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The Eurotiales is a relatively large order of Ascomycetes with members frequently having positive and negative impact on human activities. Species within this order gain attention from various research fields such as food, indoor and medical mycology and biotechnology. In this article we give an overview of families and genera present in the Eurotiales and introduce an updated subgeneric, sectional and series classification for Aspergillus and Penicillium. Finally, a comprehensive list of accepted species in the Eurotiales is given. The classification of the Eurotiales at family and genus level is traditionally based on phenotypic characters, and this classification has since been challenged using sequence-based approaches. Here, we re-evaluated the relationships between families and genera of the Eurotiales using a nine-gene sequence dataset. Based on this analysis, the new family Penicillaginaceae is introduced and four known families are accepted: Aspergillaceae, Elaphomycetaceae, Thermoascaceae and Trichocomaceae. The Eurotiales includes 28 genera: 15 genera are accommodated in the Aspergillaceae (Aspergillago, Aspergillus, Evansstolkia, Hamigera, Leiothecium, Monascus, Penicilliopsis, Penicillium, Phialomyces, Pseudohamigera, Pseudopenicillium, Sclerocleista, Warcupiella, Xerochrysium and Xeromyces), eight in the Trichocomaceae (Acidotalaromyces, Ascospirella, Dendrosphaera, Rasamsonia, Sagenomella, Talaromyces, Thermomyces, Trichocoma), two in the Thermoascaceae (Paecilomyces, Thermoascus) and one in the Penicillaginaceae (Penicillago). The classification of the Elaphomycetaceae was not part of this study, but according to literature two genera are present in this family (Elaphomyces and Pseudotulostoma). The use of an infrageneric classification system has a long tradition in Aspergillus and Penicillium. Most recent taxonomic studies focused on the sectional level, resulting in a well-established sectional classification in these genera. In contrast, a series classification in Aspergillus and Penicillium is often outdated or lacking, but is still relevant, e.g., the allocation of a species to a series can be highly predictive in what functional characters the species might have and might be useful when using a phenotype-based identification. The majority of the series in Aspergillus and Penicillium are invalidly described and here we introduce a new series classification. Using a phylogenetic approach, often supported by phenotypic, physiologic and/or extrolite data, Aspergillus is subdivided in six subgenera, 27 sections (five new) and 75 series (73 new, one new combination), and Penicillium in two subgenera, 32 sections (seven new) and 89 series (57 new, six new combinations). Correct identification of species belonging to the Eurotiales is difficult, but crucial, as the species name is the linking pin to information. Lists of accepted species are a helpful aid for researchers to obtain a correct identification using the current taxonomic schemes. In the most recent list from 2014, 339 Aspergillus, 354 Penicillium and 88 Talaromyces species were accepted. These numbers increased significantly, and the current list includes 446 Aspergillus (32 % increase), 483 Penicillium (36 % increase) and 171 Talaromyces (94 % increase) species, showing the large diversity and high interest in these genera. We expanded this list with all genera and species belonging to the Eurotiales (except those belonging to Elaphomycetaceae). The list includes 1â187 species, distributed over 27 genera, and contains MycoBank numbers, collection numbers of type and ex-type cultures, subgenus, section and series classification data, information on the mode of reproduction, and GenBank accession numbers of ITS, beta-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) gene sequences.
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Amanita is a worldwide-distributed fungal genus, with approximately 600 known species. Most species within the genus are ectomycorrhizal (ECM), with some saprotrophic representatives. In this study, we constructed the first comprehensive phylogeny including ECM species from Colombia collected in native Quercus humboldtii forests and in introduced Pinus patula plantations. We included 8 species (A. brunneolocularis, A. colombiana, A. flavoconia, A. fuligineodisca, A. muscaria, A. rubescens, A. sororcula, and A. xylinivolva) out of 16 species reported for the country, two new reports: A. citrina and A. virosa, and a new variety A. brunneolocularis var. pallida. Morphological taxonomic keys together with a phylogenetic approach using three nuclear gene regions: partial nuc rDNA 28S nuc rDNA internal transcribed spacers ITS1 and ITS2 and partial translation elongation factor 1-α gene (TEF1), were used to classify the specimens. Several highly supported clades were obtained from the phylogenetic hypotheses obtained by Bayesian inference and maximum likelihood approaches, allowing us to position the Colombian collections in a coherent infrageneric level and to contribute to the knowledge of local Amanita diversity.
Assuntos
Amanita/classificação , Filogenia , Amanita/isolamento & purificação , Biodiversidade , Colômbia , DNA Fúngico/genética , DNA Ribossômico/genética , DNA Espaçador Ribossômico/genética , Técnicas de Tipagem Micológica , Micorrizas/classificação , Micorrizas/isolamento & purificação , Fator 1 de Elongação de Peptídeos/genética , Pinus/microbiologia , Quercus/microbiologiaRESUMO
The genus Deutzia (Hydrangeaceae), containing ca. 60 species circumscribed in three sections, is disjunctly distributed in eastern Asia and Central America (Mexico). Although the genus is well delimited, its subdivisions into sections and series have not been the subject of an explicit test of monophyly based on molecular data. A comprehensive examination of the evolutionary relationships within the genus is thus still lacking. We present a fossil-calibrated, molecular phylogeny of Deutzia based on two nuclear ribosomal DNA (ITS and 26S) and three chloroplast DNA regions (matK, rbcL, and trnL-F intergenic spacer). Within this framework, we examine character evolution in petal arrangement, filament shape, and the number of stamens, and infer the ancestral area and biogeographic history of the genus. Our molecular phylogeny suggests that Deutzia is monophyletic. Two major clades are recovered: one composed of the species of sect. Neodeutzia from Mexico, and the other containing all remaining Deutzia species of sections Mesodeutzia and Deutzia from SW China and Northeast Asia. The latter two Asian sections were each revealed to be polyphyletic. The induplicate petals, 2-dentate filaments, and polystemonous androecia are inferred to be ancestral character states. Biogeographic reconstructions suggest a Northeast Asian origin for the genus and subsequent spread to Mexico during the Oligocene and to SW China during the Miocene. Based on our results, a new infrageneric classification of Deutzia inferred from molecular phylogeny is required. We propose to merge sections Mesodeutzia and Deutzia to ensure the monophyly at the sectional level. Cooling trends during the Oligocene resulted in isolation, separating eastern Asian and Mexican taxa, while the warm period during the middle Miocene stimulated the diversification from Northeast Asia to SW China. The uplift in the Qinghai-Tibetan Plateau and monsoon regimes are important in promoting high species diversification of Deutzia in SW China.
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Evolução Biológica , Hydrangeaceae/classificação , Filogenia , Teorema de Bayes , Núcleo Celular/genética , América Central , China , DNA de Cloroplastos/genética , DNA de Plantas/genética , DNA Ribossômico/genética , Ásia Oriental , Fósseis , Hydrangeaceae/genética , México , Modelos Genéticos , Análise de Sequência de DNARESUMO
PREMISE OF THE STUDY: Species of the endemic Chilean cactus genus Copiapoa have cylindrical or (sub)globose stems that are solitary or form (large) clusters and typically yellow flowers. Many species are threatened with extinction. Despite being icons of the Atacama Desert and well loved by cactus enthusiasts, the evolution and diversity of Copiapoa has not yet been studied using a molecular approach. METHODS: Sequence data of three plastid DNA markers (rpl32-trnL, trnH-psbA, ycf1) of 39 Copiapoa taxa were analyzed using maximum likelihood and Bayesian inference approaches. Species distributions were modeled based on geo-referenced localities and climatic data. Evolution of character states of four characters (root morphology, stem branching, stem shape, and stem diameter) as well as ancestral areas were reconstructed using a Bayesian and maximum likelihood framework, respectively. KEY RESULTS: Clades of species are revealed. Though 32 morphologically defined species can be recognized, genetic diversity between some species and infraspecific taxa is too low to delimit their boundaries using plastid DNA markers. Recovered relationships are often supported by morphological and biogeographical patterns. The origin of Copiapoa likely lies between southern Peru and the extreme north of Chile. The Copiapó Valley limited colonization between two biogeographical areas. CONCLUSIONS: Copiapoa is here defined to include 32 species and five heterotypic subspecies. Thirty species are classified into four sections and two subsections, while two species remain unplaced. A better understanding of evolution and diversity of Copiapoa will allow allocating conservation resources to the most threatened lineages and focusing conservation action on real biodiversity.
Assuntos
Evolução Biológica , Cactaceae/fisiologia , Cactaceae/classificação , Cactaceae/genética , Chile , DNA de Plantas/genética , DNA de Plantas/metabolismo , Dados de Sequência Molecular , Filogenia , Dispersão Vegetal , Plastídeos/genética , Análise de Sequência de DNARESUMO
Garcinia L. is a pantropically distributed genus comprised of at least 250 species of shrubs and trees and has centers of diversity located in Africa/Madagascar, Australasia, and Southeast Asia. The genus is notable due to its extreme diversity of floral form, common presence in lowland tropical rainforests worldwide, and potential pharmacological value. Across its entire geographic range, Garcinia lacks a recent taxonomic revision, with the last genus-level taxonomic treatment of Garcinia conducted over 40 years ago. In order to provide an evolutionary-based framework for a revised infrageneric classification of the genus and to investigate in more detail the systematics of New Caledonian species, we conducted molecular phylogenetic analyses using DNA sequence data for the nuclear ITS region on all samples, and for three chloroplast intergenic spacers (psbM-trnD, trnQ-rps16 and rps16-trnK) on a subset of our overall sampling. Our phylogenetic analyses are the most comprehensive to date for the genus, containing 111 biogeographically and morphologically diverse Garcinia species. The analyses support a broad circumscription of Garcinia, including several previously segregated genera (e.g. Allanblackia, Clusianthemum, Ochrocarpos p.p., Pentaphalangium, Rheedia, and Tripetalum). We recovered nine major clades falling within two major lineages, and we delimit 11 sections. We discuss each of the clades, assign them sectional names, discuss their distinguishing morphological features, compare our taxonomic treatment with the most recent sectional treatment, list representative species, note geographic distribution, and highlight some questions that deserve future investigations. We propose nine new nomenclatural combinations, four new names, and three new lectotypes. In New Caledonia (NC), a total of ten, all endemic, species are recognized and were included in our phylogenetic analyses, with several replicates per species (with the exception of G.virgata and G.urceolata, represented by a single accession each). New Caledonian species were retrieved within three separate clades, respectively including 1) G.balansae; 2) G.comptonii, G.neglecta, G.urceolata, G.virgata; and 3) G.amplexicaulis, G.densiflora, G.pedicellata, G.puat, G.vieillardii. Within NC, the phylogenies did not support the distinction between a putative undescribed species and G.balansae. However, it confirmed the distinction between NC species and both G.vitiensis (found in Fiji and Vanuatu) and G.adinantha (found in Fiji), suggesting that all NC species should be considered as endemics.
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The genus Cyathus was established in 1768, but more in-depth taxonomic studies with the group only occurred after 1844. In the following years, changes in the infrageneric classification of Cyathus were proposed based mainly on morphology. With advances in phylogenetic studies, the morphological classifications were tested and a new subdivision into three groups was proposed in 2007. Based on the last two classifications, this work aims to expand and understand the internal phylogenetic relationships among the fungi of the genus Cyathus and examine how these relationships are reflected in the taxonomic classification, through molecular analyses covering most of the species in the group, based on materials obtained from type specimens deposited in major fungal collections worldwide, besides expanding sampling with tropical species. Molecular analyses followed the protocols available in the literature, including the design of specific primers for Cyathus. In the phylogenetic analysis, using Maximum Parsimony and Bayesian methods, sequences of ITS and LSU regions from 41 samples of 39 species of Cyathus, 26 were placed with some nomenclatural types. The monophyly of Cyathus was confirmed with maximum support in both tests, and the infrageneric groups of the most recent classification were unchanged, but the clade striatum showed segregation into four groups and three subgroups. The phylogenetic organization is supported morphological characters, and diagnoses are presented for each group, as well as a dichotomous key for the infrageneric separation.
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Classification of the banana family (Musaceae) into three genera, Musa, Ensete and Musella, and infrageneric ranking are still ambiguous. Within the genus Musa, five formerly separated sections were recently merged into sections Musa and Callimusa based on seed morphology, molecular data and chromosome numbers. Nevertheless, other key morphological characters of the genera, sections, and species have not been clearly defined. This research aims to investigate male floral morphology, classify members of the banana family based on overall similarity of morphological traits using 59 banana accessions of 21 taxa and make inferences of the evolutionary relationships of 57 taxa based on ITS, trnL-F, rps16 and atpB-rbcL sequences from 67 Genbank and 10 newly collected banana accessions. Fifteen quantitative characters were examined using principal component analysis and canonical discriminant analysis and 22 qualitative characters were analyzed by the Unweighted Pair Group Method with an Arithmetic Mean (UPGMA). The results showed that fused tepal morphology, median inner tepal shape and length of style supported the three clades of Musa, Ensete and Musella, while shapes of median inner tepal and stigma classified the two Musa sections. In conclusion, a combination of morphological characters of male flowers and molecular phylogenetics well support the taxonomic arrangement within the banana family and the Musa genus and assist in selection of characters to construct an identification key of Musaceae.
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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.
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Epimedium L. is an important medicinal herbaceous genus that belongs to the family Berberidaceae. Epimedium campanulatum Ogisu is a plant species only inhabited in the northwestern part of Sichuan province, China. Here, we reported the complete chloroplast genome sequence, assembly, and characterization of E. campanulatum. The chloroplast genome of E. campanulatum was 157,343 bp in length, and a total of 112 unique genes were identified. Phylogenetic results revealed that E. campanulatum formed a sister relationship with the cluster of Epimedium ecalcaratum, Epimedium davidii, and Epimedium chlorandrum. Our findings provided valuable data for future taxonomic and phylogenetic research within the genus Epimedium.
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Epimedium L. is an important genus in the family Berberidaceae. Epimedium trifoliolatobinatum (Koidz.) Koidz. 1939 is inhabited on the west side of the Shikoku, Japan. In this study, the first complete chloroplast genome of E. trifoliolatobinatum was assembled with Illumina paired-end sequencing data, which was 157,272 bp in length with a total GC content of 38.70%. A total of 112 unique genes were annotated, comprising 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis suggested that E. trifoliolatobinatum was sister to E. koreanum. The current results provided fundamental information for further conducting molecular systematics and phylogenetic research of Epimedium genus.
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The genus Coryphantha includes plants with globose to cylindrical stems bearing furrowed tubercles, flowers arising at the apex, and seeds with flattened testa cells. Coryphantha is the second richest genus in the tribe Cacteae. Nevertheless, the genus lacks a phylogenetic framework. The limits of Coryphantha with its sister genus Escobaria and the infrageneric classification of Coryphantha have not been evaluated in a phylogenetic study. In this study we analyzed five chloroplast regions (matK, rbcL, psbA-trnH, rpl16, and trnL-F) using Bayesian phylogenetic analysis. We included 44 species of Coryphantha and 43 additional species of the tribe Cacteae. Our results support the monophyly of Coryphantha by excluding C.macromeris. Escobaria + Pelecyphora + C.macromeris are corroborated as the sister group of Coryphantha. Within Coryphantha our phylogenetic analyses recovered two main clades containing seven subclades, and we propose to recognize those as two subgenera and seven sections, respectively. Also, a new delimitation of Pelecyphora including C.macromeris and all species previously included in Escobaria is proposed. To accommodate this new delimitation 25 new combinations are proposed. The seven subclades recovered within Coryphantha are morphologically and geographically congruent, and partially agree with the traditional classification of this genus.
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Paraphlomis is a genus of Lamiaceae with about 30 species distributed mainly in subtropical China. In this study, we carried out the first molecular phylogenetic analyses to elucidate the relationships within the genus based on two nuclear and four plastid DNA regions. Our results, which recovered a species of Matsumurella within Paraphlomis, indicate that the genus is not monophyletic. The two sections and most of the series previously described within the genus are also shown to be polyphyletic. Combining with morphological evidence, our study indicates that nutlet morphology rather than calyx morphology is of phylogenetic value for the infrageneric classification of Paraphlomis. Moreover, P. jiangyongensis, a new species from southern China, is here described, and P . coronata, formerly treated as a variety of P . javanica, is here resurrected as a distinct species within the genus.
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Epimedium L. is the largest herbaceous genus in the family Berberidaceae which comprises more than 60 species. Epimedium sutchuenense Franch. is narrowly inhabited in the Daba Mountains of China. In the current study, we assembled the first complete chloroplast genome of E. sutchuenense through Illumina paired-end sequencing. The complete chloroplast genome of E. sutchuenense was 157,218 bp in length and the total GC content was 38.78%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis demonstrated that E. sutchuenense was sister to Epimedium wushanense T. S. Ying. Our results provided valuable information for further phylogenetic research and germplasm exploration of Epimedium genus.
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Epimedium L. is an important medicinal herbaceous genus in the family Berberidaceae. Epimedium platypetalum K. Mey. is a plant species only narrowly distributed in the western part of China. Here, the complete chloroplast genome of Epimedium platypetalum was assembled. The chloroplast genome of E. platypetalum was 159,088 bp in length, with a total GC content of 38.79%. A total of 112 unique genes were identified, among which 78 are protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic results revealed that E. platypetalum formed a sister relationship with E. membranaceum K. Mey. Our findings provided valuable data for future research on phylogenetic relationship and germplasm exploration within the genus Epimedium.
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Epimedium L. is a medicinally important herbaceous genus in the family Berberidaceae. Epimedium fargesii Franch. is only narrowly inhabited in the Daba Mountains in China. Here, we sequenced and assembled the first complete chloroplast genome of Epimedium fargesii Franch. The chloroplast genome of E. fargesii was 157,208 bp in length, with a total GC content of 38.77%. A total of 112 unique genes were identified, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis indicated that E. fargesii formed a sister relationship with E. wushanense T. S. Ying. Our results provided fundamental data for further taxonomic and phylogenetic research of the genus Epimedium.
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The species-rich genus Impatiens (Balsaminaceae) is represented in Madagascar by no less than 260 species. We conducted molecular phylogenetic analyses of the Malagasy Impatiens based on nuclear and plastid data and 52 accessions (representing 33 species) to: 1) reassess the monophyly of the Malagasy Impatiens; 2) assess the monophyly of the sections Preimpatiens (Humblotianae and Vulgare groups) with spurs and Trimorphopetalum without spurs as delimited by Perrier de la Bâthie, as well as that of the subgenera Impatiens and Trimorphopetalum as defined by Fischer and Rahelivololona; 3) infer the current status of some morphologically variable species; and 4) test whether the species of Impatiens from the Marojejy National Park form a monophyletic group. The Malagasy Impatiens are further confirmed to be paraphyletic with respect of the Comorian I.auricoma. The present sectional and subgeneric classifications of the Malagasy Impatiens are partly supported, with strong support for the monophyly of the sect. or subgen. Trimorphopetalum. Section Preimpatiens was not supported as monophyletic and neither the Humblotianae group nor the Vulgare group is monophyletic. Impatienselatostemmoides, I. "hammarbyoides", I.inaperta, I.lyallii and I.manaharensis are either para- or polyphyletic and may represent morpho-species. The Impatiens species from the Marojejy National Park do not form a monophyletic group and therefore are suggested to be derived from numerous independent colonisation events from all over Madagascar followed by subsequent diversifications.
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BACKGROUND: Paphiopedilum rungsuriyanum from Northern Laos was discovered and described in 2014. It is characterized by having miniature tessellated leaves, a flower having a helmet shaped lip with a V-shaped neckline, and a semi-lunate, 3-dentate staminode with an umbo. These morphological features distinguish P. rungsuriyanum from the other known sections/subgenera of Paphiopedilum, making it difficult to group with existing infrageneric units. RESULTS: Paphiopedilum rungsuriyanum has chromosome number of 2n = 26. Fluorescence in situ hybridization study demonstrates that there are two 45S rDNA signals in the telomeric region of chromosomes, and more than 20 5S rDNA signals dispersed signals in the pericentromeric and centromeric regions. Phylogenetic analyses based on four nuclear (i.e. ITS, ACO, DEF4 and RAD51) and four plastid (i.e. atpI-atpH, matK, trnS-trnfM and ycf1) gene regions indicate that P. rungsuriyanum is nested in subgenus Paphiopedilum and is a sister to section Paphiopedilum. CONCLUSIONS: The results in combination with karyomorphological, rDNA FISH patterns, morphological and phylogenetic analyses suggest a new section Laosianum to accommodate this species in the current sectional circumscription of subgenus Paphiopedilum.
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In this study, the genetic diversity of Iranian populations of two widespread Stenus species representing two ecomorphological forms, the "open living species" Stenus erythrocnemus Eppelsheim, 1884 and the "stratobiont" Stenus callidus Baudi di Selve, 1848, is presented using data from a fragment of the mitochondrial COI gene. We evaluate the mitochondrial cytochrome oxidase I haplotypes and the intraspecific genetic distance of these two species. Our results reveal a very low diversity of COI sequences in Stenus erythrocnemus in contrast to Stenus callidus. Moreover, the COI based phylogeny of a selection of Iranian Stenus support the monophyly of some species groups of Stenus proposed by Puthz (2008) and contradicts the traditional infrageneric classification.
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The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae stat. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra.