Taxonomic evaluation of Xylodon (Hymenochaetales, Basidiomycota) in Korea and sequence verification of the corresponding species in GenBank

Genus Xylodon consists of white-rot fungi that grow on both angiosperms and gymnosperms. With resupinate and adnate basidiomes, Xylodon species have been classified into other resupinate genera for a long time. Upon the integration of molecular assessments, the taxonomy of the genus has been revised multiple times over the years. However, the emendations were poorly reflected in studies and public sequence databases. In the present study, the genus Xylodon in Korea was evaluated using molecular and morphological analyses of 172 specimens collected in the period of 2011 to 2018. The host types and geographical distributions were also determined for species delimitation. Furthermore, public sequences that correspond to the Xylodon species in Korea were assessed to validate their identities. Nine Xylodon species were identified in Korea, with three species new to the country. Morphological differentiation and identification of some species were challenging, but all nine species were clearly divided into well-resolved clades in the phylogenetic analyses. Detailed species descriptions, phylogeny, and a key to Xylodon species in Korea are provided in the present study. A total of 646 public ITS and nrLSU sequences corresponding to the nine Xylodon species were found, each with 404 (73.1%) and 57 (61.3%) misidentified or labeled with synonymous names. In many cases, sequences released before the report of new names have not been revised or updated. Revisions of these sequences are arranged in the present study. These amendments may be used to avoid the misidentification of future sequence-based identifications and concurrently prevent the accumulation of misidentified sequences in GenBank.

A TAXONOMIC REVISION OF CYRTANDRA (GESNERIACEAE) IN SULAWESI, INDONESIA

Taxonomic evaluation of Cyrtandra (Gesneriaceae) from Sulawesi has resulted in the recognition of 39 species. Of these, four species are described as new here: Cyrtandra balgooyi H.J.Atkins & Karton., C. flavomaculata H.J.Atkins & Karton., C. longistamina H.J.Atkins & Karton. and C. parvicalyx H.J.Atkins & Karton. Eleven names are lectotypified and three names are placed in synonymy. Provisional conservation assessments suggest that seven of these species are Critically Endangered, six are Endangered, three are Vulnerable, two are Data Deficient and 21 are of Least Concern. Illustrations, distribution maps, and a key to the Cyrtandra species of Sulawesi are presented. Evaluasi taksonomi Cyrtandra (Gesneriaceae) dari Sulawesi menghasilkan pengenalan 39 jenis. Diantara jenis-jenis tersebut, empat jenis dideskripsikan sebagai jenis yang baru disini: Cyrtandra balgooyi H.J.Atkins & Karton., C. flavomaculata H.J.Atkins & Karton., C. longistamina H.J.Atkins & Karton. and C. parvicalyx H.J.Atkins & Karton. Sebelas nama telah dilektotipifikasikan dan tiga nama ditempatkan dalam sinonim. Penilaian konservasi sementara menyarankan bahwa tujuh dari jenisjenis ini dinyatakan Critically Endangered, enam dinyatakan Endangered, tiga dinyatakan Vulnerable, dua dinyatakan Data Deficient dan 21 sisanya dinyatakan Least Concern. Ilustrasi, peta distribusi dan kunci identifikasi untuk jenis-jenis Cyrtandra dari Sulawesi disajikan.

Taxonomic Evaluation of a Bioherbicidal Isolate of Albifimbria verrucaria, Formerly Myrothecium verrucaria

The fungal genus Myrothecium was once polyphyletic but a recent reconsideration of the family Stachybotryaceae spilt it into several genera. The ex-neotype specimen of the species Myrothecium verrucaria is now recognized as Albifimbria verrucaria. The well-studied plant pathogen and candidate bioherbicide CABI-IMI 368023, previously identified as M. verrucaria, was analyzed morphologically and genetically and found to be most consistently aligned with the other representatives of A. verrucaria.

Arganiella Giusti & Pezzoli, 1980 (Caenogastropoda: Truncatelloidea: Hydrobiidae): a widespread genus or several narrow-range endemic genera?

Most valvatiform genera of the gastropod family Hydrobiidae are narrow-range taxa. One exception is the genus Arganiella, which is comprised of three congeners: the type species A. pescei from the Apennine Peninsula, A. wolfi from the Iberian Peninsula and A. tabanensis from the Balkans. The genus assignment of the latter two species was based on morphological similarities with A. pescei in the shell, operculum, radula and genitalia. Given that the morphology of hydrobiids is sometimes susceptible to convergence, this study re-evaluates the taxonomic status of species of Arganiella by analysing mitochondrial (mtCOI) and nuclear (18S rRNA) sequences of topotypes or near topotypes to infer their phylogenetic position. Our phylogenetic analyses depicted Arganiella as a non-monophyletic group within Hydrobiidae, and sequence divergence among the three species ranged from 14.5 to 16.7% for mtCOI and 2.0 to 3.8% for 18S. We also re-examined the extent of morphological variation among species of Arganiella and found a few differences among them and other valvatiform genera. Consequently, we propose two new genera for A. wolfi and A. tabanensis. Our results conflict with the classification of valvatiform hydrobiid species solely based on traditional phenotypical methods and suggest further taxonomic evaluation within a molecular framework.

Taxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences

The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599T) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356T) and Heyndrickxia vini (JCM 19841T) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H. sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.

Taxonomic evaluation of Nymphoides (Menyanthaceae) in eastern Asia

According to recent taxonomic treatments, up to 13 Nymphoides species exist in eastern Asia, with some species purported to be narrowly endemic. However, these treatments have largely covered rather limited geographic areas, whereas the genus can be found worldwide. In order to evaluate the global distinctness of currently accepted Nymphoides species in eastern Asia, we quantitatively examined their distinguishing morphological characters using information from published treatments and data from herbarium specimens. Out of 13 evaluated species, nine were found to be morphologically distinct (N. aurantiaca, N. cambodiana, N. coreana, N. hastata, N. hydrophylla, N. indica, N. lungtanensis, N. parviflora, N. peltata), and the remaining species (N. coronata, N. cristata, N. siamensis, N. tonkinensis) lacked characters that clearly could distinguish them. We thus propose that the morphologically indistinct species should be considered synonymous with other Nymphoides species. Herein we establish N. parviflora comb. nov., to accommodate the species that was heretofore known by the invalid name N. parvifolia. Lectotypes are designated for Limnanthemum calycinum, L. coreanum, L. coronatum, L. hastatum, L. kleinianum, and L. tonkinense, and neotypes are designated for Menyanthes hydrophylla and M. nymphoides.

Taxonomic Reevaluation of Endemic Hawaiian Planchonella (Sapotaceae)

Planchonella (Sapotaceae) in Hawaii has a complicated taxonomic history that has resulted in considerable confusion among botanists and conservation practitioners. Up to seven different species and several varieties have been described in Hawaii, with the most recent taxonomic evaluation recognizing one species, P. sandwicensis. We have conducted a phylogenetic study of Hawaiian Planchonella using molecular(ETS, ITS, and RPB2) and morphological data to infer whether one or several species can be distinguished. In line with earlier research based on molecular data, we find that Planchonella in Hawaii is comprised of two well-supported clades distinguished by fruit color: yellow or purple. The purple-fruited clade contains individuals with flat leaf blades, long pedicels, and greenish corollas, a species corresponding to P. sandwicensis, distributed on all Hawaiian Islands except the island of Hawaii. The yellow-fruited clade possesses leaves that are frequently longitudinally rolled, wavy or distally deflexed, short pedicels, and yellow or cream (rarely greenish) corollas, a species corresponding to P. spathulata that is distributed on all Hawaiian Islands but is believed rare in Kauai. Both species can set fruit with aborted ovules, resulting in small fruits that look dissimilar to well-developed fruit. The species can occur in sympatry, where P. sandwicensis seems to be better adapted to slightly wetter forests and higher altitudes, whereas P. spathulata usually occurs at lower elevations in mesic to dry forests. Both species exhibit large morphological variation and overlap, resulting in many previous collections with inadequate label information, which has impeded correct taxonomic determinations. We refrain from recognizing infraspecific taxa because there is no morphological coherence, no molecular support, and it is unhelpful for species conservation. Five lectotypes are here designated. Both species are assessed for conservation status according to IUCN guidelines and are tentatively proposed as species of Least Concern.

A taxonomic evaluation of Astrophytum myriostigma var. Nudum (Cactaceae)

The absence of epidermal trichomes has been used as a diagnostic character to distinguish Astrophytum myriostigma var. nudum from other infraspecific taxa. In the Huizache region of San Luis Potosi, Mexico, between the elevations of 1320 m and 1700 m, the local populations of A. myriostigma are polymorphic, comprised of nude, semi-nude, and flecked plants. However, this polymorphism is non-discrete as there is considerable variation and intermediacy among plants. Also, the proportion of nude plants increases gradually with elevation, which suggests clinal variation correlated with altitude. Exclusively nude populations are currently known only from near Santa Rita del Rucio (? 1710 m) and south of Entronque Huizache (? 1750 m). Farther south, flecked plants were recorded at 1726 m elevation at 6 km E of Guadalcazar, and to the north near El Realejo flecked plants occur as high as 1920 m. At localities southeast of the Sierra San Pedro (Sierra Guadalcazar), nude and semi-nude plants are absent or present at relatively low frequencies in local populations. Epidermal trichomes provide shading and reflectance that protects the cactus stem against excessive solar radiation and moderates stem temperature. The majority of nude A. myriostigma growing in exposed locations at the margins of Hechtia colonies were found to suffer from chlorophyll degeneration due to excessive exposure to solar radiation. A comparative morphological study did not find any characters which can be used in combination to diagnose the var. nudum. Given the lack of a suite of discrete, or nearly discrete diagnostic characters, and given that exclusively nude populations do not have a definable geographic distribution we suggest that the nude phenotype should be treated taxonomically as a “form” rather than as a geographical “variety,” or subspecies.

Molecular phylogeny and taxonomic evaluation of the genus Asaccus Dixon and Anderson, 1973 (Reptilia: Phyllodactylidae) in Iran

The Iranian species of the phyllodactylid geckos of the genus Asaccus are found only in the valleys of the Zagros Mountains, a region which represents an important area of endemism in western Iran. Recently, many relict species have been described from the central and southern parts of the Zagros Mountains, which were previously known as A. elisae. The recent descriptions of species within this complex suggest that diversity within the genus may be higher than expected and that its taxonomy and systematics should be revised. In the present study, phylogenetic relationships within the genus Asaccus were evaluated using two mitochondrial and one nuclear gene. Genetically, the genus shows high levels of variability. The molecular phylogeny of the genus suggests the presence of three main clades along the Zagros Mountains with the southern population (from the Hormozgan province) and one clade (A. sp8 and A. sp9) being sister taxon to A. montanus from UAE. The remaining samples are separated into two reciprocally monophyletic groups: the northern (Kurdistan, Kermanshah and Ilam provinces) and the central (Lorestan, Khuzestan, Kohgilouye-Bouyer Ahmad and Fars provinces) Zagros groups. The results of the present study suggest that populations attributed to A. elisae in Iran correspond to distinct lineages with high genetic distances. In brief, our results suggest that the genus needs a major taxonomical revision The Arabian origin of the genus has not been confirmed, because two populations from Zagros were located within the A. montanus, A. gallagheri and A. platyrhynchus clade. Further morphological analyses are needed to systematically define each genetic lineage as a new taxon.

Determination of phytoplankton composition by microscopy and HPLC-derived pigment analysis in the Sea of Marmara

This study is an integrated overview of pigment and microscopic analysis of phytoplankton composition in the Sea of Marmara. The study was conducted from 27 sampling stations during spring (May 2017 and 2018) and summer (August 2016 and 2018). The phytoplankton community was represented mostly by diatoms and dinoflagellates, as the major groups, and also other phytoflagellate groups as shown by both techniques. Chlorophyll-a, chlorophyll-c1+c2, peridinin, 19’-butanoyloxyfucoxanthin, fucoxanthin, zeaxanthin, alloxanthin, 19’-hexanoyloxyfucoxanthin, diadinoxanthin, chlorophyll-b and ß-carotene concentratios were determined by High Performance Liquid Chromatography (HPLC). A total of 124 eukaryotic taxa belonging to eight algal classes were found through microscopic analysis. 60 taxa of them were dinoflagellates, 52 taxa were diatoms and 12 taxa were other phytoflagellates. The number of diatoms and dinoflagellates, as the major groups, accounted for 90.4% of the total phytoplankton species. Chlorophyll-a, fucoxanthin and peridinin concentrations varied between 0.03-7.20, 0.01-5.23 and 0.01-2.14 μg L-1, throughout the research period, respectively. The highest chlorophyll-a values were measured at stations MD26 (7.20 µg L-1) and MD22 (6.61 µg L-1) in May 2018, which were located at Gemlik and Bandirma bays. There was a significant correlation (r:0.87, p<0.001 n:54) between HPLC determined fucoxanthin concentrations and diatom abundances in August 2016 and 2018. Also, higher chlorophyll-c1+c2 concentrations revealed consistency with high diatom abundances and fucoxanthin concentrations in August 2016 and 2018. This result confirmed that diatoms are the most important carrier of fucoxanthin and it can be used for taxonomic evaluation of diatom community of the Sea of Marmara.