Wasabi Gone Wild? Origin and Characterization of the Complete Plastomes of Ulleung Island Wasabi (Eutrema japonicum; Brassicaceae) and Other Cultivars in Korea.

Korean wasabi occurs naturally on the young oceanic, volcanic Ulleung Island off the east coast of the Korean Peninsula. Although the Ulleung Island wasabi is reported as Eutrema japonicum and has been suggested to be morphologically identical to cultivars in Korea, very little is known about its taxonomic identity and relationship with other cultivars. In this study, we sequenced the complete chloroplast DNA sequences of three naturally occurring Ulleung Island wasabi plants and six cultivars ('Daewang', 'Daruma', 'Micado', 'Orochi', 'Green Thumb', and 'Shogun') from continental Korea and determined the taxonomic identity of Korean wasabi on Ulleung Island. The size and organization of the complete chloroplast genomes of the nine accessions were nearly identical to those of previously reported wasabi cultivars. In addition, phylogenetic analysis based on the complete plastomes suggested that Ulleung Island wasabi most likely comprises various wasabi cultivars with three chlorotypes ('Shogun', 'Green Thumb', and a unique Chusan type). Based on the complete plastomes, we identified eight chlorotypes for the major wasabi cultivars and the Ulleung Island wasabi. Two major groups (1-'Mazuma' and 'Daruma', and 2-'Fujidaruma'/'Shimane No. 3'/Ulleung Island wasabi/five cultivars in Korea) were also identified based on mother line genealogical history. Furthermore, different types of variations (mutations, insertions/deletions (indels), mononucleotide repeats, and inversions) in plastomes were identified to distinguish different cultivar lines and five highly divergent hotspots. The nine newly obtained complete plastomes are valuable organelle genomic resources for species identification and infraspecific phylogeographic studies on wild and cultivated wasabi.

New insights into the phylogenetic relationships among wild onions (Allium, Amaryllidaceae), with special emphasis on the subgenera Anguinum and Rhizirideum, as revealed by plastomes.

The genus Allium, with over 900 species, is one of the largest monocotyledonous genera and is widely accepted with 15 recognized subgenera and 72 sections. The robust subgeneric and sectional relationships within Allium have long been not resolved. Based on 76 species of Allium (a total of 84 accessions), we developed a highly resolved plastome phylogenetic framework by integrating 18 newly sequenced species (20 accessions) in this study and assessed their subgeneric and sectional relationships, with special emphasis on the two subgenera Anguinum and Rhizirideum. We retrieved the three major evolutionary lines within Allium and found that the two subgenera Anguinum and Rhizirideum are monophyletic whereas others are highly polyphyletic (e.g., Allium, Cepa, Polyprason, and Melanocrommyum). Within the subgenus Anguinum, two strongly supported sublineages in East Asian and Eurasian-American were found. Allium tricoccum in North America belonged to the Eurasian clade. The distinct taxonomic status of A. ulleungense and its sister taxon were further determined. In subg. Rhizirideum, the Ulleung Island endemic A. dumebuchum shared its most recent common ancestor with the species from Mongolia and the narrow Korean endemic A. minus. Two Ulleung Island endemics were estimated to originate independently during the Pleistocene. In addition, a separate monotypic sectional treatment of the east Asian A. macrostemon (subg. Allium) and sister relationship between A. condensatum and A. chinense was suggested.

Genome-Wide Single Nucleotide Polymorphism Analysis Elucidates the Evolution of Prunus takesimensis in Ulleung Island: The Genetic Consequences of Anagenetic Speciation.

Of the two major speciation modes of endemic plants on oceanic islands, cladogenesis and anagenesis, the latter has been recently emphasized as an effective mechanism for increasing plant diversity in isolated, ecologically homogeneous insular settings. As the only flowering cherry occurring on Ulleung Island in the East Sea (concurrently known as Sea of Japan), Prunus takesimensis Nakai has been presumed to be derived through anagenetic speciation on the island. Based on morphological similarities, P. sargentii Rehder distributed in adjacent continental areas and islands has been suggested as a purported continental progenitor. However, the overall genetic complexity and resultant non-monophyly of closely related flowering cherries have hindered the determination of their phylogenetic relationships as well as the establishment of concrete continental progenitors and insular derivative relationships. Based on extensive sampling of wild flowering cherries, including P. takesimensis and P. sargentii from Ulleung Island and its adjacent areas, the current study revealed the origin and evolution of P. takesimensis using multiple molecular markers. The results of phylogenetic reconstruction and population genetic structure analyses based on single nucleotide polymorphisms detected by multiplexed inter-simple sequence repeat genotyping by sequencing (MIG-seq) and complementary cpDNA haplotypes provided evidence for (1) the monophyly of P. takesimensis; (2) clear genetic differentiation between P. takesimensis (insular derivative) and P. sargentii (continental progenitor); (3) uncertain geographic origin of P. takesimensis, but highly likely via single colonization from the source population of P. sargentii in the Korean Peninsula; (4) no significant reduction in genetic diversity in anagenetically derived insular species, i.e., P. takesimensis, compared to its continental progenitor P. sargentii; (5) no strong population genetic structuring or geographical patterns in the insular derivative species; and (6) MIG-seq method as an effective tool to elucidate the complex evolutionary history of plant groups.

Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea.

Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen-deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.

Characterization and Comparison of Two Complete Plastomes of Rosaceae Species (Potentilla dickinsii var. glabrata and Spiraea insularis) Endemic to Ulleung Island, Korea.

Potentilla dickinsii var. glabrata and Spiraea insularis in the family Rosaceae are species endemic to Ulleung Island, Korea, the latter of which is listed as endangered. In this study, we characterized the complete plastomes of these two species and compared these with previously reported plastomes of other Ulleung Island endemic species of Rosaceae (Cotoneaster wilsonii, Prunus takesimensis, Rubus takesimensis, and Sorbus ulleungensis). The highly conserved complete plastomes of P. dickinsii var. glabrata and S. insularis are 158,637 and 155,524 base pairs with GC contents of 37% and 36.9%, respectively. Comparative phylogenomic analysis identified three highly variable intergenic regions (trnT-UGU/trnL-UAA, rpl32/trnL-UAG, and ndhF/rpl32) and one variable genic region (ycf1). Only 14 of the 75 protein-coding genes have been subject to strong purifying selection. Phylogenetic analysis of 23 representative plastomes within the Rosaceae supported the monophyly of Potentilla and the sister relationship between Potentilla and Fragaria and indicated that S. insularis is sister to a clade containing Cotoneaster, Malus, Pyrus, and Sorbus. The plastome resources generated in this study will contribute to elucidating the plastome evolution of insular endemic Rosaceae on Ulleung Island and also in assessing the genetic consequences of anagenetic speciation for various endemic lineages on the island.

Penicillium ulleungdoense sp. nov. from Ulleung Island in Korea.

In a study of the fungal diversity on Ulleung Island in Korea, three novel strains of Penicillium were isolated. Different sites on Ulleung Island were selected for collecting endophytic fungi, and three endophytic fungal strains showed unique morphological characteristics. DNA sequence of the internal transcribed spacer, ß-tubulin, calmodulin, and RNA polymerase II second largest subunit regions of the strains were analyzed and they showed unique taxonomic position from the other species of Penicillium section Sclerotiora. The new strains were named Penicillium ulleungdoense sp. nov. As the novel endophytic Penicillium taxa were discovered in a unique environment, the data could be meaningful for understanding the geographical distribution of Ascomycetes on Ulleung Island.

Complete chloroplast genome of Ulleung Island endemic pokeweed, Phytolacca insularis (Phytolaccaceae), in Korea.

The first complete chloroplast genome sequences of Korean endemic pokeweed in Ulleung Island, Phytolacca insularis, were reported in this study. The P. insularis plastome was 156,419 bp long, with the large single copy (LSC) region of 86,106 bp, the small single copy (SSC) region of 18,335 bp, and two inverted repeat (IR) regions of 25,989 bp. The plastome contained 132 genes, including 84 protein-coding, eight ribosomal RNA, and 39 transfer RNA genes. The overall GC content was 36.8%. Phylogenetic analysis of 13 representative plastomes within the order Caryophyllales suggests that P. insularis is closely related to the species in family Aizoaceae.

Complete chloroplast genome of Lamium takesimese Nakai (Lamiaceae): an endemic species in South Korea.

The complete chloroplast genome of Lamium takesimense (Lamiaceae), an endemic species in South Korea, are presented in this article. The genome size is 150,626 bp in length, with 38.6% of GC content. It consists a large single-copy (LSC) region (82,527bp) and a small single-copy region (SSC) (17,185bp) which were separated by two inverted repeat (IRs) regions (25,457bp). The complete chloroplast genome contains 111 unique genes, including 77 protein-coding genes, 4 rRNA genes, and 30 tRNA genes.

Chloroplast genome of critically endangered Cotoneaster wilsonii (Rosaceae) endemic to Ulleung Island, Korea.

Cotoneaster wilsonii Nakai is an endangered species endemic to Ulleung Island, Korea. Here we reported the first complete chloroplast gnome sequences of C. wilsonii, which is 159,999 bp in total length with the large single copy (LSC) region of 87,868 bp, the small single copy (SSC) region of 19,335 bp, and two inverted repeat (IR) regions of 26,399 bp. The plastome contains 131 genes, including 84 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content is 42.6% and those in the LSC, SSC, and IR regions are 34.2, 30.3, and 42.6%, respectively. Phylogenetic analysis of 21 representative plastomes within the family Rosaceae suggests strongly the monophyly of Cotoneaster and C. wilsonii being sister to the clade of Cotoneaster franchetii and Cotoneaster horizontalis.

Development of 26 microsatellite markers in Bupleurum latissimum (Apiaceae), an endangered plant endemic to Ulleung Island, Korea.

PREMISE OF THE STUDY: To enhance our understanding of evolutionary consequences and to establish a suitable conservation strategy, we isolated microsatellite markers for the endangered Bupleurum latissimum (Apiaceae), which is endemic to the oceanic Ulleung Island. We also attempted cross-amplification in B. euphorbioides and B. longeradiatum to investigate its continental progenitors. METHODS AND RESULTS: Using high-throughput sequencing data, we developed 26 polymorphic microsatellite loci in three multiplexes, of which 13 loci were polymorphic in the two related species. For B. latissimum, alleles numbered two to four and the observed and expected heterozygosity ranged from 0.000 to 0.500 and 0.061 to 0.529, respectively. CONCLUSIONS: These developed markers will be useful for understanding evolutionary patterns of B. latissimum in an oceanic island system and for establishing suitable conservation strategies at the genetic level.

The complete plastome sequence of Rubus takesimensis endemic to Ulleung Island, Korea: Insights into molecular evolution of anagenetically derived species in Rubus (Rosaceae).

Previous phylogenetic studies have suggested that Rubus takesimensis (Rosaceae), which is endemic to Ulleung Island, Korea, is closely related to R. crataegifolius, which is broadly distributed across East Asia. A recent phylogeographic study also suggested the possible polyphyletic origins of R. takesimensis from multiple source populations of its continental progenitor R. crataegifolius in China, Japan, Korea, and the Russian Far East. However, even though the progenitor-derivative relationship between R. crataegifolius and R. takesimensis has been established, little is known about the chloroplast genome (i.e., plastome) evolution of anagenetically derived species on oceanic islands and their continental progenitor species. In the present study, we characterized the complete plastome of R. takesimensis and compared it to those of R. crataegifolius and four other Rubus species. The R. takesimensis plastome was 155,760 base pairs (bp) long, a total of 46 bp longer than the plastome of R. crataegifolius (28 from LSC and 18 from SSC). No structural or content rearrangements were found between the species pairs. Four highly variable intergenic regions (rpl32/trnL, rps4/trnT, trnT/trnL, and psbZ/trnG) were identified between R. takesimensis and R. crataegifolius. Compared to the plastomes of other congeneric species (R. corchorifolius, R. fockeanus, and R. niveus), six highly variable intergenic regions (ndhC/psaC, rps16/trnQ, trnK/rps16, trnL/trnF, trnM/atpE, and trnQ/psbK) were also identified. A total of 116 simple sequence repeats (SSRs), including 48 mononucleotide, 64 dinucleotide, and four trinucleotide repeat motifs were characterized in R. takesimensis. The plastome resources generated by the present study will help to elucidate plastome evolution within the genus and to resolve phylogenetic relationships within highly complex and reticulated lineages. Phylogenetic analysis supported both the monophyly of Rubus and the sister relationship between R. crataegifolius and R. takesimensis.

Complete chloroplast genome of Ulleung Island endemic flowering cherry, Prunus takesimensis (Rosaceae), in Korea.

Prunus takesimensis is an endemic flowering cherry on Ulleung Island, Korea. The complete chloroplast (cp) genome of P. takesimensis was generated by de novo assembly using whole-genome next-generation sequencing approach. The cp genome size was 157,948 bp in length consisting of four regions; large single copy region (85,959 bp), small single copy region (19,117 bp), and a pair of inverted repeat regions (26,436 bp). The genome contained a total of 128 genes, including 83 coding genes, 8 rRNA genes, and 37 tRNA genes. Phylogenetic analysis for 20 reported genomes within the family Rosaceae showed the monophyly of the genus Prunus including newly sequenced P. takesimensis.

The plastome sequence of Ulleung Rowan, Sorbus ulleungensis (Rosaceae), a new endemic species on Ulleung Island, Korea.

The complete chloroplast genome sequence of Sorbus ulleungensis, a recently described endemic species to Ulleung Island of Korea, was determined. The genome size was 159,632 bp in length with 36.5% GC content. It included a pair of inverted repeats (IRa and IRb) of 26,402 bp, which were separated by small single copy (SSC: 18,824 bp) and large single copy (LSC: 88,003 bp) regions. The cp genome contained 111 genes, including 78 protein coding genes, 29 tRNA genes, and four rRNA genes. Phylogenetic analysis of the combined 78 protein coding genes and four rRNA genes showed that S. ulleungensis was most closely related to Pyrus pyrifolia.

Complete chloroplast genome of Ulleung Island endemic basswood, Tilia insularis (Malvaceae), in Korea.

The first complete chloroplast genome sequences of Korean endemic basswood in Ulleung Island, Tilia insularis, were reported in this study. The T. insularis plastome was 162,565 bp long, with the large single-copy (LSC) region of 91,100 bp, the small single-copy (SSC) region of 20,381 bp, and two inverted repeat (IR) regions of 25,542 bp. The plastome contained 131 genes, including 86 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 36.5%. Phylogenetic analysis of 14 representative plastomes within the family Malvaceae suggests that T. insularis is closely related to other congeneric species in subfamily Tilioideae.

Complete chloroplast genome of Ulleung Island endemic, Epilobium ulleungensis (Onagraceae), in Korea.

The first complete chloroplast genome sequences of Korean endemic Epilobium in Ulleung Island, Epilobium ulleungensis, were reported in this study. The E. ulleungensis plastome was 160,912 bp long, with the large single copy (LSC) region of 88,915 bp, the small single copy (SSC) region of 17,327 bp, and two inverted repeat (IR) regions of 27,335 bp. The plastome contained 131 genes, including 84 protein-coding, eight ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 36.5%. Phylogenetic analysis of nine representative plastomes within the family Onagraceae suggests strongly that E. ulleungensis is sister to the clade containing species of Oenothera in tribe Onagreae.

Seroprevalence of Coxiella burnetii infection in cattle on Ulleung Island, Korea / 대한수의학회지

We assessed the seroprevalence of Coxiella burnetii (C. burnetii) in cattle on Ulleung Island, Korea in a population-based follow up study for 4 years and determined the spatial distribution and risk factors associated with C. burnetii. The seroprevalence of C. burnetii was determined to be 1.4–2.0% during 2011–2014. Overall, nine cattle from three farms that tested seropositive showed C. burnetii antibody seroconversions between 2011 and 2014. The number of seropositive cattle was low, suggesting that movement of and contact between animals was possible risk factors for the transmission of C. burnetii.

Three New Recorded Species of the Physalacriaceae on Ulleung Island, Korea.

Most known species in the Physalacriaceae are saprotrophs that grow on decaying leaves and wood, and approximately 21 genera in the Physalacriaceae have been reported worldwide. During an ongoing survey of indigenous fungi in Korea, four specimens belonging to the Physalacriaceae were collected on Ulleung Island. These specimens were identified as three species based on morphological characteristics and molecular analysis of rDNA-internal transcribed spacer sequences. Three species in three genera were shown to be new records in Korea: Hymenopellis orientalis, Paraxerula hongoi, and Ponticulomyces orientalis. The latter two are the first records of these genera in Korea. In this study, we provide detailed morphological descriptions of these species and describe their phylogenetic position within the Physalacriaceae.

Biodiversity hotspot for marine invertebrates around the Dokdo, East Sea, Korea: Ecological checklist revisited.

We extensively reviewed the macrozoobenthos around Dokdo, Korea, by analyzing metadata collected over the past 50years. The Dokdo macrozoobenthos was represented by 578 species belonging to 243 families from 12 phyla, where four major phyla (or classes) collectively accounted for 86% to total. Mollusks, arthropods, and cnidarians were semi-equally occurred in intertidal and subtidal areas, while polychetes dominated the subtidal zone. The northern most region of Dokdo had the greatest biodiversity (173 species). The taxonomic distinctness analysis (delta+) indicated a close association between species by region, although the number of species varied greatly. About half of the species did not occur cross the locations (n=20), indicating strong habitat preferences of Dokdo macrofaunal assemblages. Overall, the diversity of Dokdo was greater than that of Ulleung Island (east coast), but comparable to that of the well-developed tidal flats in the western Korean waters, highlighting its status as a biodiversity hotspot.

Ten New Recorded Species of Macrofungi on Ulleung Island, Korea.

Ulleung Island is a biodiversity hotspot in South Korea. During a survey of indigenous fungal species from Ulleung Island conducted from 2015 to 2016, we discovered 10 unrecorded macrofungi in Korea. These macrofungi were identified to the species level using morphological features and phylogenetic analysis based on the internal transcribed spacer region: Deconica phyllogena, Mycena zephirus, Phaeomarasmius proximans, Phlebia radiata, Pluteus semibulbosus, Postia alni, Resinicium pinicola, Scytinostroma portentosum, Tricholomopsis flammula, and Tyromyces kmetii. We also provide detailed morphological descriptions for these 10 species.

Three New Recorded Species of the Physalacriaceae on Ulleung Island, Korea

Most known species in the Physalacriaceae are saprotrophs that grow on decaying leaves and wood, and approximately 21 genera in the Physalacriaceae have been reported worldwide. During an ongoing survey of indigenous fungi in Korea, four specimens belonging to the Physalacriaceae were collected on Ulleung Island. These specimens were identified as three species based on morphological characteristics and molecular analysis of rDNA-internal transcribed spacer sequences. Three species in three genera were shown to be new records in Korea: Hymenopellis orientalis, Paraxerula hongoi, and Ponticulomyces orientalis. The latter two are the first records of these genera in Korea. In this study, we provide detailed morphological descriptions of these species and describe their phylogenetic position within the Physalacriaceae.