification. Finally, MATO v4.2 software [36] was used to measure the pollen size, including the polar axis length (P) and the equatorial axis length (E) of pollen. In addition, we also calculated the ratio of polar axis length and equatorial axis length (P/E). ...
The genus Sanicula L. possesses many medically important plants, belonging to the family Apiaceae. It is one of the most taxonomically difficult taxa, largely due to the great variability in habit, foliage, flowers and fruits. Previous studies have mainly focused on the molecular studies of this genus, and the morphological research for this genus was limited, especially in the micromorphological research. In the current study, we newly obtained leaf materials from twenty-two Sanicula members, fruit and pollen materials from twenty Sanicula members and performed comprehensively micromorphological analyses for this complicated genus. The results of the leaf epidermis showed that the upper and lower epidermis were smooth and glabrous, and the cell shape was polygonal or irregular. The patterns of anticlinal wall were shallowly undulating, deeply undulating, subflat or flat. The cuticular membrane ornamentations were diverse, and some species had epidermal appendage. All Sanicula species observed the stomata in the lower epidermis, and only five species (S. rugulosa, S. elongata, S. hacquetioides, S. tienmuensis and S. elata) observed stomata in the upper epidermis, which can easily identify them from other Sanicula members. In addition, we found that the fruits scarcely compressed, and some fruits had their distinctive shape, such as the fruit shape of S. tienmuensis was subglobose, S. subgiraldii was broadly ovate and S. pengshuiensis was ellipsoid. All Sanicula taxa fruits surfaces were covered with prickles, bristles, protuberance, or tubercles, prickles were either long or short, uncinate or straight, rarely scale-like, ribs inconspicuous or slightly prominent, but the prickles/bristles/tubercles were different in shape, sparseness and arrangement. The vittae were distinct in S. rubriflora, S. chinensis, S. caerulescens, S. pengshuiensis, S. pauciflora, S. lamelligera, S. oviformis, S. flavovirens and S. elata, and the remaining taxa were obscure. These findings indicated that the fruits can clearly distinguish these Sanicula members. Furthermore, the micromorphological characteristics of pollen showed that the equatorial view included four shapes: ellipsoid, subrectangular, equatorially constricted and super-rectangular-equatorially constricted; and the polar view possessed four shapes: triangular, triangular–circular, suborbicular and trilobate circular. The germ furrow and the outer wall ornamentation of all Sanicula taxa were quite similar, indicating that the genus was a natural unit. In summary, our study promoted the improvement of a taxonomic system for the genus and also provided additional evidence for future taxonomic study of the genus Sanicula.
... There were thirty representative fruit samples for each species (ten individuals from each species, each with three fruits) selected to observe their morphological characters, and then their overall structure and anatomy were photographed using a stereo microscope (SMZ25, Nikon Corp., Tokyo, Japan). The software MATO (Liu et al., 2023b) was used to measure the thirty representative fruit samples for each species, and then the average value was calculated. The terminology followed the reported study (Kljuykov et al., 2004). ...
Introduction
The genus Sanicula L. is a taxonomically complicated taxa within Apiaceae, as its high variability in morphology. Although taxonomists have performed several taxonomic revisions for this genus, the interspecific relationships and species boundaries have not been satisfactorily resolved, especially for those endemic to China. This study mainly focused on S. giraldii var. ovicalycina, S. tienmuensis var. pauciflora, and S. orthacantha var. stolonifera and also described two new members of the genus.
Methods
We newly sequenced sixteen plastomes from nine Sanicula species. Combined with eleven plastomes previously reported by us and one plastome downloaded, we performed a comprehensively plastid phylogenomics analysis of 21 Sanicula taxa.
Results and Discussion
The comparative results showed that 21 Sanicula plastomes in their structure and features were highly conserved and further justified that two new species were indeed members of Sanicula. Nevertheless, eleven mutation hotspot regions were still identified. Phylogenetic analyses based on plastome data and the ITS sequences strongly supported that these three varieties were clearly distant from three type varieties. The results implied that these three varieties should be considered as three independent species, which were further justified by their multiple morphological characters. Therefore, revising these three varieties into three independent species was reasonable and convincing. Moreover, we also identified and described two new Sanicula species (S. hanyuanensis and S. langaoensis) from Sichuan and Shanxi, China, respectively. Based on their distinct morphological characteristics and molecular phylogenetic analysis, two new species were included in Sanicula. In summary, our study impelled the revisions of Sanicula members and improved the taxonomic system of the genus.
Taxonomy of Populus is a challenging task, especially in regions with complex topography, such as the Qinghai–Tibet Plateau because of the effect of hybridization, incomplete lineage sorting, phenotypic plasticity, and convergence. In the Flora of China , Populus pseudoglanca and Populus wuana are classified into sect. Leucoides and sect. Tacamahaca , respectively, but their taxonomy remains unclear. By conducting a systematic investigation for all taxa of Populus on the plateau, we found 31 taxa from the two sections . Through identification based on morphology and habitats, we confirmed that the “ P. pseudoglanca ” recorded in the Flora of Sichuan is not true P. pseudoglanca , while P. pseudoglanca and P. wuana recorded in the Flora of China may refer to the same species. By performing whole‐genome re‐sequencing of 150 individuals from the 31 taxa, we derived 2.28 million single nucleotide polymorphisms (SNPs). Further genetic and phylogenetic analyses demonstrated that the genetic structure of P. wuana is extremely consistent with P. pseudoglanca , and they all originate through the natural hybridization between Populus ciliata in sect. Leucoides and Populus curviserrata in sect. Tacamahaca . Our results suggested that P. wuana should be merged with P. pseudoglanca taxonomically. This study not only clarifies the taxonomic confusions related to P. pseudoglanca and P. wuana but also provides a new framework based on the integration of morphology, distribution, habitat, and genome to solve complex taxonomic problems.
Nothapodytes burmanica Y.H.Tan & S.K.Shen, sp. nov. (Icacinaceae) from Kachin State, Myanmar is described and illustrated. It belongs to Nothapodytes due to the lorate hairy petals being connate at the base and a fleshy foliaceous disk divided into five leaflike lobes. Morphological and phylogenetic evidence indicates that it is close to N. pittosporoides . Morphologically, both species have oblanceolate or oblong leaf blades that are adaxially sparsely pubescent, but the new species is distinguished by its leaf base usually being oblique, and the paniculate inflorescence that has more numerous but smaller flowers with shorter petals. Phylogenetic results indicate that N. burmanica is deeply nested within the genus and forms a sister group of N. pittosporoides .
The advancement of next‐generation sequencing (NGS) technologies has been revolutionary for the field of evolutionary biology. This technology has led to an abundance of available genomes and transcriptomes for researchers to mine. Specifically, researchers can mine for various types of molecular markers that are vital for phylogenetic, evolutionary and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to an insufficient number of well‐annotated reference genomes for non‐model organisms, it remains challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner combines the reference‐guided de Bruijn graph assembly with seed self‐discovery and greedy extension. Additionally, it includes a verification step using a parameter‐bootstrap method to reduce the pitfalls associated with using a relatively distant reference. Our results, using both experimental and simulation data, showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic and other NGS data. GeneMiner is designed to be user‐friendly, fast and memory‐efficient. Further, it is compatible with Linux, Windows and macOS. All source codes are publicly available on GitHub ( https://github.com/sculab/GeneMine r) and Gitee ( https://gitee.com/sculab/GeneMiner ) for easy accessibility and transparency.
Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well‐resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes ( ndhC, ndhJ , and petG ) related to photosynthesis appear to have undergone significant selective pressure. Through high‐resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa . However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long‐obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.
The advancement of Next-generation Sequencing (NGS) technologies has led to a revolution in the field of evolutionary biology. With the increasing number of available genomes and transcriptomes, researchers can mine various types of molecular markers that are vital for phylogenetic, evolutionary, and ecological studies. Numerous tools have been developed to extract these molecular markers from NGS data. However, due to a limited number of well-annotated reference genomes for non-model organisms, it is still challenging to obtain these markers accurately and efficiently. Here, we present GeneMiner, an improved and expanded version of our previous tool, Easy353. GeneMiner involves the reference-guided de Bruijn Graph assembly with seed self-discovery and greedy extension. Additionally, it includes a verification step using a parameter-bootstrap method to reduce the negative impact on assembly caused by the relatively distant reference. Our results using both experimental and simulation data showed GeneMiner can accurately acquire phylogenetic molecular markers for plants using transcriptomic, genomic, and other NGS data. GeneMiner is designed to be user-friendly, fast, and memory-efficient, and is compatible with Linux, Windows, and macOS. All source codes are publicly available on GitHub for easy accessibility and transparency (https://github.com/happywithxpl/GeneMiner).
