From White to Black, from Darkness to Light: Species Delimitation and UNITE Species Hypothesis Testing in the Russula Albonigra Species Complex.

Abstract Russula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata that is blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological amplitude and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s.l. represents a species complex consisting of at least five European, three North-American and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra lineage is proposed and a key to the described European species of R. subg. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta and R. ustulata. UNITE species hypotheses at different thresholds were tested against the taxonomic data. The species hypotheses at the similarity threshold 0.5% give a perfect match to the phylogenetically defined species within the R. albonigra lineage. Publicly available sequence data can contribute to species delimitation and expand knowledge on ecology and distribution, but the pitfalls are short and low quality sequences. The importance of updating public taxonomic data and using correct sequence similarity thresholds is emphasised.

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Enlightening the black and white: species delimitation and UNITE species hypothesis testing in the Russula albonigra species complex

IMA Fungus ◽

10.1186/s43008-021-00064-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ruben De Lange ◽

Slavomír Adamčík ◽

Katarína Adamčíkova ◽

Pieter Asselman ◽

Jan Borovička ◽

...

Keyword(s):

Species Delimitation ◽

Species Complex ◽

Sequence Data ◽

Perfect Match ◽

Distribution Area ◽

Nuclear Markers ◽

Traditional Concept ◽

Distance Threshold ◽

European Species ◽

Black And White

ABSTRACTRussula albonigra is considered a well-known species, morphologically delimited by the context of the basidiomata blackening without intermediate reddening, and the menthol-cooling taste of the lamellae. It is supposed to have a broad ecological range and a large distribution area. A thorough molecular analysis based on four nuclear markers (ITS, LSU, RPB2 and TEF1-α) shows this traditional concept of R. albonigra s. lat. represents a species complex consisting of at least five European, three North American, and one Chinese species. Morphological study shows traditional characters used to delimit R. albonigra are not always reliable. Therefore, a new delimitation of the R. albonigra complex is proposed and a key to the described European species of R. subgen. Compactae is presented. A lectotype and an epitype are designated for R. albonigra and three new European species are described: R. ambusta, R. nigrifacta, and R. ustulata. Different thresholds of UNITE species hypotheses were tested against the taxonomic data. The distance threshold of 0.5% gives a perfect match to the phylogenetically defined species within the R. albonigra complex. Publicly available sequence data can contribute to species delimitation and increase our knowledge on ecology and distribution, but the pitfalls are short and low quality sequences.

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Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Phytotaxa ◽

10.11646/phytotaxa.188.2.2 ◽

2014 ◽

Vol 188 (2) ◽

pp. 78 ◽

Cited By ~ 3

Author(s):

Nelson Menolli Jr. ◽

ALFREDO JUSTO ◽

PEDRO ARRILLAGA ◽

C. K. PRADEEP ◽

ANDREW M. MINNIS ◽

...

Keyword(s):

Dna Sequence ◽

Species Delimitation ◽

Species Complex ◽

Democratic Republic ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sensu Stricto ◽

Type Collection ◽

Data Support ◽

Republic Of The Congo

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-examined here. Four other species are recognized in this complex and described herein as new: P. izurun from Spain, P. meridionalis from Brazil, P. padanilus from India and P. thoenii from Africa. Phylogenetic analyses based on nrITS + tef1 sequence data support the recognition of all species in this complex.

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Species diversity within the Helvella crispa group (Ascomycota: Helvellaceae) in China

Phytotaxa ◽

10.11646/phytotaxa.239.2.2 ◽

2015 ◽

Vol 239 (2) ◽

pp. 130 ◽

Cited By ~ 9

Author(s):

QI ZHAO ◽

TOLGOR B ◽

YONGCHANG ZHAO ◽

ZHULIANG YANG ◽

KEVIN D. HYDE

Keyword(s):

New Species ◽

Species Diversity ◽

Species Complex ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Similar Species ◽

Phylogenetic Species ◽

European Species

The white saddle-mushroom, a well-known European species, has long been named as Helvella crispa in China. In this study, phylogenetic analyses of combined ITS, nrLSU, tef1-α, rpb2 and mcm7 sequence data, showed that the Chinese H. crispa-like samples represent a species complex, which contains at least six phylogenetic species. Three of these species, H. involuta, H. orienticrispa and H. pseudoreflexa, are introduced as new species in this paper. The remaining two taxa are not described due to paucity of material. Among the six phylogenetic species, H. zhongtiaoensis is more closely related to European H. crispa than the remaining Chinese species. They are provided with descriptions, photographs and are compared with similar species. A key to the Chinese morphologically recognizable taxa of this complex is provided.

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Correcting values of DNA sequence similarity for errors in sequencing

10.1101/237990 ◽

2017 ◽

Author(s):

Timothy J. Hackmann

Keyword(s):

Ribosomal Dna ◽

Dna Sequences ◽

Sequence Similarity ◽

Single Equation ◽

Error Rates ◽

Sequencing Error ◽

Original Sequence ◽

Sequencing Errors ◽

Correct Sequence ◽

Similarity Thresholds

AbstractThe similarity between two DNA sequences is one of the most important measures in bioinformatics, but errors introduced during sequencing make values of similarity lower than they should be. Here we develop a method to correct raw sequence similarity for sequencing errors and estimate the original sequence similarity. Our method is simple and consists of a single equation with terms for 1) raw sequence similarity and 2) error rates (e.g., from Phred quality scores). We show the importance of this correction for 16S ribosomal DNA sequences from bacterial communities, where 97% similarity is a frequent threshold for clustering sequences for analysis. At that threshold and typical error rate of 0.2%, correcting for error increases similarity by 0.36 percentage points. This result shows that, if uncorrected, sequencing error would increase similarity thresholds and generate false clusters for analysis. Our method could be used to adjust thresholds for cluster-based analyses. Alternatively, because it requires no clustering to correct sequence similarity, it could usher in a new age of analyzing ribosomal DNA sequences without clustering.

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Predicting bacteriophage hosts based on sequences of annotated receptor-binding proteins

Scientific Reports ◽

10.1038/s41598-021-81063-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Dimitri Boeckaerts ◽

Michiel Stock ◽

Bjorn Criel ◽

Hans Gerstmans ◽

Bernard De Baets ◽

...

Keyword(s):

Machine Learning ◽

Predictive Model ◽

Receptor Binding ◽

Bacterial Infections ◽

Sequence Data ◽

Sequence Similarity ◽

Area Under The Curve ◽

Local Alignment ◽

Search Tool ◽

Different Levels

AbstractNowadays, bacteriophages are increasingly considered as an alternative treatment for a variety of bacterial infections in cases where classical antibiotics have become ineffective. However, characterizing the host specificity of phages remains a labor- and time-intensive process. In order to alleviate this burden, we have developed a new machine-learning-based pipeline to predict bacteriophage hosts based on annotated receptor-binding protein (RBP) sequence data. We focus on predicting bacterial hosts from the ESKAPE group, Escherichia coli, Salmonella enterica and Clostridium difficile. We compare the performance of our predictive model with that of the widely used Basic Local Alignment Search Tool (BLAST). Our best-performing predictive model reaches Precision-Recall Area Under the Curve (PR-AUC) scores between 73.6 and 93.8% for different levels of sequence similarity in the collected data. Our model reaches a performance comparable to that of BLASTp when sequence similarity in the data is high and starts outperforming BLASTp when sequence similarity drops below 75%. Therefore, our machine learning methods can be especially useful in settings in which sequence similarity to other known sequences is low. Predicting the hosts of novel metagenomic RBP sequences could extend our toolbox to tune the host spectrum of phages or phage tail-like bacteriocins by swapping RBPs.

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Species delimitation in the Stenocereus griseus (Cactaceae) species complex reveals a new species, S. huastecorum

PLoS ONE ◽

10.1371/journal.pone.0190385 ◽

2018 ◽

Vol 13 (1) ◽

pp. e0190385 ◽

Cited By ~ 2

Author(s):

Hernán Alvarado-Sizzo ◽

Alejandro Casas ◽

Fabiola Parra ◽

Hilda Julieta Arreola-Nava ◽

Teresa Terrazas ◽

...

Keyword(s):

New Species ◽

Species Delimitation ◽

Species Complex ◽

A New Species

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Whole genome characterization of strains belonging to the Ralstonia solanacearum species complex and in silico analysis of TaqMan assays for detection in this heterogenous species complex

European Journal of Plant Pathology ◽

10.1007/s10658-020-02190-8 ◽

2021 ◽

Author(s):

Viola Kurm ◽

Ilse Houwers ◽

Claudia E. Coipan ◽

Peter Bonants ◽

Cees Waalwijk ◽

...

Keyword(s):

Ralstonia Solanacearum ◽

In Silico ◽

Species Complex ◽

Sequence Data ◽

In Silico Analysis ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Pcr Assays

AbstractIdentification and classification of members of the Ralstonia solanacearum species complex (RSSC) is challenging due to the heterogeneity of this complex. Whole genome sequence data of 225 strains were used to classify strains based on average nucleotide identity (ANI) and multilocus sequence analysis (MLSA). Based on the ANI score (>95%), 191 out of 192(99.5%) RSSC strains could be grouped into the three species R. solanacearum, R. pseudosolanacearum, and R. syzygii, and into the four phylotypes within the RSSC (I,II, III, and IV). R. solanacearum phylotype II could be split in two groups (IIA and IIB), from which IIB clustered in three subgroups (IIBa, IIBb and IIBc). This division by ANI was in accordance with MLSA. The IIB subgroups found by ANI and MLSA also differed in the number of SNPs in the primer and probe sites of various assays. An in-silico analysis of eight TaqMan and 11 conventional PCR assays was performed using the whole genome sequences. Based on this analysis several cases of potential false positives or false negatives can be expected upon the use of these assays for their intended target organisms. Two TaqMan assays and two PCR assays targeting the 16S rDNA sequence should be able to detect all phylotypes of the RSSC. We conclude that the increasing availability of whole genome sequences is not only useful for classification of strains, but also shows potential for selection and evaluation of clade specific nucleic acid-based amplification methods within the RSSC.

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Atlas of leaf surface micromorphology in Aloe L. (Asphodelaceae) from the Horn of Africa region

Phytotaxa ◽

10.11646/phytotaxa.524.4.3 ◽

2021 ◽

Vol 524 (4) ◽

pp. 261-282

Author(s):

ESHETU FENTAW ◽

KELDA F.V.A. ELLIOTT ◽

SEBSEBE DEMISSEW ◽

DAVID CUTLER ◽

OLWEN M. GRACE

Keyword(s):

Species Delimitation ◽

Plant Material ◽

Species Complex ◽

Leaf Surface ◽

Detailed Comparison ◽

Species Variation ◽

Leaf Epidermis ◽

Horn Of Africa ◽

Surface Micromorphology ◽

Leaf Surface Micromorphology

The confident identification to species rank of fragmentary and sterile plant material is often challenged by the absence of diagnostic characters, which are present in intact specimens, reproductive parts, and plants in habitat. Here, we consider leaf surface micromorphology for the identification of the genus Aloe in the Horn of Africa region. Primary and secondary sculpturing of the leaf epidermis and stomata were characterised from SEM micrographs of 35 taxa representing 31 species of Aloe (Asphodelaceae subfam. Alooideae). Detailed comparison revealed that leaf surface characters are conserved between species and within-species variation is modest. Closely related taxa in the Aloe adigratana—A. camperi—A. sinana species complex could be distinguished using leaf surface micromorphology alone. These characters also guide species delimitation; in the species complex including A. schoelleri and A. steudneri, a narrow circumscription is supported, whereas with A. ankoberensis and A. pulcherrima, a wider circumscription merits consideration. The observed trait combinations are characteristic of plants in xeric environments, with the most notable feature being stomata that are most deeply sunken in species in more arid habitats. Our findings support the use of comparative study of micromorphological leaf surface characters for species identification and taxonomy in the genus Aloe.

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