Genome Size and Chromosome Number Evolution in Korean Iris L. Species (Iridaceae Juss.)

The return of natural dyes: the case of logwood tree (Haematoxylum campechianum L.)

In recent years, a worldwide reassessment of natural dyes has occurred, driven by the health and environmental issues associated with synthetic dyes. Haematoxylum campechianum L. is a tropical tree from which wood extracts were widely used in the textile industry during the 16th century. The logwood tree extract serves as a contemporary source of hematoxylin, a key dye in the globally prevalent hematoxylin-eosin staining method, a cornerstone in histopathological procedures. This paper will initially explore the re-emergence of natural dyes. Subsequently, it will focus on the historical, conventional, and innovative applications of logwood in the fields of medicine, histopathology, and nanotechnology, along with the status and alternative uses of the hematoxylin-eosin stain. Lastly, this paper will examine the current state of conservation and utilization of Haematoxylum campechianum in Campeche, Mexico, a leading global producer of hematoxylin.

Evolutionary patterns of variations in chromosome counts and genome sizes show positive correlations with taxonomic diversity in tropical gingers

PREMISE

Cytogenetic traits such as an organism's chromosome number and genome size are taxonomically critical as they are instrumental in defining angiosperm diversity. Variations in these traits can be traced to evolutionary processes such as polyploidization, although geographic variations across cytogenetic traits remain underexplored. In the pantropical monocot family Zingiberaceae (~1500 species), cytogenetic traits have been well documented; however, the role of these traits in shaping taxonomic diversity and biogeographic patterns of gingers is not known.

METHODS

A time-calibrated Bayesian phylogenetic tree was constructed for 290 taxa covering three of the four subfamilies in Zingiberaceae. We tested models of chromosome number and genome size evolution within the family and whether lineage age, taxonomic diversity, and distributional range explain the variations in the cytogenetic traits. Tests were carried out at two taxonomic ranks: within Zingiberaceae and within genus Hedychium using correlations, generalized linear models and phylogenetic least square models.

RESULTS

The most frequent changes in chromosome number within Zingiberaceae were noted to be demi-polyploidization and polyploidization (~57% of the time), followed by ascending dysploidy (~27%). The subfamily Zingiberoideae showed descending dysploidy at its base, while Alpinioideae showed polyploidization at its internal nodes. Although chromosome counts and genome sizes did not corroborate with each other, suggesting that they are not equivalent; higher chromosome number variations and higher genome size variations were associated with higher taxonomic diversity and wider biogeographic distribution.

CONCLUSIONS

Within Zingiberaceae, multiple incidences of polyploidization were discovered, and cytogenetic events appear to have reduced the genome sizes and increased taxonomic diversity, distributional ranges and invasiveness.

Complete plastid genome of Iris orchioides and comparative analysis with 19 Iris plastomes

Iris is a cosmopolitan genus comprising approximately 280 species distributed throughout the Northern Hemisphere. Although Iris is the most diverse group in the Iridaceae, the number of taxa is debatable owing to various taxonomic issues. Plastid genomes have been widely used for phylogenetic research in plants; however, only limited number of plastid DNA markers are available for phylogenetic study of the Iris. To understand the genomic features of plastids within the genus, including its structural and genetic variation, we newly sequenced and analyzed the complete plastid genome of I. orchioides and compared it with those of 19 other Iris taxa. Potential plastid markers for phylogenetic research were identified by computing the sequence divergence and phylogenetic informativeness. We then tested the utility of the markers with the phylogenies inferred from the markers and whole-plastome data. The average size of the plastid genome was 152,926 bp, and the overall genomic content and organization were nearly identical among the 20 Iris taxa, except for minor variations in the inverted repeats. We identified 10 highly informative regions (matK, ndhF, rpoC2, ycf1, ycf2, rps15-ycf, rpoB-trnC, petA-psbJ, ndhG-ndhI and psbK-trnQ) and inferred a phylogeny from each region individually, as well as from their concatenated data. Remarkably, the phylogeny reconstructed from the concatenated data comprising three selected regions (rpoC2, ycf1 and ycf2) exhibited the highest congruence with the phylogeny derived from the entire plastome dataset. The result suggests that this subset of data could serve as a viable alternative to the complete plastome data, especially for molecular diagnoses among closely related Iris taxa, and at a lower cost.

A Flow Cytometry-Based Assessment of the Genomic Size and Ploidy Level of Wild Musa Species in India

The genome size variation is an important attribute in evolutionary and species characterization. Musa L. is regarded as one of the taxonomically complicated genera within the order Zingiberales, with more than 75 species from wild seeded to seedless cultivars that may be diploid, triploid or tetraploid. The knowledge of total nuclear DNA content in terms of genome size and ploidy level in wild species of Musa is absolutely important in evolutionary and genomic studies.

METHODS

In this paper, chromosome spreading was performed via protoplast isolation and a fast air-dry dropping method and flow cytometry were used with Raphanus sativus L. (Brassicaceae) as a standard for ploidy and genome size estimation.

RESULTS

The results showed that genome size (2C) varied amongst Musa species, based on the ratio of G1 peak positions. The lowest genome size (2C) was found in M. balbisiana var. andamanica (1.051 ± 0.060 pg) and the highest genome size (2C) was recorded for Musa ABB.cv. Meitei-hei (1.812 ± 0.108 pg) for the section Eumusa. Among the species belonging to the section Rhodochlamys, M. rosae had the lowest 2C content of 1.194 ± 0.033 pg whereas the highest nuclear DNA content (2C) was observed in M. velutina (1.488 ± 0.203 pg). Cytogenetic analysis revealed that the chromosome number of 14 wild Musa species was 2n = 22, while 1 species-Ensete glaucum-showed a chromosome number of 2n = 18 (diploid), and for 3 species, the chromosome number was 2n = 33 (triploids). An association study based on the Pearson correlation coefficient showed 2C nuclear DNA content was significant and positively correlated with ploidy level (R = 0.9) and chromosome number (R = 0.84).

CONCLUSIONS

The present study provides reliable information on the genome size and ploidy level of wild Musa species from the Indian region through flow cytometric analysis, which could be further utilized in taxonomic and crop improvement programs. For the first time, the nuclear DNA content of eight wild diploid and three triploid Indian species were estimated and reported. Genome size could be an effective indicator in identification of species and evolutionary studies in Musa with varying ploidy levels and morphological similarities.

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

Iris Koreana NAKAI Inhibits Osteoclast Formation via p38-Mediated Nuclear Factor of Activated T Cells 1 Signaling Pathway

BACKGROUND

Iris Koreana NAKAI (IKN) is a flowering perennial plant that belongs to the Iridaceae family. In this study, we aimed to demonstrate the effects of IKN on osteoclast differentiation in vitro and in vivo. We also sought to verify the molecular mechanisms underlying its anti-osteoclastogenic effects.

METHODS

Osteoclasts were formed by culturing mouse bone marrow macrophage (BMM) cells with macrophage colony-stimulating factor and receptor activator of nuclear factor-κB ligand (RANKL). Bone resorption assays were performed on dentin slices. mRNA expression levels were analyzed by quantitative polymerase chain reaction. Western blotting was performed to detect protein expression or activation. Lipopolysaccharide (LPS)-induced osteoclast formation was performed using a mouse calvarial model.

RESULTS

In BMM cultures, an ethanol extract of the root part of IKN suppressed RANKL-induced osteoclast formation and bone resorptive activity. In contrast, an ethanol extract of the aerial parts of IKN had a minor effect on RANKL-induced osteoclast formation. Mechanistically, the root part of IKN suppressed RANKL-induced p38 mitogen-activated protein kinase (MAPK) activation, effectively abrogating the induction of c-Fos and nuclear factor of activated T cells 1 (NFATc1) expression. IKN administration decreased LPS-induced osteoclast formation in a calvarial osteolysis model in vivo.

CONCLUSIONS

Our study suggested that the ethanol extract of the root part of IKN suppressed osteoclast differentiation and function partly by downregulating the p38 MAPK/c-Fos/NFATc1 signaling pathways. Thus, the root part.

Comparative Analyses of Complete Chloroplast Genomes and Karyotypes of Allotetraploid Iris koreana and Its Putative Diploid Parental Species (Iris Series Chinenses, Iridaceae)

The Iris series Chinenses in Korea comprises four species (I. minutoaurea, I. odaesanensis, I. koreana, and I. rossii), and the group includes some endangered species, owing to their high ornamental, economic, and conservation values. Among them, the putative allotetraploid, Iris koreana (2n = 4x = 50), is hypothesized to have originated from the hybridization of the diploids I. minutoaurea (2n = 2x = 22) and I. odaesanensis (2n = 2x = 28) based on morphological characters, chromosome numbers, and genome size additivity. Despite extensive morphological and molecular phylogenetical studies on the genus Iris, little is known about Korean irises in terms of their complete chloroplast (cp) genomes and molecular cytogenetics that involve rDNA loci evolution based on fluorescence in situ hybridization (FISH). This study reports comparative analyses of the karyotypes of the three Iris species (I. koreana, I. odaesanensis, and I. minutoaurea), with an emphasis on the 5S and 35S rDNA loci number and localization using FISH together with the genome size and chromosome number. Moreover, the cp genomes of the same individuals were sequenced and assembled for comparative analysis. The rDNA loci numbers, which were localized consistently at the same position in all species, and the chromosome numbers and genome size values of tetraploid Iris koreana (four 5S and 35S loci; 2n = 50; 1C = 7.35 pg) were additively compared to its putative diploid progenitors, I. minutoaurea (two 5S and 35S loci; 2n = 22; 1C = 3.71 pg) and I. odaesanensis (two 5S and 35S loci; 2n = 28; 1C = 3.68 pg). The chloroplast genomes were 152,259–155,145 bp in length, and exhibited a conserved quadripartite structure. The Iris cp genomes were highly conserved and similar to other Iridaceae cp genomes. Nucleotide diversity analysis indicated that all three species had similar levels of genetic variation, but the cp genomes of I. koreana and I. minutoaurea were more similar to each other than to I. odaesanensis. Positive selection was inferred for psbK and ycf2 genes of the three Iris species. Phylogenetic analyses consistently recovered I. odaesanensis as a sister to a clade containing I. koreana and I. minutoaurea. Although the phylogenetic relationship, rDNA loci number, and localization, together with the genome size and chromosome number of the three species, allowed for the inference of I. minutoaurea as a putative maternal taxon and I. odaesanensis as a paternal taxon, further analyses involving species-specific molecular cytogenetic markers and genomic in situ hybridization are required to interpret the mechanisms involved in the origin of the chromosomal variation in Iris series Chinenses. This study contributes towards the genomic and chromosomal evolution of the genus Iris.

Comparative analysis of two Korean irises (Iris ruthenica and I. uniflora, Iridaceae) based on plastome sequencing and micromorphology

Iris ruthenica Ker Gawl. and I. uniflora Pall. ex Link, which are rare and endangered species in Korea, possess considerable horticultural and medicinal value among Korean irises. However, discrimination of the species is hindered by extensive morphological similarity. Thus, the aim of the present study was to identify discriminating features by comparing the species’ complete plastid genome (i.e., plastome) sequences and micromorphological features, including leaf margins, stomatal complex distribution (hypostomatic vs. amphistomatic leaves), anther stomata density, and tepal epidermal cell patterns. Plastome comparison revealed slightly divergent regions within intergenic spacer regions, and the most variable sequences, which were distributed in non-coding regions, could be used as molecular markers for the discrimination of I. ruthenica and I. uniflora. Phylogenetic analysis of the Iris species revealed that I. ruthenica and I. uniflora formed a well-supported clade. The comparison of plastomes and micromorphological features performed in this study provides useful information for elucidating taxonomic, phylogenetic, and evolutionary relationships in Iridaceae. Further studies, including those based on molecular cytogenetic approaches using species specific markers, will offer insights into species delimitation of the two closely related Iris species.

Implications of foliar epidermal micromorphology using light and scanning electron microscopy: A useful tool in taxonomy of Korean irises

The genus Iris L., comprising approximately 210 species, is one of the most species-rich genera in the family Iridaceae. In this study, the first comprehensive leaf micromorphological characters of Korean irises were studied using light and scanning electron microscopy. Our objective was to evaluate the foliar micromorphological characteristics (namely epidermal cells, stomata types, and guard cell size) of Korean Iris taxa in a systematic context. All the investigated Korean Iris taxa had amphistomatic or hypostomatic leaves with anomocytic stomatal complexes. Guard cell length varied among species, ranging from 24.8 μm (I. rossii) to 56.0 μm (I. domestica). Although the presence of papillae on the outer periclinal wall is not of taxonomic significance, leaf margin pattern, guard cell size, and sunken stomata type were useful for species-level identification of Korean Iris species. The occurrence of polymorphic stomatal types was reported here for the first time, and the correlation between genome size and epidermal guard cell length was discussed.

Bioactive Constituents of Iris hybrida (Iridaceae): processing effect

Iris genus plants are a valuable source of bioactive compounds, which are an important component for pharmaceutical development. The present article shows the potential of mineral nutrition with applied of magnesium sulfate, iron chelates, and potassium oxide on affecting the phenolic compounds content in Iris hybrida 'Tsikavynka', I. hybrida 'Tambo', and I. hybridа 'Widecombe Fire'. The effect of mineral processing was specific to plant organs and varied in the components composition. The Irises rhizomes had an increased total phenolic compounds content after treatment (up to 10% of the total isoflavonoids content, up to 8% of phenolic acids; up to 5% of γ-pyrones; up to 13% of flavonoids) by UV-Vis spectroscopy method. A positive effect of nutrition on the biosynthesis and content of individual isoflavonoids (tectoridin, nigricin D-glucoside, genistin, iristectorigenin B, nigricin, irigenin, irisolidone) and xanthone mangiferin in Irises rhizomes by HPLC has been established. In addition, an increase of chlorogenic acid amount in Irises leaves was noted. The results demonstrate the sensitivity of Iris phenylpropanoid metabolism to mineral nutrition and can be used for predicted medical plant cultivation with increased content of bioactive constituents.

Cytological Study of Cypripedium japonicum Thunb. (Orchidaceae Juss.): An Endangered Species from Korea

Changes in chromosome number and karyotype evolution are important to plant diversification, as they are both major drivers of speciation processes. Herein, chromosome number, karyotype, and genome size of the Korean lady's slipper orchid Cypripedium japonicum Thunb., an endangered species, were investigated in natural populations. Furthermore, all cytological data from this species are reported herein for the first time. The chromosome number of all investigated C. japonicum plants was diploid (2n = 2x = 22), with x = 11 as base chromosome number, whereby the species can now be clearly distinguished from the Japanese lady's slipper orchid. The karyotypes of all studied individuals were of similar length, symmetrical, and rather unimodal. Flow cytometry of the C. japonicum revealed that the genome size ranged from 28.38 to 30.14 pg/1C. Data on chromosome number and karyotypes were largely consistent with previous results indicating that Korean (x = 11) populations of C. japonicum are more closely related to Chinese populations (x = 11) compared to Japanese (x = 10) populations. These comprehensive cytological results will benefit the efforts to discriminate the geographically isolated and endangered Eastern Asian (China, Japan, and Korea) lady's slipper orchid species.

Micromorphological differentiation of Korean Disporum species using light and scanning electron microscopy

The genus Disporum Salisb. is widely distributed in East Asia, yet phylogenetically relevant morphological traits useful for differentiating many of the small, perennial, herbaceous species remain poorly described. To address this, leaf, floral, pollen, and orbicule micromorphology of four Korean Disporum species was investigated using light and scanning electron microscopy. All Korean Disporum species examined had hypostomatic leaves, with anomocytic stomatal complexes found only on the abaxial epidermis. Guard cell length varied among species, ranging from 44.30 μm in D. viridescens to 53.49 μm in D. uniflorum. The epidermal cells of the investigated Disporum taxa had sinuate anticlinal cell walls on both adaxial and abaxial surfaces. The surface of the guard and subsidiary cells were either smooth with weak striations or had strongly wrinkled striations. The pollen grains of all Korean Disporum taxa were monads, monosulcate with granular aperture membranes, subprolate to prolate in shape with microreticulate or verrucate exine surfaces. The mean size of pollen grains ranged from 46.38 to 49.92 μm in polar length and from 34.39 to 39.58 μm in equatorial diameter across species. Sexine ornamentation was a taxonomically relevant trait for differentiating Korean Disporum taxa. Additionally, the presence of orbicules as well as the orbicular characters (e.g., size, shape, ornamentation, and association pattern) are described for the first time in species from this genus. The present investigation of leaf and floral micromorphology using light and scanning electron microscopy provides valuable information for the taxonomic differentiation and identification of Disporum species in Korea. RESEARCH HIGHLIGHTS: A detailed micromorphological description of leaf, floral characters (tepal, stigma, style), pollen and orbicule is provided for Korean Disporum species using scanning electron microscopy (SEM) and light microscopy (LM). The presence of orbicules and their taxonomic implications in Korean Disporum species are described for the first time. Phylogenetically informative pollen and orbicule micromorphological characters are described, improving understanding the systematic relationships of Korean species in the genus Disproum.

Genome Size Evolution and Dynamics in Iris, with Special Focus on the Section Oncocyclus

Insights into genome size dynamics and its evolutionary impact remain limited by the lack of data for many plant groups. One of these is the genus Iris, of which only 53 out of c. 260 species have available genome sizes. In this study, we estimated the C-values for 41 species and subspecies of Iris mainly from the Eastern Mediterranean region. We constructed a phylogenetic framework to shed light on the distribution of genome sizes across subgenera and sections of Iris. Finally, we tested evolutionary models to explore the mode and tempo of genome size evolution during the radiation of section Oncocyclus. Iris as a whole displayed a great variety of C-values; however, they were unequally distributed across the subgenera and sections, suggesting that lineage-specific patterns of genome size diversification have taken place within the genus. The evolutionary model that best fitted our data was the speciational model, as changes in genome size appeared to be mainly associated with speciation events. These results suggest that genome size dynamics may have contributed to the radiation of Oncocyclus irises. In addition, our phylogenetic analysis provided evidence that supports the segregation of the Lebanese population currently attributed to Iris persica as a distinct species.