Insight into the Systematics of Microfungi Colonizing Dead Woody Twigs of Dodonaea viscosa in Honghe (China)

Members of Dodonaea are broadly distributed across subtropical and tropical areas of southwest and southern China. This host provides multiple substrates that can be richly colonized by numerous undescribed fungal species. There is a severe lack of microfungal studies on Dodonaea in China, and consequently, the diversity, phylogeny and taxonomy of these microorganisms are all largely unknown. This paper presents two new genera and four new species in three orders of Dothideomycetes gathered from dead twigs of Dodonaea viscosa in Honghe, China. All new collections were made within a selected area in Honghe from a single Dodonaea sp. This suggests high fungal diversity in the region and the existence of numerous species awaiting discovery. Multiple gene sequences (non-translated loci and protein-coding regions) were analysed with maximum likelihood and Bayesian analyses. Results from the phylogenetic analyses supported placing Haniomyces dodonaeae gen. et sp. in the Teratosphaeriaceae family. Analysis of Rhytidhysteron sequences resulted in Rhytidhysteron hongheense sp. nov., while analysed Lophiostomataceae sequences revealed Lophiomurispora hongheensis gen. et sp. nov. Finally, phylogeny based on a combined dataset of pyrenochaeta-like sequences demonstrates strong statistical support for placing Quixadomyceshongheensis sp. nov. in Parapyrenochaetaceae. Morphological and updated phylogenetic circumscriptions of the new discoveries are also discussed.

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Fenestelloid clades of the Cucurbitariaceae

Persoonia - Molecular Phylogeny and Evolution of Fungi ◽

10.3767/persoonia.2020.44.01 ◽

2020 ◽

Vol 44 (1) ◽

pp. 1-40

Author(s):

W.M. Jaklitsch ◽

H. Voglmayr

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Fungal Species ◽

Lsu Rdna ◽

Phylogenetic Structure ◽

Protein Coding ◽

Molecular Phylogenetic ◽

Type Studies ◽

Asexual Morphs ◽

One New Species

Fresh collections and their ascospore and conidial isolates backed up by type studies and molecular phylogenetic analyses of a multigene matrix of partial nuSSU-, complete ITS, partial LSU rDNA, rpb2, tef1 and tub2 sequences were used to evaluate the boundaries and species composition of Fenestella and related genera of the Cucurbitariaceae. Eight species, of which five are new, are recognised in Fenestella s.str., 13 in Parafenestella with eight new species and two in the new genus Synfenestella with one new species. Cucurbitaria crataegi is combined in Fenestella, C. sorbi in Synfenestella, Fenestella faberi and Thyridium salicis in Parafenestella. Cucurbitaria subcaespitosa is distinct from C. sorbi and combined in Neocucurbitaria. Fenestella minor is a synonym of Valsa tetratrupha, which is combined in Parafenestella. Cucurbitaria marchica is synonymous with Parafenestella salicis, Fenestella bavarica with S. sorbi, F. macrospora with F. media, and P. mackenziei is synonymous with P. faberi, and the latter is lectotypified. Cucurbitaria sorbi, C. subcaespitosa and Fenestella macrospora are lecto- and epitypified, Cucurbitaria crataegi, Fenestella media, F. minor and Valsa tetratrupha are epitypified in order to stabilise the names in their phylogenetic positions. A neotype is proposed for Thyridium salicis. A determinative key to species is given. Asexual morphs of fenestelloid fungi are phoma-like and do not differ from those of other representatives of the Cucurbitariaceae. The phylogenetic structure of the fenestelloid clades is complex and can only be resolved at the species level by protein-coding genes, such as rpb2, tef1 and tub2. All fungal species studied here occur, as far as has been possible to determine, on members of Diaporthales, most frequently on asexual and sexual morphs of Cytospora.

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Morpho-Phylo Taxonomy of Novel Dothideomycetous Fungi Associated With Dead Woody Twigs in Yunnan Province, China

Frontiers in Microbiology ◽

10.3389/fmicb.2021.654683 ◽

2021 ◽

Vol 12 ◽

Author(s):

Peter E. Mortimer ◽

Rajesh Jeewon ◽

Jian-Chu Xu ◽

Saisamorn Lumyong ◽

Dhanushka N. Wanasinghe

Keyword(s):

Yunnan Province ◽

Phylogenetic Analyses ◽

Protein Coding ◽

Research Attention ◽

Multiple Gene ◽

Asexual Morph ◽

Coding Regions ◽

Extant Species ◽

Ocular Chamber ◽

Taxonomic Novelties

Within the field of mycology, macrofungi have been relatively well-studied when compared to microfungi. However, the diversity and distribution of microfungi inhabiting woody material have not received the same degree of research attention, especially in relatively unexplored regions, such as Yunnan Province, China. To help address this knowledge gap, we collected and examined fungal specimens from different plants at various locations across Yunnan Province. Our investigation led to the discovery of four species that are clearly distinct from extant ones. These taxonomic novelties were recognized based on morphological comparisons coupled with phylogenetic analyses of multiple gene sequences (non-translated loci and protein-coding regions). The monotypic genus Neoheleiosa gen. nov. (type: N. lincangensis) is introduced in Monoblastiaceae (Monoblastiales) for a woody-based saprobic ascomycete that possesses globose to subglobose or obpyriform ascomata with centric or eccentric, papillate ostioles, an ascomatal wall with thin-walled cells of textura globulosa, cylindric, pedicellate asci with an ocular chamber, and 1-septate, brown, guttulate, longitudinally striated, bicellular ascospores. Neoheleiosa has a close phylogenetic affinity to Heleiosa, nevertheless, it is morphologically dissimilar by its peridium cells and ornamented ascospores. Acrocalymma hongheense and A. yuxiense are described and illustrated as new species in Acrocalymmaceae. Acrocalymma hongheense is introduced with sexual and asexual (coelomycetous) features. The sexual morph is characterized by globose to subglobose, ostiolate ascomata, a peridium with textura angularis cells, cylindric-clavate asci with a furcate to truncate pedicel and an ocular chamber, hyaline, fusiform, 1-septate ascospores which are surrounded by a thick, distinct sheath, and the asexual morph is featured by pycnidial conidiomata, subcylindrical, hyaline, smooth, annelledic, conidiogenous cells, hyaline, guttulate, subcylindrical, aseptate conidia with mucoid ooze at the apex and with a rounded hilum at the base. Acrocalymma yuxiense is phylogenetically distinct from other extant species of Acrocalymma and differs from other taxa in Acrocalymma in having conidia with three vertical eusepta. Magnibotryascoma kunmingense sp. nov. is accommodated in Teichosporaceae based on its coelomycetous asexual morph which is characterized by pycnidial, globose to subglobose, papillate conidiomata, enteroblastic, annelledic, discrete, cylindrical to oblong, hyaline conidiogenous cells arising from the inner layer of pycnidium wall, subglobose, oval, guttulate, pale brown and unicelled conidia.

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Comparative Mitogenomics and Phylogenetic Analyses of Pentatomoidea (Hemiptera: Heteroptera)

Genes ◽

10.3390/genes12091306 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1306

Author(s):

Shiwen Xu ◽

Yunfei Wu ◽

Yingqi Liu ◽

Ping Zhao ◽

Zhuo Chen ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Analyses ◽

Heterogeneous Mixture ◽

Protein Coding ◽

Coding Regions ◽

The Third ◽

The Family ◽

Long Time ◽

Codon Positions ◽

Tree Topologies

Pentatomoidea is the largest superfamily of Pentatomomorpha; however, the phylogenetic relationships among pentatomoid families have been debated for a long time. In the present study, we gathered the mitogenomes of 55 species from eight common families (Acanthosomatidae, Cydnidae, Dinidoridae, Scutelleridae, Tessaratomidae, Plataspidae, Urostylididae and Pentatomidae), including 20 newly sequenced mitogenomes, and conducted comparative mitogenomic studies with an emphasis on the structures of non-coding regions. Heterogeneity in the base composition, and contrasting evolutionary rates were encountered among the mitogenomes in Pentatomoidea, especially in Urostylididae, which may lead to unstable phylogenetic topologies. When the family Urostylididae is excluded in taxa sampling or the third codon positions of protein coding genes are removed, phylogenetic analyses under site-homogenous models could provide more stable tree topologies. However, the relationships between families remained the same in all PhyloBayes analyses under the site-heterogeneous mixture model CAT + GTR with different datasets and were recovered as (Cydnidae + (((Tessaratomidae + Dinidoridae) + (Plataspidae + Scutelleridae)) + ((Acanthosomatidae + Urostylididae) + Pentatomidae)))). Our study showed that data optimizing strategies after heterogeneity assessments based on denser sampling and the use of site-heterogeneous mixture models are essential for further analysis of the phylogenetic relationships of Pentatomoidea.

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Additions to the Knowledge of Corticioid Xylodon (Schizoporaceae, Hymenochaetales): Introducing Three New Xylodon Species from Southern China

Diversity ◽

10.3390/d13110581 ◽

2021 ◽

Vol 13 (11) ◽

pp. 581

Author(s):

Kai-Yue Luo ◽

Meng-Han Qu ◽

Chang-Lin Zhao

Keyword(s):

New Species ◽

Southern China ◽

Phylogenetic Analyses ◽

Fungal Species ◽

Molecular Evidence ◽

Similar Function ◽

Rotten Wood ◽

Three New Species ◽

Inference Methods ◽

High Support

Three wood-inhabiting fungal species, Xylodon gossypinus, X. macrosporus, and X. sinensis spp. nov. were collected from southern China, with the similar function to decompose rotten wood, which are here proposed as new taxa based on a combination of morphological features and molecular evidence. Xylodon gossypinus is characterized by the resupinate basidiomata with cotton hymenophore, and ellipsoid basidiospores; X. macrosporus is characterized by the resupinate basidiomata having the cracking hymenophore with pale yellowish hymenial surface, and larger basidiospores 8–10.5 × 7.5–9 µm; and X. sinensis differs by its grandinioid hymenial surface and subglobose basidiospores measuring as 3–5 × 2.5–4 µm. Sequences of ITS and nLSU rRNA markers of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony, and Bayesian inference methods. The ITS+nLSU analysis in Hymenochaetales revealed that the three new species clustered into the Schizoporaceae family, located in genus Xylodon; based on the ITS dataset, X. gossypinus was a sister to X. ussuriensis; X. macrosporus closely grouped with X. follis with a high support; and X. sinensis was retrieved as two sisters to X. attenuatus and X. yarraensis with a lower support.

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One Hundred Mitochondrial Genomes of Cicadas

Journal of Heredity ◽

10.1093/jhered/esy068 ◽

2018 ◽

Vol 110 (2) ◽

pp. 247-256 ◽

Cited By ~ 6

Author(s):

Piotr Łukasik ◽

Rebecca A Chong ◽

Katherine Nazario ◽

Yu Matsuura ◽

De Anna C Bublitz ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Purifying Selection ◽

Evolutionary Rates ◽

Future Research ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Coding Regions ◽

Mitochondrial Genome Evolution ◽

Taxonomic Framework

Abstract Mitochondrial genomes can provide valuable information on the biology and evolutionary histories of their host organisms. Here, we present and characterize the complete coding regions of 107 mitochondrial genomes (mitogenomes) of cicadas (Insecta: Hemiptera: Auchenorrhyncha: Cicadoidea), representing 31 genera, 61 species, and 83 populations. We show that all cicada mitogenomes retain the organization and gene contents thought to be ancestral in insects, with some variability among cicada clades in the length of a region between the genes nad2 and cox1, which encodes 3 tRNAs. Phylogenetic analyses using these mitogenomes recapitulate a recent 5-gene classification of cicadas into families and subfamilies, but also identify a species that falls outside of the established taxonomic framework. While protein-coding genes are under strong purifying selection, tests of relative evolutionary rates reveal significant variation in evolutionary rates across taxa, highlighting the dynamic nature of mitochondrial genome evolution in cicadas. These data will serve as a useful reference for future research into the systematics, ecology, and evolution of the superfamily Cicadoidea.

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The 287,403 bp Mitochondrial Genome of Ectomycorrhizal Fungus Tuber calosporum Reveals Intron Expansion, tRNA Loss, and Gene Rearrangement

Frontiers in Microbiology ◽

10.3389/fmicb.2020.591453 ◽

2020 ◽

Vol 11 ◽

Author(s):

Xiaolin Li ◽

Lijiao Li ◽

Zhijie Bao ◽

Wenying Tu ◽

Xiaohui He ◽

...

Keyword(s):

Large Scale ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Fungal Species ◽

Ectomycorrhizal Fungus ◽

Open Reading Frames ◽

Rrna Genes ◽

Trna Genes ◽

Total Size ◽

Protein Coding

In the present study, the mitogenome of Tuber calosporum was assembled and analyzed. The mitogenome of T. calosporum comprises 15 conserved protein-coding genes, two rRNA genes, and 14 tRNAs, with a total size of 287,403 bp. Fifty-eight introns with 170 intronic open reading frames were detected in the T. calosporum mitogenome. The intronic region occupied 69.41% of the T. calosporum mitogenome, which contributed to the T. calosporum mitogenome significantly expand relative to most fungal species. Comparative mitogenomic analysis revealed large-scale gene rearrangements occurred in the mitogenome of T. calosporum, involving gene relocations and position exchanges. The mitogenome of T. calosporum was found to have lost several tRNA genes encoding for cysteine, aspartate, histidine, etc. In addition, a pair of fragments with a total length of 32.91 kb in both the nuclear and mitochondrial genomes of T. calosporum was detected, indicating possible gene transfer events. A total of 12.83% intragenomic duplications were detected in the T. calosporum mitogenome. Phylogenetic analysis based on mitochondrial gene datasets obtained well-supported tree topologies, indicating that mitochondrial genes could be reliable molecular markers for phylogenetic analyses of Ascomycota. This study served as the first report on mitogenome in the family Tuberaceae, thereby laying the groundwork for our understanding of the evolution, phylogeny, and population genetics of these important ectomycorrhizal fungi.

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Comparative Chloroplast Genome Analysis of Rhubarb Botanical Origins and the Development of Specific Identification Markers

Molecules ◽

10.3390/molecules23112811 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2811 ◽

Cited By ~ 8

Author(s):

Yuxin Zhou ◽

Jing Nie ◽

Ling Xiao ◽

Zhigang Hu ◽

Bo Wang

Keyword(s):

Chinese Medicine ◽

Chloroplast Genome ◽

Phylogenetic Analyses ◽

Genetic Identification ◽

Protein Coding ◽

Variable Regions ◽

Specific Identification ◽

Coding Regions ◽

Botanical Species ◽

Chloroplast Genomes

Rhubarb is an important ingredient in traditional Chinese medicine known as Rhei radix et rhizome. However, this common name refers to three different botanical species with different pharmacological effects. To facilitate the genetic identification of these three species for their more precise application in Chinese medicine we here want to provide chloroplast sequences with specific identification sites that are easy to amplify. We therefore sequenced the complete chloroplast genomes of all three species and then screened those for suitable sequences describing the three species. The length of the three chloroplast genomes ranged from 161,053 bp to 161,541 bp, with a total of 131 encoded genes including 31 tRNA, eight rRNA and 92 protein-coding sequences. The simple repeat sequence analysis indicated the differences existed in these species, phylogenetic analyses showed the chloroplast genome can be used as an ultra-barcode to distinguish the three botanical species of rhubarb, the variation of the non-coding regions is higher than that of the protein coding regions, and the variations in single-copy region are higher than that in inverted repeat. Twenty-one specific primer pairs were designed and eight specific identification sites were experimentally confirmed that can be used as special DNA barcodes for the identification of the three species based on the highly variable regions. This study provides a molecular basis for precise medicinal plant selection, and supplies the groundwork for the next investigation of the closely related Rheum species comparing and correctly identification on these important medicinal species.

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Morphological and molecular identification of a new species of Cinereomyces (Polyporales, Basidiomycota) in southern China

Phytotaxa ◽

10.11646/phytotaxa.459.1.5 ◽

2020 ◽

Vol 459 (1) ◽

pp. 51-60

Author(s):

RUN-ZHI WANG ◽

ZHI-YONG YUAN ◽

CHANG-ZHI HAN ◽

CHANG-LIN ZHAO

Keyword(s):

Ribosomal Rna ◽

Internal Transcribed Spacer ◽

Southern China ◽

Phylogenetic Analyses ◽

Its Region ◽

Fungal Species ◽

Molecular Characteristics ◽

Monophyletic Lineage ◽

Inference Methods ◽

A New Species

A new poroid wood-inhabiting fungal species, Cinereomyces fimbriatus sp. nov., is proposed based on morphological and molecular characteristics. The species is characterized by resupinate, brittle basidiomata with cream pore surface, a dimitic hyphal system with clamped generative hyphae, broad allantoid, hyaline, thin-walled, smooth basidiospores (3.6–4.6 × 0.8–1.1 µm). The internal transcribed spacer (ITS) region of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood, maximum parsimony and bayesian inference methods. The phylogenetic analysis based on ITS sequences showed that C. fimbriatus formed a monophyletic lineage with strong supports (100% BS, 100% BT, 1.00 BPP) sister to C. lindbladii.

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Comparative analysis of the complete chloroplast genome sequences of three Amaranthus species

Plant Genetic Resources ◽

10.1017/s1479262118000485 ◽

2019 ◽

Vol 17 (03) ◽

pp. 245-254 ◽

Cited By ~ 2

Author(s):

Su-Young Hong ◽

Kyeong-Sik Cheon ◽

Ki-Oug Yoo ◽

Hyun-Oh Lee ◽

Manjulatha Mekapogu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Sister Group ◽

Amino Acid Sequences ◽

Genome Sequences ◽

Inverted Repeat Region ◽

Protein Coding ◽

Amaranthus Hypochondriacus ◽

Coding Regions ◽

Homologous Locus ◽

Cp Genome

AbstractThe complete chloroplast (cp) genome sequences of three Amaranthus species (Amaranthus hypochondriacus, A. cruentus and A. caudatus) were determined by next-generation sequencing. The cp genome sequences of A. hypochondriacus, A. cruentus and A. caudatus were 150,523, 150,757 and 150,523 bp in length, respectively, each containing 84 genes with identical contents and orders. Expansion or contraction of the inverted repeat region was not observed among the three Amaranthus species. The coding regions were highly conserved with 99.3% homology in nucleotide and amino acid sequences. Five genes – matK, accD, ndhJ, ccsA and ndhF – showed relatively high non-synonymous/synonymous values (Ka/Ks > 0.1). Sequence comparison identified two insertion/deletion (InDels) greater than 40 bp in length, and polymerase chain reaction markers that could amplify these InDel regions were applied to diverse Korean Genbank accessions, which could discriminate the three Amaranthus species. Phylogenetic analyses based on 62 protein-coding genes showed that the core Caryophyllales were monophyletic and Amaranthoideae formed a sister group with the Betoideae and Chenopodioideae clade. Comparing each homologous locus among the three Amaranthus species, identified eight regions with high Pi values (>0.03). Seven of these loci, except for rps19-trnH (GUG), were considered to be useful molecular markers for further phylogenetic studies.

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An updated tribal classification of Lamiaceae based on plastome phylogenomics

BMC Biology ◽

10.1186/s12915-020-00931-z ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Fei Zhao ◽

Ya-Ping Chen ◽

Yasaman Salmaki ◽

Bryan T. Drew ◽

Trevor C. Wilson ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Character Evolution ◽

Bayesian Analyses ◽

Protein Coding ◽

Future Studies ◽

The Past ◽

Phylogenetic Framework ◽

Tribal Classification ◽

Stable Classification

Abstract Background A robust molecular phylogeny is fundamental for developing a stable classification and providing a solid framework to understand patterns of diversification, historical biogeography, and character evolution. As the sixth largest angiosperm family, Lamiaceae, or the mint family, consitutes a major source of aromatic oil, wood, ornamentals, and culinary and medicinal herbs, making it an exceptionally important group ecologically, ethnobotanically, and floristically. The lack of a reliable phylogenetic framework for this family has thus far hindered broad-scale biogeographic studies and our comprehension of diversification. Although significant progress has been made towards clarifying Lamiaceae relationships during the past three decades, the resolution of a phylogenetic backbone at the tribal level has remained one of the greatest challenges due to limited availability of genetic data. Results We performed phylogenetic analyses of Lamiaceae to infer relationships at the tribal level using 79 protein-coding plastid genes from 175 accessions representing 170 taxa, 79 genera, and all 12 subfamilies. Both maximum likelihood and Bayesian analyses yielded a more robust phylogenetic hypothesis relative to previous studies and supported the monophyly of all 12 subfamilies, and a classification for 22 tribes, three of which are newly recognized in this study. As a consequence, we propose an updated phylogenetically informed tribal classification for Lamiaceae that is supplemented with a detailed summary of taxonomic history, generic and species diversity, morphology, synapomorphies, and distribution for each subfamily and tribe. Conclusions Increased taxon sampling conjoined with phylogenetic analyses based on plastome sequences has provided robust support at both deep and shallow nodes and offers new insights into the phylogenetic relationships among tribes and subfamilies of Lamiaceae. This robust phylogenetic backbone of Lamiaceae will serve as a framework for future studies on mint classification, biogeography, character evolution, and diversification. Graphical abstract

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