Publications by authors named "Mario Amalfi"

10 Publications

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Genome skimming reveals novel plastid markers for the molecular identification of illegally logged African timber species.

PLoS One 2021 11;16(6):e0251655. Epub 2021 Jun 11.

Meise Botanic Garden, Meise, Belgium.

Tropical forests represent vast carbon stocks and continue to be key carbon sinks and buffer climate changes. The international policy constructed several mechanisms aiming at conservation and sustainable use of these forests. Illegal logging is an important threat of forests, especially in the tropics. Several laws and regulations have been set up to combat illegal timber trade. Despite significant enforcement efforts of these regulations, illegal logging continues to be a serious problem and impacts for the functioning of the forest ecosystem and global biodiversity in the tropics. Microscopic analysis of wood samples and the use of conventional plant DNA barcodes often do not allow to distinguish closely-related species. The use of novel molecular technologies could make an important contribution for the identification of tree species. In this study, we used high-throughput sequencing technologies and bioinformatics tools to obtain the complete de-novo chloroplast genome of 62 commercial African timber species using the genome skimming method. Then, we performed a comparative genomic analysis that revealed new candidate genetic regions for the discrimination of closely-related species. We concluded that genome skimming is a promising method for the development of plant genetic markers to combat illegal logging activities supporting CITES, FLEGT and the EU Timber Regulation.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0251655PLOS
June 2021

An Unexpectedly High Number of New (Boletaceae) Species From Northern and Northeastern Thailand.

Front Microbiol 2021 12;12:643505. Epub 2021 Apr 12.

School of Science, Mae Fah Luang University, Chiang Rai, Thailand.

is a poroid genus in Boletaceae that typically has chocolate brown to reddish brown or purplish brown basidiomata with a finely scaly stipe and produces a reddish brown spore deposit. During the survey on diversity of boletes in Northern and Northeastern Thailand, several collections were obtained. Combined evidence from morphology and phylogenetic analyses of a combined three-gene data set (6, 1 and 2) of the collections along with selected Boletaceae in the group indicated that Thai collections represent seven new species. The analyses also indicated that belongs in . Therefore, the transfer of to is proposed. Full descriptions and illustrations of the seven new species and are presented in this study. With the seven new species and the new combination, eight of the eleven described species are known to occur in Northern and Northeastern Thailand, whereas only one species is known from each of two continents, the Americas and Australia.
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http://dx.doi.org/10.3389/fmicb.2021.643505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072293PMC
April 2021

Two new species (Boletaceae) from Thailand, with two new combinations of American species.

MycoKeys 2019 21;55:29-57. Epub 2019 Jun 21.

Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium.

is a lamellate genus in the family Boletaceae that has been recently described from China based on , the only known species. Typical characters of are reddish-orange to yellowish-red basidiomata, including lamellae, bright yellow basal mycelium and smooth, broadly ellipsoid, ellipsoid to nearly ovoid basidiospores. During our survey on diversity of Boletaceae in Thailand, several yellowish-orange to reddish- or brownish-orange lamellate boletes were collected. Based on both morphological evidence and molecular analyses of a four-gene dataset (6, 1, 2 and 3), they were recognised as belonging in and different from the already known species. Two new species, and are therefore introduced from Thailand with detailed descriptions and illustrations. Moreover, two previously described species, and , were also revised and recombined in . A key to all known species is provided.
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http://dx.doi.org/10.3897/mycokeys.55.34570DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6598938PMC
June 2019

Two new species of Amanitasect.Phalloideae from Africa, one of which is devoid of amatoxins and phallotoxins.

MycoKeys 2019 6;53:93-125. Epub 2019 Jun 6.

Meise Botanic Garden, 38 Nieuwelaan, 1860 Meise, Belgium Meise Botanic Garden Meise Belgium.

Two new species of Amanitasect.Phalloideae are described from tropical Africa (incl. Madagascar) based on both morphological and molecular (DNA sequence) data. was collected, associated with , in Rwanda, Burundi and Tanzania. It is consumed by local people and chemical analyses showed the absence of amatoxins and phallotoxins in the basidiomata. Surprisingly, molecular analysis performed on the same specimens nevertheless demonstrated the presence of the gene sequence encoding for the phallotoxin phallacidin (PHA gene, member of the MSDIN family). The second species, was collected in Tanzania and Madagascar. It is also characterised by a complete PHA gene sequence and is suspected to be deadly poisonous. Both species clustered together in a well-supported terminal clade in multilocus phylogenetic inferences (including nuclear ribosomal partial LSU and ITS-5.8S, partial -α, and β-tubulin genes), considered either individually or concatenated. This, along with the occurrence of other species in sub-Saharan Africa and their phylogenetic relationships, are briefly discussed. Macro- and microscopic descriptions, as well as pictures and line drawings, are presented for both species. An identification key to the African and Madagascan species of Amanitasect.Phalloideae is provided. The differences between the two new species and the closest species are discussed.
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http://dx.doi.org/10.3897/mycokeys.53.34560DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6565643PMC
June 2019

Multilocus, DNA-based phylogenetic analyses reveal three new species lineages in the Phellinus gabonensis-P. caribaeo-quercicola species complex, including P. amazonicus sp. nov.

Mycologia 2016 09 29;108(5):939-953. Epub 2016 Jul 29.

Mycothèque de l'Université catholique de Louvain (MUCL, BCCM™), Earth and Life Institute-Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348 Louvain-la-Neuve, Belgium

Species complexes in the poroid Hymenochaetaceae are well documented in the temperate areas. Potential species complexes are less known in tropical areas, however. In the last ten years, four phylogenetically and morphologically closely related species of Phellinus (Hymenochaetaceae) were described from various tropical/subtropical areas viz. P. caribaeo-quercicola, P. gabonensis, P. ellipsoideus, and P. castanopsidis They are characterized by cushion-shaped basidiomata, ventricose, commonly hamate hymenial setae, and broadly ellipsoid, thick-walled, pale yellowish basidiospores. Pursuing the studies of this complex, a phylogenetic approach based on DNA sequence data from the nuc rDNA regions ITS1-5.8S-ITS2 (ITS) and partial 28S (including the domains D1, D2, D3) and on part of the translation elongation factor 1-α (tef1, region between exons 4 and 8) revealed three new lineages or phylogenetic species. Two of these phylogenetic species are composed of exclusively on Neotropical specimens. One of them, described below as Phellinus amazonicus sp. nov., is represented by multiple collections originating from Neotropical, lowland, dense, moist forest at the western edge of the Amazon Basin in Ecuador, the Guiana Shield in French Guiana and (more likely) Trinidad. The second Neotropical phylogenetic species is represented in our phylogenetic analyses by a single collection from northeastern Argentina. It is also potentially known from two herbarium specimens originating from southern Brazil, for which no sequence data is available. It is left for now as Phellinus sp. 1, waiting to gather more specimens and DNA sequences data. The third new phylogenetic species is known by a single collection (pure culture) of uncertain origin. It is thought to represent Phellinus setulosus, a Southeast Asian taxa. From an evolutionary perspective, tree species occurring in the Neotropics (P. amazonicus, P. caribaeo-quercicola, and Phellinus sp. 1) have a closely related genetic background and form a well supported Neotropical lineage.
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http://dx.doi.org/10.3852/15-173DOI Listing
September 2016

Hymenochaetaceae from the Guineo-Congolian rainforest: three new species of Phylloporia based on morphological, DNA sequences and ecological data.

Mycologia 2015 Sep-Oct;107(5):996-1011. Epub 2015 Aug 3.

Mycothèque de l'Université catholique de Louvain (MUCL, BCCM™), Earth and Life Institute- Microbiology (ELIM), Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, Louvain-la-Neuve, Belgium B-1348

Four species are added to Phylloporia. Three species, originating from the western edge of the Guineo-Congolian rainforest in Gabon (central Africa), are described as new. Phylloporia afrospathulata sp. nov. forms seasonal, stipitate, solitary basidiomata emerging from soil, more likely connected to buried roots, and has broadly ellipsoid basidiospores. Phylloporia inonotoides sp. nov. forms seasonal sessile, soft basidiomata, solitary at the base of small-stemmed trees including Crotonogyne manniana (Euphorbiaceae) and Garcinia cf. smeathmannii (Clusiaceae). It has a homogeneous context, large pores (2-3 mm), and oblong-ellipsoid to suballantoid basidiospores. Phylloporia fulva sp. nov. forms sessile, conchate, mostly pendant, gregarious basidiomata emerging from the trunk of an unidentified small-stemmed tree and has small, subglobose basidiospores. This species is compared to Polyporus pullus and Phylloporia pulla comb. nov. and proposed based on the study of the type specimen. Phylogenetic inferences using partial nuc 28S DNA sequence data (region including the D1/D2/D3 domains) and the most exhaustive dataset available to date resolved these new morphospecies as three distinct terminal lineages. No sequence data of P. pulla currently is available. The 28S-based phylogenic inferences poorly resolved the interspecific relationships within the Phylloporia clade.
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http://dx.doi.org/10.3852/14-298DOI Listing
November 2015

Fomitiporia castilloi sp. nov. and multiple clades around F. apiahyna and F. texana in Meso- and South America evidenced by multiloci phylogenetic inferences.

Mycologia 2013 Jul-Aug;105(4):873-87. Epub 2013 May 25.

Université catholique de Louvain, Louvain-la-Neuve, Belgium.

Fomitiporia castilloi sp. nov. from the lowland rainforest in French Guyana is described, illustrated and its phylogenetic affinities are discussed. This species is characterized by pileate basidiomata, a plicate margin, abundant, variably shaped hymenial setae and basidiospores averaging ≅ 6 × 5 μm. In phylogenetic inferences based on a DNA sequence dataset of four loci (5' end of the LSU, ITS-5.8S, partial tef1 and rpb2), F. castilloi occupies an isolated position, basal to a clade that is composed exclusively of Neotropical species with resupinate basidiomata. The phylogenetic inferences also provide evidence of an unreported complexity within the Neotropical taxa, with multiple clades closely related to F. apiahyna and F. texana, representing additional potential species.
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http://dx.doi.org/10.3852/11-423DOI Listing
September 2013

Fomitiporia cupressicola sp. nov., a parasite on Cupressus arizonica, and additional unnamed clades in the southern USA and northern Mexico, determined by multilocus phylogenetic analyses.

Mycologia 2012 Jul-Aug;104(4):880-93. Epub 2012 Mar 31.

Université catholique de Louvain, Louvain-la-Neuve, Belgium.

Fomitiporia cupressicola sp. nov., found in living Cupressus arizonica, is described on the basis of several collections originating from a high altitude forest in the northern Sierra Madre Occidental, Mexico. The species forms a monophyletic clade, basal to a larger lineage comprising species originating mainly from temperate to Mediterranean areas of the northern hemisphere. The phylogenetic approach in Fomitiporia also revealed multiple unnamed clades within the F. robusta complex in the southern USA and northern Mexico, representing potential species. The status of the F. robusta complex in North America is discussed briefly.
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http://dx.doi.org/10.3852/11-196DOI Listing
September 2012

Fomitiporia in sub-Saharan Africa: morphology and multigene phylogenetic analysis support three new species from the Guineo-Congolian rainforest.

Mycologia 2010 Nov-Dec;102(6):1303-17. Epub 2010 May 26.

Mycothèque de l'Université Catholique de Louvain (MUCL, BCCM™), Earth and Life Institute Mycology, Université Catholique de Louvain, Croix du Sud 3, B-1348 Louvain-la-Neuve, Belgium.

Fomitiporia nobilissima sp. nov., F. gabonensis sp. nov. and F. ivindoensis sp. nov., three species from the rainforest of the Guineo-Congolian phytogeographic region in Gabon, are described and illustrated. These species share a pileate basidiome, small basidiospores and an absence of setae. The critical morphological features that differentiate them are the pileus habit or shape, pore surface color, pore diameter and possibly ecology. Each new species forms distinct but closely related clades in phylogenetic analysis of DNA sequences from nuclear ribosomal LSU, ITS and translation elongation factor 1-α. Other species in sub-Saharan Africa are discussed briefly. A key to six species of Fomitiporia from sub-Saharan Africa is provided. The new combination Fomitiporia apiahyna is proposed.
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http://dx.doi.org/10.3852/09-083DOI Listing
December 2010

Perenniporiella chaquenia sp. nov. and further notes on Perenniporiella and its relationships with Perenniporia (poriales, basidiomycota).

Mycologia 2009 Sep-Oct;101(5):657-73

IMBIV-CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina.

Perenniporiella chaquenia sp. nov. is described from Argentina. New records of P. pendula and P. micropora are discussed. A key to Perenniporiella species is presented. Preliminary phylogenetic relationships of Perenniporiella are inferred from parsimony and Bayesian analysis of a combined set of DNA sequence data (nuclear ribosomal partial LSU and ITS). It demonstrated that Perenniporiella forms a well resolved monophyletic clade distantly related to Perenniporia s.s. It also clearly showed that within Perenniporia as usually conceived other morphologically homogeneous group of taxa, such as the P. ochroleuca or P. vicina alliances, form well resolved clades, which could be recognized as distinct genera. The differentiation of the hyphal system and the basidiospores morphology are outlined as critical features for the definition of genera in the Perenniporia complex.
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http://dx.doi.org/10.3852/08-040DOI Listing
October 2009