Using active learning methodologies to teach sequence analysis and molecular phylogeny

The great development of high-throughput molecular biology techniques and the consequent generation of massive data have made Bioinformatics essential for undergraduate Bioscience students. The importance of this scientific discipline is evidenced by the huge number of specialized publications, tools, and databases available. Training in Bioinformatics equips undergraduates with transferable skills that can be applied in all fields of Biology, such as programming abilities, data analysis, database management, biological knowledge, statistics, problem solving, and interdisciplinary collaboration. Over the past decade, there has been a notable increase in the number of higher education institutions worldwide that have adopted a competency-based curricula. This approach places a significant emphasis on the actions and skills that students are expected to develop, rather than merely focusing on the information, they are required to memorize. In this educational context, the use of active learning strategies has been demonstrated to enhance student comprehension and competency development. This paper describes the implementation of an active learning approach in a hands-on lesson performed by undergraduate students of Biology at the University of Malaga (Spain). Its main objective is to introduce students to molecular databases and information search systems on genes, proteins, and phylogeny. This is achieved within the framework of a smart campus, which integrates technological and sustainable resources to promote a positive and productive learning environment for the university community. This work presents the content and procedure of this practical activity, as well as the evaluation method and the results of a student survey to assess their opinions.

Morphological and phylogenetic analyses reveal eight novel species of Pestalotiopsis (Sporocadaceae, Amphisphaeriales) from southern China

Plants play an important role in maintaining the ecological balance of the biosphere, but often suffer from pathogenic fungi during growth. During our continuing mycological surveys of plant pathogens from terrestrial plants in Jiangxi and Yunnan provinces, China, 24 strains of Pestalotiopsis isolated from diseased and healthy tissues of plant leaves represented eight new species, viz. P.alpinicola, P.camelliicola, P.cyclosora, P.eriobotryae, P.gardeniae, P.hederae, P.machiliana and P.mangifericola. Multi-locus (ITS, tef1-α and tub2) phylogenetic analyses were performed using maximum-likelihood and Bayesian inference to reveal their taxonomic placement within Pestalotiopsis. Both molecular phylogenetic analyses and morphological comparisons supported them as eight independent taxa within Pestalotiopsis. Illustrations and descriptions of these eight taxa were provided, in conjunction with comparisons with closely related taxa in the genus. This work highlights the large potential for new fungal species associated with diseased plant leaves.

Revision of the Most Primitive Taxa of the Family Gyrodactylidae (van Beneden et Hesse, 1864) (Platyhelminthes, Monopisthocotyla) Based on ITS rDNA Phylogeny

BACKGROUND

For the past 25 years, the ITS rDNA (ITS1-5.8S-ITS2) of Gyrodactylidae has been crucial for species identification, description, and phylogeny. This family includes 25 genera parasitizing marine and freshwater fish, initially distinguished by morphological differences in attachment and/or male copulatory organs. Gyrodactylus Nordmann, 1832, the most species-rich genus, has approximately 500 described species and an additional 25,000 species suspected. The genus is not monophyletic, and the functionally adaptive nature of morphological diagnostic characters complicates the delimitation of new genera.

METHODS

A phylogeny based on ITS rDNA was proposed to address these challenges, using only complete sequences of primitive taxa. Fifty-four sequences were aligned with the MUSCLE v5.1 algorithm, creating a 1590 ps long matrix. Maximum Likelihood (ML) and Bayesian Inference (BI) methods with the models TVM+F+G4 and SYM+G4 for ITS1-ITS2 and 5.8S, respectively, were inferred using IQ-TREE v2.3.5 and BEAST v2.7.6.0.

RESULTS

The findings revealed eleven main lineages. Four of them are proposed for classification into new genera: Cichlidarus gen. nov., Iraqemembranatus gen. nov., Macracanthus gen. nov., and Rysavyius gen. nov. Elevating the subgenus G. (Gyrodactylus) to genus rank was supported.

CONCLUSIONS

The presented phylogeny provides a foundation for developing a classification system within Gyrodactylidae that is both reasonable and comprehensive.

Melitapanda, a new species of Melitidae (Crustacea, Amphipoda) from Japan

A new intertidal species of the melitid amphipod, Melitapanda, from the Wakayama Prefecture, Japan, is identified and described. Melitapanda sp. nov. differs from the similar M.koreana and M.nagatai by its black-and-white body color, well-developed anterodistal projection of the male gnathopod 1 propodus, and telson armature. Molecular phylogenetic analyses based on the nuclear 28S rRNA and mitochondrial COI genes support that M.panda sp. nov. is closely related to M.koreana and M.nagatai.

Two new species of Dendrostoma (Erythrogloeaceae, Diaporthales) associated with Castaneamollissima canker disease in China

The genus Dendrostoma is known to inhabit tree barks associated with branch canker diseases in China and several countries of Europe. Previous studies indicated that species of Dendrostoma prefer inhabiting fagaceous hosts, especially species of Castanea. In the present study, we obtained four isolates from cankered branches of Chinese chestnut (C.mollissima) in Rizhao City, Shandong Province, China. Morphological comparisons and phylogenetical analyses of a combined ITS-tef1-rpb2 sequence matrix were conducted, which revealed two new species named Dendrostomarizhaoense sp. nov. and D.tianii sp. nov. The new taxa are compared with other Dendrostoma species and comprehensive descriptions and illustrations are provided herein.

Thrombospondins: Conserved mediators and modulators of metazoan extracellular matrix

This review provides a personal overview of significant scientific developments in the thrombospondin field during the course of my career. Thrombospondins are multidomain, multimeric, calcium-binding extracellular glycoproteins with context-specific roles in tissue organisation. They act at cell surfaces and within ECM to regulate cell phenotype and signalling, differentiation and assembly of collagenous ECM, along with tissue-specific roles in cartilage, angiogenesis and synaptic function. More recently, intracellular, homeostatic roles have also been identified. Resolution of structures for the major domains of mammalian thrombospondins has facilitated major advances in understanding thrombospondin biology from molecule to tissue; for example, in illuminating molecular consequences of disease-causing coding mutations in human pseudoachrondroplasia. Although principally studied in vertebrates, thrombospondins are amongst the most ancient of animal ECM proteins, with many invertebrates encoding a single thrombospondin and the thrombospondin gene family of vertebrates originating through gene duplications. Moreover, thrombospondins form one branch of a thrombospondin superfamily that debuted at the origin of metazoans. The super-family includes additional sub-groups, present only in invertebrates, that differ in N-terminal domain organisation, share the distinctive TSP C-terminal region domain architecture and, to the limited extent studied to date, apparently contribute to tissue development and organisation. Finally, major lines of translational research are discussed, related to fibrosis; TSP1, TSP2 and inhibition of angiogenesis; and the alleviation of chronic cartilage tissue pathologies in pseudoachrondroplasia.

Morphology of the wings and attachment apparatus in the evolution of the family Hippoboscidae (Diptera)

Using a complex analysis of the molecular genetics, morphological, and ecological characteristics of Hippoboscidae flies, the phylogenetic structure and trends in the evolution of morphological characters that contribute to the ectoparasitic lifestyle of hippoboscid flies of the north of Eurasia were studied for the first time. The research was carried out on 26 Palearctic species from 10 genera. The analysis of molecular phylogeny revealed the levels of clustering of the family with the species predominantly parasitizing mammals or birds, the time of cluster formation, and the divergence of species in the Palearctic conditions. An independent adaptation to birds occurred in the genera Icosta, Pseudolynchia, Ornithoica, and others. Bird parasites are characterized by bifid tarsal claws, long hooks on pulvilli, and long empodium setae (except genus Ornithoica). Mammalian parasites are characterized by simple tarsal claws, short lobes of hooks on pulvilli, and zones on empodium with short setae. Specialization in empodium and pulvillus morphotypes and wing reduction are higher diverged in mammalian parasites than in bird parasites. The decrease of flight ability and wing reduction independently arose in different subfamilies of Hippoboscidae flies. Our results assume that the tribe Ornithomyini is a paraphyletic group, since, according to the complex of morphological features, the genus Ornithoica can be considered a separate lineage of evolution.

Revision of Alternaria sections Pseudoulocladium and Ulocladioides: Assessment of species boundaries, determination of mating-type loci, and identification of Russian strains

Alternaria is a large genus within Pleosporaceae and consists of fungi that have up to recently been considered to be 15 separate genera, including Ulocladium. The majority of Ulocladium species after incorporation into Alternaria were placed in three sections: Ulocladioides, Pseudoulocladium, and Ulocladium. In this study, phylogeny of 26 reference strains of 22 species and 20 Russian Ulocladium-like isolates was recovered. The partial actin gene (act), Alternaria major allergen (alta1), calmodulin (cal), glyceraldehyde-3-phosphate dehydrogenase (gapdh), RNA polymerase II second largest subunit (rpb2), and translation elongation factor 1-α (tef1) were sequenced for Russian isolates. All these fungi were examined using multilocus phylogenetic analysis according to the genealogical concordance phylogenetic species recognition (GCPSR) principle and the coalescent-based model Poisson tree processes (PTP, mPTP) and evaluated for the presence of recombination. All strains were combined into two clades that corresponded to the Pseudoulocladium and Ulocladioides sections. The Pseudoulocladium clade included four reference strains and nine local isolates and considered to be a single species, whereas the Ulocladioides section comprises 11 species, instead of 17 names previously adopted. Nine species were abolished by joining four other species. Species A. atra and A. multiformis were combined into the single species A. atra. Five species, A. brassicae-pekinensis, A. consortialis, A. cucurbitae, A. obovoidea, and A. terricola, were united in the species A. consortialis. Alternaria heterospora and A. subcucurbitae were combined into one species, A. subcucurbitae. Alternaria aspera, A. chartarum, A. concatenata, and A. septospora were combined into a single species, A. chartarum. Also, amplification with two different primer sets was performed to define mating-type locus 1 (MAT1) idiomorph. All studied isolates were heterothallic, contradicting some prior studies. Twenty Russian Ulocladium-like isolates were assigned to five species of two sections, A. atra, A. cantlous, A. chartarum, A. consortialis, and A. subcucurbitae. Species A. cantlous and A. subcucurbitae were found in Russia for the first time.

Intergrative Taxonomic Study of the Frullania parvistipula Complex with a Modern Circumscription of the Section Trachycolea (Frullaniaceae, Marchantiphyta)

Frullania (subg. Trachycolea) sect. Trachycolea has been studied using integrative taxonomy methods and utilizing sampling from almost all areas of distribution of the species previously referred to this section. A phylogenetic analysis based on nuclear ribosomal ITS1-2 and chloroplast trnL-F sequence data and a morphological study reveal a wide range of morphological variability within specimens that has largely disguised the overall taxonomic diversity. Frullania parvistipula, previously regarded as a widespread species, has been found to represent a group of separate species within different sections of F. subg. Trachycolea: F. caucasica and F. conistipula in F. sect. Trachycolea, F. parvistipula in F. sect. Australes, and F. fukuzawana in F. sect. Integristipulae II. Illustrations of the type specimens of F. conistipula, F. fukuzawana, and F. parvistipula, as well as illustrations of the sequenced specimens belonging to two of the discussed species (F. conistipula and F. parvistipula), are provided. The morphological differences separating the highly similar F. caucasica, F. conistipula, F. fukuzawana, F. koponenii, and F. parvistipula are discussed. A dichotomous key is presented for accepted species. New combinations are provided for two taxa.

Updated Taxonomy of Iris scariosa (Iridaceae) Inferred from Morphological and Chloroplast DNA Sequence Data with Remarks on Classification of Iris subg. Iris

Iris scariosa is a rhizomatous perennial whose taxonomy and distribution range still remain unclear. The results of our examination of literature, specimens, and wild plants have shown that I. glaucescens, described from Kazakhstan, and I. timofejewii, considered to be endemic to the Republic of Dagestan, Russia, are very closely related to I. scariosa. We have carried out molecular phylogenetic analyses for the first time to clarify the taxonomy of I. scariosa. For this, we sequenced six chloroplast DNA regions of an extended sampling that comprised the accepted species I. glaucescens and I. timofejewii, which has revealed their strong affinity to the accession of I. scariosa from the vicinity of Astrakhan, Russia. A thorough revision of the morphological characters has confirmed the lack of evident differences between I. scariosa and I. timofejewii. Thus, the analyses support a broad species circumscription of I. scariosa. We here reduce I. timofejewii, as well as I. curvifolia, considered to be endemic to Xinjiang, western China, to synonymy of I. scariosa. Color illustrations, updated nomenclature, and data on distribution of I. scariosa are provided. A lectotype for I. astrachanica and a neotype for I. timofejewii are designated here. Also, the phylogenetic relationships within I. subg. Iris are outlined, and an updated classification of the subgenus is proposed. We have recovered six major lineages within four major clades which we recognize as sections. Here, we propose two new nomenclatural combinations, a revised taxonomic treatment, and a new identification key to I. subg. Iris.

Arthrocatenales, a new order of extremophilic fungi in the Dothideomycetes

The widely treated order Capnodiales is one of the most important orders in the class Dothideomycetes. Recently, the order Capnodiales s. lat. was reassessed and split into seven orders (Capnodiales s. str., Cladosporiales, Comminutisporales, Mycosphaerellales, Neophaeothecales, Phaeothecales and Racodiales) based on multi-locus phylogeny, morphology and life strategies. In this study, two Arthrocatena strains isolated from sooty mould communities on the leaves of Tiliacordata and needles of Pinusnigra in southern Poland were analyzed. Multi-locus phylogenetic analyses (ITS-LSU-SSU-rpb2-tef1) along with morphological examination showed that they belong to Capnobotryellaantalyensis, which represents a sister taxon to Arthrocatenatenebrosa. Capnobotryellaantalyensis is a rock-inhabiting fungus described from Turkey. The following new combination is proposed: Arthrocatenaantalyensis. Phylogenetic analyses also showed that Arthrocatena and related genus Hyphoconis, both known previously only from rocks, form a sister lineage to orders Cladosporiales and Comminutisporales. The new order Arthrocatenales and new family Arthrocatenaceae are proposed to this clade. Representatives of this order are extremophilic fungi that live on rocks and in sooty mould communities.

A New Species of Cyrtodactylus tibetanus Group (Reptilia: Squamata: Gekkonidae) from Xizang Autonomous Region, China

A new Cyrtodactylus species, C. laevissp. nov., from the dry-hot valleys near the Yarlung Zangbo River in Re Village, Jindong Countryside, Lang County, Linzhi City, Xizang Autonomous Region, China, is described herein based upon the integrative taxonomic results combining molecular phylogenetic systematics and morphological characteristic comparisons. Our molecular phylogeny was inferred by combining three mitochondrial gene fragments (16S/CO1/ND2), and it indicated a distinct differentiation between the new species and C. tibetanus species complex, with obvious genetic distances (16S 9.9-11.8%/CO1 16.5-18.2%/ND2 16.6-18.5%) detected, supporting its validity. Morphologically, the new species can be easily distinguished from its congers by the following characters: (1) medium size (SVL 48.58-50.92 mm), (2) tubercles on dorsum sparse, (3) tail segments absent and tubercles on tails absent, (4) supralabials 10-12 and infralabials 8-10, (5) interorbital scales between anterior corners of the eyes 28-32, (6) scale rows at midbody 96-98, (7) ventral scales between mental and cloacal slit 145-153, (8) ventral scale rows 41-45, and (9) 4 to 5 white-yellow transverse bands with brown dots and black merges between the nape and sacrum. The description of C. laevissp. nov. increased the total species number of C. tibetanus group to three, and the total Cyrtodactylus species number in Xizang to six and in China to eleven. The new species is currently only known from the type locality with its extremely small populations and needs future surveys to reveal its distribution range, population status, natural history, and mechanisms so that the new species can coexist with Altiphylax medogense.

Phylogenetic classification of arbuscular mycorrhizal fungi: new species and higher-ranking taxa in Glomeromycota and Mucoromycota (class Endogonomycetes)

Arbuscular mycorrhizal (AM) fungi - Glomeromycota and Endogonomycetes - comprise multiple species and higher-level taxa that have remained undescribed. We propose a mixed morphology- and DNA-based classification framework to promote taxonomic communication and shed light into the phylogenetic structure of these ecologically essential fungi. Based on eDNA samples and long reads as type materials, we describe 15 new species and corresponding genera (Pseudoentrophosporakesseensis, Hoforsarebekkae, Kahvenarebeccae, Kelottijaerviashannonae, Kungsaengenashadiae, Langduoadianae, Lehetuaindrekii, Lokrumastenii, Moosteastephanieae, Nikkaluoktamahdiehiae, Parniguacraigii, Riederbergasylviae, Ruuacoralieae, Tammsaareavivikae and Unemaeeanathalieae), the genus Parvocarpum as well as 19 families (Pseudoentrophosporaceae, Hoforsaceae, Kahvenaceae, Kelottijaerviaceae, Kungsaengenaceae, Langduoaceae, Lehetuaceae, Lokrumaceae, Moosteaceae, Nikkaluoktaceae, Parniguaceae, Riederbergaceae, Ruuaceae, Tammsaareaceae, Unemaeeaceae, Bifigurataceae, Planticonsortiaceae, Jimgerdemanniaceae and Vinositunicaceae) and 17 orders (Hoforsales, Kahvenales, Kelottijaerviales, Kungsaengenales, Langduoales, Lehetuales, Lokrumales, Moosteales, Nikkaluoktales, Parniguales, Riederbergales, Ruuales, Tammsaareales, Unemaeeales, Bifiguratales and Densosporales), and propose six combinations (Diversisporabareae, Diversisporanevadensis, Fuscutatacerradensis, Fuscutatareticulata, Viscosporadeserticola and Parvocarpumbadium) based on phylogenetic evidence. We highlight further knowledge gaps in the phylogenetic structure of AM fungi and propose an alphanumeric coding system for preliminary communication and reference-based eDNA quality-filtering of the remaining undescribed genus- and family-level groups. Using AM fungi as examples, we hope to offer a sound, mixed framework for classification to boost research in the alpha taxonomy of fungi, especially the "dark matter fungi".

Molecular phylogeny of the Lecudinoidea (Apicomplexa): A major group of marine gregarines with diverse shapes, movements and hosts

Gregarine apicomplexans are ubiquitous endosymbionts of invertebrate hosts. Despite their ecological and evolutionary importance, inferences about the phylogenetic relationships of major gregarine groups, such as the Lecudinidae and Urosporidae, have been hindered by vague taxonomic definitions and limited molecular and morphological data. In this study, we investigated five gregarine species collected from four families of polychaete hosts (Nereididae, Oenonidae, Hesionidae, and Phyllodocidae) using light microscopy (LM) and scanning electron microscopy (SEM). We also generated small subunit ribosomal DNA sequences from these species and conducted molecular phylogenetic analyses to elucidate the evolutionary relationships within the Lecudinoidea. Our results include new molecular and morphological data for two previously described species (Lecudina cf. platynereidis and Lecudina cf. arabellae), the discovery of a new species of Lecudina (L. oxydromus n. sp.), and the discovery of two novel species, namely Amplectina cordis n. gen. et. n. sp. and Sphinctocystis inclina n. sp. These two species exhibited unique shapes and movements, resembling those of urosporids but with a phylogenetic affinity to lecudinids, blurring the border between lecudinids and urosporids. Our study emphasizes the need for further investigations into this highly diverse group, which has achieved great success across multiple animal phyla with diverse shapes and movements.

Fusarium amaranthi sp. nov. from Amaranth Is an Emergent Species Closely Related to F. circinatum

Amaranth (Amaranthus spp. L) is not native to South Korea but is cultivated in small scales for ornamental purposes as well as leafy vegetables and pseudo cereals. In this study, a new species within the genus Fusarium was isolated from amaranth, showing stem rot symptoms from a farmer field in Hwaseong, South Korea. The disease is characterized by dark-brown spots with black borders, leading to withering. Phylogenetic analysis-based concatenated sequences of translation elongation factor 1-alpha (TEF1), beta-tubulin (tub2), calmodulin (cmdA), RNA polymerase largest subunit (RPB1), and RNA polymerase II second largest subunit (RPB2) genes revealed that the obtained isolates formed a distinct clad within the Fusarium fujikuroi species complex and is closely related to F. circinatum. Cultural and morphological characteristics and pathogenicity on healthy amaranth plants (stem and leaves) were examined. The isolates readily differentiated from F. circinatum based on one- to five-septate macroconidia and the absence of sterile hyphae. Based on molecular and morphological characteristics, this fungus is demonstrated to be a new species and is described here as F. amaranthi, the causal agent of stem rot of amaranth in South Korea.

Mycenabrunnescens (Basidiomycota, Mycenaceae), a new species of Mycena sect. Pterigenae from China

Background

Mycena (Pers.) Roussel (1806) is a large genus of Mycenaceae known for having small to medium-sized basidiomata. It is typified by the species Mycenagalericulata (Scop.) Gray. For years, many mycologists have made important contributions to understanding Mycena and several monographs have been published. Three specimens were collected from China that belonged to the genus Mycena. On the basis of morphological analysis and phylogenetic analyses employing DNA sequences, a new species is described.

New information

Mycenabrunnescens sp. nov. is described as a new species from subtropical areas of China. It is characterised by its brown pileus, whitish lamellae that turns brown when bruised, orange to brown lamellae edges, the absence of pleurocystidia and cheilocystidia with simple or branched excrescences at the apex containing yellowish-brown contents. We performed phylogenetic analyses on a concatenated dataset comprising the internal transcribed spacer and large subunit regions of nuclear ribosomal RNA using Bayesian Inference and Maximum Likelihood methods. The result showed that the new taxon clustered in an independent group and is closely related to M.albiceps and M.flosoides.

Diversity and New Species of Ascomycota from Bamboo in China

Bamboo is an economically important crop that has gained prominence as an alternative to wood to reduce deforestation and ecosystem destruction. Diseases of bamboo that typically occur on leaves and stems can cause significant loss, reducing the quality and yield of the bamboo. However, there are few reports identifying the fungal species diversity and potential pathogens of bamboo. Here, we describe four new species of plant fungi from the leaves of bamboo within Fujian provinces, China. Fungi were isolated from diseased leaves collected within Fujian province and identified based on their morphological characteristics and multilocus phylogenies using nucleotide sequences derived from combined datasets of the intervening 5.8S nrRNA gene (ITS), the 28S large subunit of nuclear ribosomal RNA gene (LSU), the large subunit of RNA polymerase I (rpb1), the translation elongation factor 1-α gene (tef1-α), and the partial beta-tubulin gene (tub2). These analyses helped reveal and clarify taxonomic relationships in the family Magnaporthaceae. The new species of bambusicolous fungi identified include two species of Bifusisporella, described as B. fujianensis sp. nov. and B. bambooensis sp. nov., and two species of Apiospora, described as A. fujianensis sp. nov. and A. fuzhouensis sp. nov. This study further expands the characterization and distribution of fungi associated with bamboo.

Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Cnidaria, Anthozoa, Scleractinia), a new coral species previously considered as a variant of Paragoniastreadeformis, from Japan and northern Taiwan

A new zooxanthellate scleractinian coral, Paragoniastreavariabilis Kishi, Nomura & Fukami, sp. nov. (Scleractinia, Merulinidae), is described from non-coral reef regions of Japan and northern Taiwan. This new species was previously recognized as a morphological variant of Paragoniastreadeformis (Veron, 1990) and can be morphologically distinguished from that species by lacking groove-and-tube structures on corallite wall joints, and by having larger calices, numerous septa, and up to three corallites in one valley. The new species also formed an independent clade from its congeners, P.australensis (Milne Edwards & Haime, 1857), P.deformis and P.russelli (Wells, 1954), in the molecular phylogeny based on the mitochondrial intergenic region and nuclear ribosomal internal transcribed spacers.

Revision of Trigastrotheca Cameron (Hymenoptera, Braconidae, Braconinae) with descriptions of 13 new species

The Old World braconine wasp genus Trigastrotheca Cameron is revised. The genus is recorded from the island of Madagascar for the first time based on two new species, T.christianhenrichi Quicke & Butcher, sp. nov. and T.formosa Quicke & Friedman, sp. nov. Trigastrothecagriffini Quicke, sp. nov. is described from Australia; T.aethiopica Quicke & Friedman, sp. nov. is described from Ethiopia; T.braeti Quicke & Butcher, sp. nov. is described from Congo; T.simba van Noort, sp. nov. is described from Tanzania; T.freidbergi Quicke & Friedman, sp. nov., T.carinata Ranjith, sp. nov., T.flava Ranjith, sp. nov. and T.similidentata Ranjith, sp. nov. are described from India; T.khaoyaiensis Quicke & Butcher, sp. nov., T.naniensis Quicke & Butcher, sp. nov., and T.sublobata Quicke & Butcher, sp. nov. are described from Thailand. Trigastrothecatridentata is recorded from Thailand for the first time. A putative female of T.sureeratae is described for the first time. Acroceriliatricolor Quicke & Ingram, 1993 is transferred into Trigastrotheca, as T.acroceropsis nom. nov. A key is provided for the identification of species.

Sequencing and analysis of the complete mitochondrial genome of Amrasca biguttula biguttula Ishida, 1913 (Hemiptera: Cicadellidae: Typhlocybinae: Empoascini)

The complete mitogenome of the cotton leafhopper, Amrasca biguttula biguttula Ishida, 1913, was sequenced and annotated. The mitogenome is 14,474 bp long and contains 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes, as well as a control region. The nucleotide composition of the mitogenome is as follows: A, 39.17%; T, 39.3%; C, 11.13%; and G, 10.39%. The total length of the 13 PCGs is 10,496 bp, which encodes 3503 amino acids. All PCGs start with the ATG codon, except for ATA, ATC, GTG, and ATT. Most of the PCGs stop with TGA, and the remaining with CCT, GAA, GGT, TCA, CCA, CTA, TTA, AAA, ATT, or ATA. The phylogenetic tree shows that A. biguttula biguttula belongs to Empoascini of the subfamily Typhlocybinae, but is different from other species within the subfamily.

Acquisition of green algal photobionts enables both chlorolichens and chloro-cyanolichens to activate photosynthesis at low humidity without liquid water

Cyanobacteria require liquid water for photosynthesis, whereas green algae can photosynthesise with water vapour alone. We discovered that several Lobaria spp. which normally have cyanobacteria as the sole photobiont, in some regions of the trans-Himalayas also harboured green algae. We tested whether green algal acquisition was: limited to high elevations; obtained from neighbouring chloro-Lobaria species; enabled photosynthesis at low humidity. Lobaria spp. were collected from 2000 to 4000 m elevation. Spectrophotometry quantified green algal abundance by measuring chlorophyll b (absent in cyanobacteria). Thalli cross-sections visually confirmed green algal presence. We sequenced gene regions: Lobaria (ITS-EF-1α-RPB2), green algae (18S-RBC-L) and Nostoc (16S). Phylogenetic analysis determined myco-photobiont associations. We used a custom closed-circuit gas exchange system with an infrared gas analyser to measure CO2 exchange rates for desiccated specimens at 33%, 76%, 86% and 98% humidity. Cross-sections revealed that the photobiont layers in putative cyano-Lobaria contained both cyanobacteria and green algae, indicating that they should be considered chloro-cyanolichens. Chloro-Lobaria had no visible cephalodia nor cyanobacteria in the photobiont layer. Chloro-Lobaria and chloro-cyano-Lobaria had comparable levels of chlorophyll b. Chloro-Lobaria usually contained Symbiochloris. Chloro-cyano-Lobaria mainly associated with Parachloroidium and Nostoc; infrequently with Symbiochloris, Apatococcus, Chloroidium, Pseudochlorella, Trebouxia. Sequences from two green algal genera were obtained from within some thalli. Desiccated specimens of every Lobaria species could attain net photosynthesis with light exposure and 33% humidity. CO2 exchange dynamics over a five-day period differed between species. At all elevations, chloro-cyano-Lobaria spp. had abundant green algae in the photobiont layer, but green algal strains mostly differed to those of chloro-Lobaria spp. Both chloro-Lobaria and chloro-cyano-Lobaria were capable of conducting photosynthesis without liquid water. The data strongly suggest that they attained positive net photosynthesis.

Two new Mycena section Calodontes species: One newly discovered and the other new to Japan

In 2017, two candidate species of Mycena were reported from Japan, with the Japanese names "Togari-sakura-take" and "Mitsuhida-sakura-take". However, to date, no taxonomic study or formal description has been undertaken for these two species. In the present study, we conducted comprehensive morphological and molecular phylogenetic examinations of "Togari-sakura-take" and "Mitsuhida-sakura-take", and compared them to known species within the genus Mycena. We performed phylogenetic analyses on a concatenated dataset, including the internal transcribed spacer region of ribosomal RNA, RNA polymerase II largest subunit, and translation elongation factor-1 alpha genes. "Togari-sakura-take" formed a clade with Mycena subulata, which was recently described from China, whereas "Mitsuhida-sakura-take" formed a distinct independent clade. We identified the former as M. subulata based on molecular phylogenetic analyses and morphological observations. However, the Japanese specimens displayed dextrinoid cheilocystidia and caulocystidia as well as the inamyloidity of basidiospores, which differed from the original description of M. subulata based on the materials from China. "Mitsuhida-sakura-take" was characterized by its remarkably dense lamellae and could be distinguished from known Mycena species by the combination of absent pleurocystidia and presence of bowling pin-shaped cheilocystidia. Here, we describe "Mitsuhida-sakura-take" as a new species, named Mycena densilamellata, in the section Calodontes.

Coniocybe Ach. Revisited

Calicioids form a research field that has encompassed ascomycetous fungi with stalked ascomata similar to those of the lichen genus Calicium. Early generic circumscriptions of calicioid lichens and fungi were mainly based on morphological and secondary chemistry information. After the introduction of molecular data, taxonomy in the group has been reconsidered. Here, based on a broad geographical sampling, Coniocybe Ach. was revised using molecular and morphological features. Three loci (ITS, LSU and rpb1) were compared to infer its phylogenetic position, and a total of 52 new sequences (14 ITS, 24 LSU and 14 rpb1) were produced. Apart from its type C. furfuracea, Coniocybe was revised and emended to also include C. brachypoda and C. confusa. In addition, a new species, Coniocybe eufuracea, was described, and a key to the species of Coniocybe was provided.

Revision of the Genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera: Sphingidae) from China, Based on Morphological and Phylogenetic Analyses

Here, the taxonomy of the genus Rhagastis Rothschild & Jordan, 1903 (Lepidoptera, Sphingidae, Macroglossinae, Macroglossini) from China is revised based on differences in wing morphology, male and female genitalia, and the phylogenetic relationship of the DNA barcodes. Subspecies of Rhagastis albomarginatus (Rothschild, 1894) and R. castor (Walker, 1856) are treated as "good" species, namely Rhagastis dichroae Mell, 1922 stat. nov.; R. everetti Rothschild & Jordan, 1903 stat. nov.; R. aurifera (Butler, 1875) stat. rev.; R. chinensis Mell, 1922 stat. nov.; R. formosana Clark, 1925 stat. nov.; and R. jordani Oberthür, 1904 stat. rev. The distribution maps, biological notes, and ecological records of the genus Rhagastis Rothschild & Jordan, 1903 from China are given, and a species inventory of genus Rhagastis in the world is also included.

Four New Species and a New Combination of Boletaceae (Boletales) from Subtropical and Tropical China

Previous studies have shown that boletes are abundant and diverse in China, especially in tropical and subtropical regions. In the present study, morphological, ecological, host relationship, and a four-locus (28S, tef1, rpb1, and rpb2) molecular phylogenetic analyses were used to study the family Boletaceae in subtropical and tropical China. Four new bluing species are described from three genera, viz. Boletellus verruculosus (Chinese name), Xerocomellus tenuis (Chinese name), Xer. brunneus (Chinese name), and Xerocomus zhangii (Chinese name). Moreover, the genus Nigroboletus is treated as a synonym of Xerocomellus, and a new combination, namely Xer. roseonigrescens (Chinese name), is proposed.