molecular phylogenetic
Recently Published Documents





Antioxidants ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 163
Martin Hofrichter ◽  
Harald Kellner ◽  
Robert Herzog ◽  
Alexander Karich ◽  
Jan Kiebist ◽  

Unspecific peroxygenases (UPOs), whose sequences can be found in the genomes of thousands of filamentous fungi, many yeasts and certain fungus-like protists, are fascinating biocatalysts that transfer peroxide-borne oxygen (from H2O2 or R-OOH) with high efficiency to a wide range of organic substrates, including less or unactivated carbons and heteroatoms. A twice-proline-flanked cysteine (PCP motif) typically ligates the heme that forms the heart of the active site of UPOs and enables various types of relevant oxygenation reactions (hydroxylation, epoxidation, subsequent dealkylations, deacylation, or aromatization) together with less specific one-electron oxidations (e.g., phenoxy radical formation). In consequence, the substrate portfolio of a UPO enzyme always combines prototypical monooxygenase and peroxidase activities. Here, we briefly review nearly 20 years of peroxygenase research, considering basic mechanistic, molecular, phylogenetic, and biotechnological aspects.

Mammalia ◽  
2022 ◽  
Vol 0 (0) ◽  
Wenhua Yu ◽  
Chuyan Lin ◽  
Zhenglanyi Huang ◽  
Shuo Liu ◽  
Qiaoyan Wang ◽  

Abstract In April 2019, 15 (10♂, 5♀) Kerivoula bats were collected by harp traps from Xishuangbanna, Yunnan Province, China. External and craniodental examination, multivariate statistical analyses and molecular phylogenetic inference (CoI, Cytb and Rag2 gene markers) indicated they are Kerivoula kachinensis and Kerivoula titania, respectively. Former represents a new chiropteran record from China, while the latter is a valid occurrence of K. titania in this region because recent study indicate a misidentification of “K. titania” in Guangdong, Guangxi and Hainan, China. All specimens are presently preserved at Key Laboratory of Conservation and Application in Biodiversity of South China in Guangzhou University, Guangzhou, China. Nowadays, four woolly bats occur in China including, Kerivoula furva, K. kachinensis, Kerivoula picta and K. titania, whilst there is a risk of underestimation the actual species diversity in China region when comparing those of neighboring region such as Vietnam. Supports for field survey need to be continued in future.

Plant Disease ◽  
2022 ◽  
Qing Sun ◽  
Yongjing Xie ◽  
Tangmin Chen ◽  
Jianping Zhang ◽  
Pedro Laborda ◽  

In May 2021, canker symptoms were detected on ‘Xuxiang’ kiwi trees in southwestern Shaanxi (Hanzhong municipality; 107.27° E, 33.23° N) in China. Seven-year-old trees exhibited black necrotic lesions and cracked areas in the trunk (Figure 1). The symptoms were observed in approximately 10% of the trees in 6 orchards (31 ha in total). Application of commercial fungicides did not control the advancement of the pathogen, and infected trees were removed to control the spread. Three samples, approximately 1 cm2 in size, of symptomatic tissue were collected and surface sterilized in 2% NaOCl for 1 min, and washed with sterile ddH2O. Four isolates showing white mycelium with yellow pigmentation were obtained after 4 days of incubation on PDA, containing chloramphenicol (50 µg/mL), at 28 ºC. The pathogen was isolated from all collected samples. ITS, EF1-α, TUB2, RPB1 and RPB2 genes were amplified using ITS1/ITS4, EF1-728F/EF1-986R, T1/T22, RPB1-5F/RPB1-8R and RPB2-5F/RPB2-7cR (strain NJC06), or RPB2-c7F/RPB2-11aR (strains NJC07 and NJC08), primers, respectively. Two isolates shared the same sequences (strain NJC08). Obtained sequences were submitted to GenBank under accession numbers MZ669205 and OL347898-OL347899 (ITS), OL439731-OL439733 (EF1-α), OL439734-OL439736 (TUB2), OL439737-OL439739 (RPB1), and OL439740-OL439742 (RPB2). The sequences shared >99% (ITS; F. avenaceum CBS 128538, MH864972), >99% (EF1-α; F. avenaceum 55-2, MN473124), 100% (TUB2; F. avenaceum SICAUCC 18-0001, MK253102), >98% (RPB1; F. avenaceum NRRL 26911, MG282372), and >98% (RPB2; F. avenaceum SICAUCC 18-0001, MK396098; or F. avenaceum FRC R-09495, CQ915486) homology to multiple F. avenaceum strains. Molecular phylogenetic tree (Figure 2) was constructed using MEGA7 with Fusarium strains found causing rot in various hosts (Wang et al. 2015), and other fungal species, such as Cadophora nalorum, Diaporthe ambigua, D. australafricana, and Neofusicoccum parvum, which were reported to cause cordon dieback on kiwi tree in Chile (Diaz et al. 2021). Microscope observations after cultivation of all isolates on barley-honey-tryptone medium (Song et al. 2020) showed the presence of septate mycelium, fusiform microconidia (8-15 µm in length, containing between 0 and 3 septa; n = 77) and chlamydospores (n = 21), and agree with the morphology of F. avenaceum (Zhao et al. 2020). To confirm pathogenicity, a sterilized spatula was used to make wounds (3 mm diameter, 1 mm depth) on the trunk of 3-months-old ‘Xuxiang’ kiwi trees. Solutions containing 1 × 106 spores/mL (20 µL) of the isolates were injected in the wounds. Sterile ddH2O was used for the control experiment. Inoculated plants were maintained in a growth chamber at 28 °C and 80% relative humidity for 4 days. The pathogen was recovered from the canker lesions, which were similar to those observed in the orchards, and its identity was confirmed by sequence analysis. The pathogen only infected wounded trees, and probably invaded the orchards during the pruning in February 2021. F. avenaceum was reported to cause canker on almond tree (Stack et al. 2020), stem rot on Anthoxanthum aristatum and Polygonatum cyrtonema (Pieczul et al. 2018; Xu et al. 2019), and root rot on carrot, Coptis chinensis and wheat (Le Moullec-Rieu et al. 2020; Mei et al. 2020; Ozer et al. 2020). Recently, F. avenaceum was found causing fruit blotch in kiwi fruit in Anhui (China) (Zhao et al. 2020). Here, F. avenaceum was found causing canker disease in kiwi tree, demonstrating the host and tissue promiscuity of this pathogen. Kiwi is an important crop in China with nearly 1.5 million tons produced in 2019. This report will help to better understand the pathogens reducing kiwi production in China.

Phytotaxa ◽  
2022 ◽  
Vol 530 (2) ◽  
pp. 177-188

Types and recently collected samples of two Paxillus species namely P. rhytidophyllus and P. yunnanensis, originally described from southwestern China, were critically restudied based on morphology and molecular phylogenetic data of DNA sequences from the large subunit of the nuclear ribosomal RNA (nrLSU), the nuclear ribosomal internal transcribed spacer (ITS), and the translation elongation factor 1-α (tef1-α). The results showed that these two species belong to Boletinellus and Tricholomopsis, respectively. Thus, two new combinations, Boletinellus rhytidophyllus and Tricholomopsis yunnanensis are proposed. Boletinellus rhytidophyllus is characterized by a deeply decurrent and shallow hymenophore which is poroid-lamellate to alveolate, slightly thick-walled (0.6–1 μm) basidiospores, occasionally 2- to 4-spored basidia, rare or infrequent hymenial cystidia, and a trichodermal pileipellis. Tricholomopsis yunnanensis is characterized by a convex pileus densely covered by red-violet to red-brown fibrillose squamules, a yellowish stipe sparsely covered with red to red-brown fibrillose squamules, subglobose to broadly ellipsoid basidiospores, prominent large cheilocystidia measuring 60–195 × 11–39 μm, and a palisadic pileipellis. New descriptions and line drawings of these two species and their comparisons with allied taxa are presented.

Genki Kobayashi ◽  
Tatsuya Sakamoto

Abstract Bioluminescence is widespread in the marine environment. The bioluminescence of some species of the fireworm Odontosyllis (Annelida: Syllidae: Eusyllinae) has been well studied, although the presence or absence of bioluminescence in most species of this genus is yet to be revealed. The bioluminescent worms were observed after sunset around the new moon day in July and October 2020 and in July to October 2021 in Nagasaki Prefecture, Japan. Molecular phylogenetic analysis based on two mitochondrial and one nuclear gene sequence showed that the worms were closely related to Odontosyllis australiensis, but the partial 16S rRNA gene sequences differed by 2% between those of the Japanese and Australian material. Because only epitokes, i.e. morphologically modified sexually mature worms, were collected, further studies on morphological characters of atokes would be required in the future. We therefore tentatively refer to them as Odontosyllis cf. australiensis. Molecular phylogenetic analysis also showed that known bioluminescent Odontosyllis species belong to various lineages.

Phytotaxa ◽  
2022 ◽  
Vol 530 (1) ◽  
pp. 21-37
DanFeng Bao ◽  

Diversity of lignicolous freshwater fungi in northwestern Yunnan, China is currently being studied. Four fresh collections of tubeufiaceous taxa were collected and identified. Among of them, Parahelicomyces yunnanensis sp. nov and Tubeufia nigroseptum sp. nov. are introduced as new species based on morphology and molecular phylogenetic analysis of combined ITS, SSU, TEF1-α and RPB2 sequence data. The detailed descriptions and illustrations of the new species are provided, as well as the morphological comparison with similar taxa are discussed. Two strains of Neohelicomyces aquaticus and Tubeufia cylindrothecia are provided.

2022 ◽  
Ignacio Ramos-Gutierrez ◽  
Herlander Lima ◽  
Rafael Molina-Venegas

The increasing availability of molecular information has lifted our understanding of species evolutionary relationships to unprecedent levels. However, current estimates of the world's biodiversity suggest that about a fifth of all extant species are yet to be described, and we still lack molecular information for many of the known species. Hence, evolutionary biologists will have to tackle phylogenetic uncertainty for a long time to come. This prospect has urged the development of software to expand phylogenies based on non-molecular phylogenetic information, and while the available tools provide some valuable features, major drawbacks persist and some of the proposed solutions are hardly generalizable to any group of organisms. Here, we present a completely generalized and flexible framework to expand incomplete molecular phylogenies. The framework is implemented in the R package "randtip", a toolkit of functions that was designed to randomly bind phylogenetically uncertain taxa in backbone phylogenies through a fully customizable and automatic procedure that uses taxonomic ranks as a major source of phylogenetic information. Although randtip is capable of automatically generating fully operative phylogenies for any group of organisms using just a list of species and a backbone tree, we stress that the "blind" expansion of phylogenies (using randtip or any other available software) often leads to suboptimal solutions. Thus, we discuss a variety of circumstances that may require customizing simulation parameters beyond default settings to optimally expand the trees, including a detailed step-by-step workflow. Phylogenetic uncertainty should be tackled with caution, assessing potential pitfalls and opportunities to optimize parameter space prior to launch any simulation. Used judiciously, our framework will help evolutionary biologists to efficiently expand incomplete molecular phylogenies and thereby account for phylogenetic uncertainty in quantitative analyses.

Diversity ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 30
Daniel Fernández Marchán ◽  
Thibaud Decaëns ◽  
Jorge Domínguez ◽  
Marta Novo

Earthworm systematics have been limited by the small number of taxonomically informative morphological characters and high levels of homoplasy in this group. However, molecular phylogenetic techniques have yielded significant improvements in earthworm taxonomy in the last 15 years. Several different approaches based on the use of different molecular markers, sequencing techniques, and compromises between specimen/taxon coverage and phylogenetic information have recently emerged (DNA barcoding, multigene phylogenetics, mitochondrial genome analysis, transcriptome analysis, targeted enrichment methods, and reduced representation techniques), providing solutions to different evolutionary questions regarding European earthworms. Molecular phylogenetics have led to significant advances being made in Lumbricidae systematics, such as the redefinition or discovery of new genera (Galiciandrilus, Compostelandrilus, Vindoboscolex, Castellodrilus), delimitation and revision of previously existing genera (Kritodrilus, Eophila, Zophoscolex, Bimastos), and changes to the status of subspecific taxa (such as the Allolobophorachaetophora complex). These approaches have enabled the identification of problems that can be resolved by molecular phylogenetics, including the revision of Aporrectodea, Allolobophora, Helodrilus, and Dendrobaena, as well as the examination of small taxa such as Perelia, Eumenescolex, and Iberoscolex. Similar advances have been made with the family Hormogastridae, in which integrative systematics have contributed to the description of several new species, including the delimitation of (formerly) cryptic species. At the family level, integrative systematics have provided a new genus system that better reflects the diversity and biogeography of these earthworms, and phylogenetic comparative methods provide insight into earthworm macroevolution. Despite these achievements, further research should be performed on the Tyrrhenian cryptic complexes, which are of special eco-evolutionary interest. These examples highlight the potential value of applying molecular phylogenetic techniques to other earthworm families, which are very diverse and occupy different terrestrial habitats across the world. The systematic implementation of such approaches should be encouraged among the different expert groups worldwide, with emphasis on collaboration and cooperation.

2022 ◽  
Vol 32 (1) ◽  
pp. 41-48
I. A. Ekimova

A new species of the family Coryphellidae, Coryphella alexanderi sp. nov. is described based on specimens collected in the Kuril Islands, NorthWest Pacific, from the upper sublittoral to 200 m depth. An integrative analysis was conducted, including a molecular phylogenetic analysis based on four markers (COI, 16S, H3, 28S), an automatic species delimitation method ABGD, and an analysis of the external and internal morphology using light and scanning electron microcopy. The distinctiveness of Coryphella alexanderi sp. nov. is well established both morphologically and genetically, and it differs from externally similar species in radular characters. Phylogenetically Coryphella alexanderi sp. nov. is closely related to Coryphella trophina, which occurs sympatrically in the same geographic and bathymetric ranges. Coryphella alexanderi sp. nov. appears to be restricted to the middle and northern Kuril Islands, which is consistent with the high numbers of endemic taxa in this area.

Sign in / Sign up

Export Citation Format

Share Document