The complete chloroplast genome and phylogentic results support the species position of Swertia banzragczii and Swertia marginata (Gentianaceae) in Mongolia.

BACKGROUND: Swertia banzragczii and S. marginata are important medicinal species in Mongolia. However, their taxonomic positions and genetic backgrounds remain unknown. In this study, we explored the complete chloroplast genomes and DNA barcoding of these species and compared them with those of closely related species within the subgenus to determine their taxonomic positions and phylogenetic relationships. RESULT: The chloroplast genomes of S. banzragczii and S. marginata encoded 114 genes, including 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among them, 16 genes contained a single intron, and 2 genes had two introns. Closely related species had a conserved genome structure and gene content. Only differences in genome length were noticed, which were caused by the expansion and contraction of the inverted repeat (IR) region and loss of exons in some genes. The trnH-GUG-psbA and trnD-GUC-trnY-GUA intergenic regions had high genetic diversity within Swertia plastomes. Overall, S. banzragczii and S. marginata are true species and belong to the subgenus Swertia. CONCLUSIONS: These results provide valuable genetic and morphological information on rare and subendemic Swertia species in Mongolia, which can be used for further advanced studies on the Swertia genus.

Comparative plastome analysis and taxonomic classification of snow lotus species (Saussurea, Asteraceae) in Central Asia and Southern Siberia.

Four species of Saussurea, namely S. involucrata, S. orgaadayi, S. bogedaensis, and S. dorogostaiskii, are known as the "snow lotus," which are used as traditional medicines in China (Xinjiang), Kyrgyzstan, Mongolia, and Russia (Southern Siberia). These species are threatened globally, because of illegal harvesting and climate change. Furthermore, the taxonomic classification and identification of these threatened species remain unclear owing to limited research. The misidentification of medicinal species can sometimes be harmful to health. Therefore, the phylogenetic and genomic features of these species need to be confirmed. In this study, we sequenced five complete chloroplast genomes and seven nuclear ITS regions of four snow lotus species and other Saussurea species. We further explored their genetic variety, selective pressure at the sequence level, and phylogenetic relationships using the chloroplast genome, nuclear partial DNA sequences, and morphological features. Plastome of the snow lotus species has a conserved structure and gene content similar to most Saussurea species. Two intergenic regions (ndhJ-ndhK and ndhD-psaC) show significantly high diversity among chloroplast regions. Thus, ITS and these markers are suitable for identifying snow lotus species. In addition, we characterized 43 simple sequence repeats that may be useful in future population genetic studies. Analysis of the selection signatures identified three genes (rpoA, ndhB, and ycf2) that underwent positive selection. These genes may play important roles in the adaptation of the snow lotus species to alpine environments. S. dorogostaiskii is close to S. baicalensis and exhibits slightly different adaptation from others. The taxonomic position of the snow lotus species, confirmed by morphological and molecular evidence, is as follows: (i) S. involucrata has been excluded from the Mongolian flora due to misidentification as S. orgaadayi or S. bogedaensis for a long time; (ii) S. dorogostaiskii belongs to section Pycnocephala subgenus Saussurea, whereas other the snow lotus species belong to section Amphilaena subgenus Amphilaena; and (iii) S. krasnoborovii is synonymous of S. dorogostaiskii. This study clarified the speciation and lineage diversification of the snow lotus species in Central Asia and Southern Siberia.

Flower morphology of Allium (Amaryllidaceae) and its systematic significance.

Allium is a complicated genus that includes approximately 1000 species. Although its morphology is well studied, the taxonomic importance of many morphological traits, including floral traits, are poorly understood. Here, we examined and measured the floral characteristics of 87 accessions of 74 Allium taxa (belonging to 30 sections and nine subgenera) from Central to Eastern Asian countries. We then examined the taxonomic relationships between select flower characteristics and a phylogenetic tree based on ITS sequences. Our results confirm that floral morphology provides key taxonomic information to assess species delimitation in Allium. We found that perianth color is an important characteristic within the subg. Melanocrommyum, Polyprason, and Reticulatobulbosa. In subg. Allium, Cepa, and Rhizirideum, significant characteristics include ovary shape, perianth shape, and inner tepal apex. For species in subg. Angunium, the key taxonomic character is ovule number (only one ovule in per locule). In the subg. Allium, Cepa, Polyprason, and Reticulatobulbosa, which belong to the third evolutionary line of Allium, hood-like appendages occur in the ovary, although these do not occur in subg. Rhizirideum. Our results also indicated that the flower morphology of several species in some sections are not clearly distinguished, e.g., sect. Sacculiferum (subg. Cepa) and sect. Tenuissima (subg. Rhizirideum). This study provides detailed photographs and descriptions of floral characteristics and information on general distributions, habitats, and phenology of the studied taxa.

Improved Understanding of the Macrofungal Diversity of Mongolia: Species Richness, Conservation Status, and An Annotated Checklist.

In this study, we updated and revised the checklist of macrofungi, along with the distribution of phytogeographical regions and the regional conservation status in Mongolia. The checklist comprises 677 macrofungal species belonging to 284 genera and 119 families in the country. Based on previous studies, 18 species are currently invasive to Mongolia. In this checklist, only four species are endemic to Mongolia. Among the 677 species, the regional conservation status of 51 species was previously assessed as threatened in the country. Furthermore, we collected all available occurrence records from various sources. A total of 4733 occurrences of 655 species across Mongolia were analyzed for species richness based on a 0.5° × 0.5° grid cell size. We found the records to be unevenly distributed across Mongolia, where records from the northern and central parts dominate. Among these, we identified 43 grids with a high diversity of macrofungal species. Most of these grids did not reside inside by protected geographical areas.

Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe.

Adonis mongolica is a threatened species that is endemic to Mongolia. It is a medicinal plant from the Adonis genus and has been used to treat heart diseases. However, the genomics and evolution of this species have not been thoroughly studied. We sequenced the first complete plastome of A. mongolica and compared it with ten Adonideae species to describe the plastome structure and infer phylogenetic relationships. The complete plastome of A. mongolica was 157,521 bp long and had a typical quadripartite structure with numerous divergent regions. The plastomes of Adonideae had relatively constant genome structures and sizes, except for those of Adonis. The plastome structure was consistent across Adonis. We identified a 44.8 kb large-scale inversion within the large single-copy region and rpl32 gene loss in the Adonis plastomes compared to other members of the Adonideae tribe. Additionally, Adonis had a smaller plastome size (156,917-157,603 bp) than the other genera within the tribe (159,666-160,940 bp), which was attributed to deletions of intergenic regions and partial and complete gene losses. These results suggested that an intramolecular mutation occurred in the ancestor of the Adonis genus. Based on the phylogenetic results, Adonis separated earlier than the other genera within the Adonideae tribe. The genome structures and divergences of specific regions in the Adonis genus were unique to the Adonideae tribe. This study provides fundamental knowledge for further genomic research in Mongolia and a better understanding of the evolutionary history of endemic plants.

Karyotypes and Physical Mapping of Ribosomal DNA with Oligo-Probes in Eranthis sect. Eranthis (Ranunculaceae).

A comparative karyotype analysis of four species of yellow-flowered Eranthis sect. Eranthis, i.e., E. bulgarica, E. cilicica, E. hyemalis, and E. longistipitata from different areas, has been carried out for the first time. All the studied specimens had somatic chromosome number 2n = 16 with basic chromosome number x = 8. Karyotypes of the investigated plants included five pairs of metacentric chromosomes and three pairs of submetacentric/subtelocentric chromosomes. The chromosome sets of the investigated species differ mainly in the ratio of submetacentric/subtelocentric chromosomes, their relative lengths, and arm ratios. A new oligonucleotide probe was developed and tested to detect 45S rDNA clusters. Using this probe and an oligonucleotide probe to 5S rDNA, 45S and 5S rDNA clusters were localized for the first time on chromosomes of E. cilicica, E. hyemalis, and E. longistipitata. Major 45S rDNA clusters were identified on satellite chromosomes in all the species; in E. cilicica, minor clusters were also identified in the terminal regions of one metacentric chromosome pair. The number and distribution of 5S rDNA clusters is more specific. In E. cilicica, two major clusters were identified in the pericentromeric region of a pair of metacentric chromosomes. Two major clusters in the pericentromeric region of a pair of submetacentric chromosomes and two major clusters in the interstitial region of a pair of metacentric chromosomes were observed in E. longistipitata. E. hyemalis has many clusters of different sizes, localized mainly in the pericentromeric regions. Summarizing new data on the karyotype structure of E. sect. Eranthis and previously obtained data on E. sect. Shibateranthis allowed conclusions to be formed about the clear interspecific karyological differences of the genus Eranthis.

A Multi-Considered Seed Coat Pattern Classification of Allium L. Using Unsupervised Machine Learning.

The seed coat sculpture is one of the most important taxonomic distinguishing features. The objective of this study is to classify coat patterns of Allium L. seeds into new groups using scanning electron microscopy unsupervised machine learning. Selected images of seed coat patterns from more than 100 Allium species described in literature and data from our samples were classified into seven types of anticlinal (irregular curved, irregular curved to nearly straight, straight, S, U, U to Ω, and Ω) and five types of periclinal walls (granule, small verrucae, large verrucae, marginal verrucae, and verrucate verrucae). We used five unsupervised machine learning approaches: K-means, K-means++, Minibatch K-means, Spectral, and Birch. The elbow and silhouette approaches were then used to determine the number of clusters required. Thereafter, we compared human- and machine-based results and proposed a new clustering. We then separated the data into six target clusters: SI, SS, SM, NS, PS, and PD. The proposed strongly identical grouping is distinct from the other groups in that the results are exactly the same, but PD is unrelated to the others. Thus, unsupervised machine learning has been shown to support the development of new groups in the Allium seed coat pattern.

Flora of Mongolia: annotated checklist of native vascular plants.

In this study, we critically revised and updated the checklist of native vascular plants of Mongolia. The checklist comprises 3,041 native vascular plant taxa (2,835 species and 206 infraspecific species) from 653 genera and 111 families, including 7 lycophytes, 41 ferns, 21 gymnosperms, and 2,972 angiosperms. In the angiosperms, we identified the 14 families with the greatest species richness, ranging from 50 to 456 taxa. Species endemism is also noted here; 102 taxa are endemic to Mongolia, and 275 taxa are sub-endemic that co-occur in adjacent countries. Since 2014, a total of 14 taxa have been described new to science based on morphological evidences. Moreover, five genera and 74 taxa were newly added to the flora of Mongolia. Based on our critical revisions, names of three families, 21 genera, and 230 species have been changed in comparison to the previous checklist, "Conspectus of the vascular plants of Mongolia" (2014).

Micro-replication platform for studying the structural effect of seed surfaces on wetting properties.

Biological surfaces in plants are critical for controlling essential functions such as wettability, adhesion, and light management, which are linked to their adaptation, survival, and reproduction. Biomimetically patterned surfaces replicating the microstructures of plant surfaces have become an emerging tool for understanding plant-environment interactions. In this study, we developed a two-step micro-replication platform to mimic the microstructure of seed surfaces and demonstrated that this initial platform can be used to study seed surface-environment interactions. The two-step process involved the extraction of a simplified seed surface model from real seeds and micro-replication of the simplified seed surface model using nanoimprint lithography. Using Allium seeds collected from Mongolia and Central Asia as the model system, we studied the wettability of biological and synthetic seed surfaces. We could independently control the material properties of a synthetic seed surface while maintaining the microstructures and, thereby, provide clear evidence that Allium seed surfaces were highly wettable owing to the high surface energy in the epidermal material rather than a microstructural effect. We expect that this platform can facilitate study of the independent effect of microstructure on the interaction of seed surfaces with their surroundings and contribute to research on the evolution of plant-environment interactions.

Seed Morphology of Allium L. (Amaryllidaceae) from Central Asian Countries and Its Taxonomic Implications.

We studied seed macro- and micro-morphological characteristics of 48 Allium species (51 accessions) belonging to 24 sections and 7 subgenera. Our taxonomic sampling focused on the central Asian regions of Uzbekistan, Kyrgyzstan, and Mongolia. The seed length ranged between 1.74 ± 0.16-4.47 ± 0.43 mm and width ranged between 1.06 ± 0.08-3.44 ± 0.23 mm, showing various shapes. The irregular and elongated polygonal testa cells occurred in all investigated species. Seed testa sculptures showed high variation in their anticlinal walls associated with different shapes: straight to with U-, S- or Omega-type undulations among the species. The moderately flat to convex periclinal walls with various sized verrucae or granules were found in all investigated taxa. Based on our research, we conclude that seed characteristics such as size, shape, and the seed testa features show their significant variability, revealing key characteristics to support taxonomic relationships and major clades recovered in the molecular phylogeny of the genus Allium. Especially, the anticlinal wall characteristics were highly variable and decisive at the both section and species levels. In addition, widely varied shapes and sizes of the seeds were remarkably effective to distinguish Allium species.

A new record of critically endangered Saussurea bogedaensis (Asteraceae) from Dzungarian Gobi, Mongolia.

A species in the family Asteraceae, Saussurea bogedaensis, was newly described from Bogeda Mountain in Xinjiang, China and is a critically endangered species in China. Morphological and genetic characteristics confirm the presence of this species in Mongolia, as it was found in Baitag Bogd Mountain (in the Dzungarian Gobi). In addition, the distribution and conservation status of S. bogedaensis are provided.