scholarly journals Genome and Metagenome of The Phytophagous Gall-Inducing Mite Fragariocoptes Setiger (Eriophyoidea): Are Symbiotic Bacteria Responsible For Gall-Formation?

2021 ◽  
Author(s):  
Pavel B. Klimov ◽  
Philipp E. Chetverikov ◽  
Irina E. Dodueva ◽  
Andrey E. Vishnyakov ◽  
Samuel J. Bolton ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Phylogenetic Position ◽  
Phylogenomic Analysis ◽  
Agricultural Pests ◽  
Gall Formation ◽  
Deep Soil ◽  
Comparative Metagenomics ◽  
Pathogenic Virus ◽  
Eriophyoid Mites ◽  
Phylogenetic Affinities

Abstract Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall-formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall-inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites; a mite pathogenic virus (Betabaculovirus) has the potential to be used in the biocontrol of agricultural pests.

scholarly journals Origins and Evolution of the Global RNA Virome

mBio ◽  
2018 ◽  
Vol 9 (6) ◽  
Author(s):  
Yuri I. Wolf ◽  
Darius Kazlauskas ◽  
Jaime Iranzo ◽  
Adriana Lucía-Sanz ◽  
Jens H. Kuhn ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Rna Viruses ◽  
Rna Virus ◽  
Phylogenomic Analysis ◽  
Rna Helicases ◽  
Sequence Alignments ◽  
Recent Advances ◽  
Wide Range ◽  
Positive Sense ◽  
Dsrna Viruses

ABSTRACTViruses with RNA genomes dominate the eukaryotic virome, reaching enormous diversity in animals and plants. The recent advances of metaviromics prompted us to perform a detailed phylogenomic reconstruction of the evolution of the dramatically expanded global RNA virome. The only universal gene among RNA viruses is the gene encoding the RNA-dependent RNA polymerase (RdRp). We developed an iterative computational procedure that alternates the RdRp phylogenetic tree construction with refinement of the underlying multiple-sequence alignments. The resulting tree encompasses 4,617 RNA virus RdRps and consists of 5 major branches; 2 of the branches include positive-sense RNA viruses, 1 is a mix of positive-sense (+) RNA and double-stranded RNA (dsRNA) viruses, and 2 consist of dsRNA and negative-sense (−) RNA viruses, respectively. This tree topology implies that dsRNA viruses evolved from +RNA viruses on at least two independent occasions, whereas −RNA viruses evolved from dsRNA viruses. Reconstruction of RNA virus evolution using the RdRp tree as the scaffold suggests that the last common ancestors of the major branches of +RNA viruses encoded only the RdRp and a single jelly-roll capsid protein. Subsequent evolution involved independent capture of additional genes, in particular, those encoding distinct RNA helicases, enabling replication of larger RNA genomes and facilitating virus genome expression and virus-host interactions. Phylogenomic analysis reveals extensive gene module exchange among diverse viruses and horizontal virus transfer between distantly related hosts. Although the network of evolutionary relationships within the RNA virome is bound to further expand, the present results call for a thorough reevaluation of the RNA virus taxonomy.IMPORTANCEThe majority of the diverse viruses infecting eukaryotes have RNA genomes, including numerous human, animal, and plant pathogens. Recent advances of metagenomics have led to the discovery of many new groups of RNA viruses in a wide range of hosts. These findings enable a far more complete reconstruction of the evolution of RNA viruses than was attainable previously. This reconstruction reveals the relationships between different Baltimore classes of viruses and indicates extensive transfer of viruses between distantly related hosts, such as plants and animals. These results call for a major revision of the existing taxonomy of RNA viruses.

scholarly journals OnProphocaandLeptophoca(Pinnipedia, Phocidae) from the Miocene of the North Atlantic realm: redescription, phylogenetic affinities and paleobiogeographic implications

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3024 ◽  
Author(s):  
Leonard Dewaele ◽  
Olivier Lambert ◽  
Stephen Louwye
Keyword(s):  
North America ◽  
Middle Miocene ◽  
New Combination ◽  
Phylogenetic Position ◽  
Appendicular Skeleton ◽  
Original Diagnosis ◽  
Sediment Samples ◽  
The North ◽  
The North Sea ◽  
Phylogenetic Affinities

BackgroundProphocaandLeptophocarepresent the oldest known genera of phocine seals, dating from the latest early to middle Miocene. Originally,Prophoca rousseauiandProphoca proximawere described based on fragmentary remains from the Miocene of Belgium. However, several researchers contested the union ofProphoca rousseauiandProphoca proximainto one genus, without providing evidence. The stratigraphic context ofProphocaremained poorly constrained due to the lack of precise data associated with the original specimens collected in the area of Antwerp (north of Belgium).MethodsProphocaandLeptophocaare redescribed and their phylogenetic position among Phocidae is reassessed using PAUP. Dinoflagellate biostratigraphy has been carried out on sediment samples associated with specimens fromProphocaandLeptophocato elucidate their approximate ages.ResultsWhereas the speciesProphoca rousseauiis redescribed,Prophoca proximais considered synonymous toLeptophoca lenis, with the proposal of a new combinationLeptophoca proxima(Van Beneden, 1877). Sediment samples from specimens of both taxa have been dated to the late Langhian–early Serravallian (middle Miocene). Following a reinvestigation ofLeptophoca amphiatlantica, characters from the original diagnosis are questioned and the specimens ofLeptophoca amphiatlanticaare consideredLeptophocacf.L. proxima. In a phylogenetic analysis,Prophoca rousseauiandLeptophoca proximaconstitute early branching stem-phocines.DiscussionLeptophoca proximafrom the North Sea Basin is younger than the oldest known find ofLeptophoca proximafrom North America, which does not contradict the hypothesis that Phocinae originated along the east coast of North America during the late early Miocene, followed by dispersal to Europe shortly after. Morphological features of the appendicular skeleton indicate thatProphoca rousseauiandLeptophoca proximahave archaic locomotory modes, retaining a more prominent use of the fore flipper for aquatic propulsion than extant Phocidae.

First pentasetacid mite from Australasian Araucariaceae: morphological description and molecular phylogenetic position of Pentasetacus novozelandicus n. sp. (Eriophyoidea, Pentasetacidae) and remarks on anal lobes in eriophyoid mites

2019 ◽  
Vol 24 (7) ◽  
pp. 1284-1309 ◽  
Author(s):  
Philipp Chetverikov ◽  
C. CRAEMER C. CRAEMER ◽  
T. CVRKOVIĆ T. CVRKOVIĆ ◽  
P.G. EFIMOV P.G. EFIMOV ◽  
P.B. KLIMOV P.B. KLIMOV ◽  
...  
Keyword(s):  
Laser Scanning ◽  
Phylogenetic Analyses ◽  
Mite Species ◽  
Laser Scanning Microscopy ◽  
Coi Gene ◽  
Confocal Laser ◽  
Phylogenetic Position ◽  
Morphological Description ◽  
Eriophyoid Mites ◽  
Molecular Phylogenetic

A new vagrant eriophyoid mite species of the archaic genus Pentasetacus (Schliesske 1985), P. novozelandicus n. sp., is described with the aid of conventional microscopy, confocal laser scanning microscopy and scanning electron microscopy. It was found on Araucaria heterophylla, which is an araucarian that is endemic to Norfolk Island and introduced to New Zealand. Partial sequences of mitochondrial barcode COI gene and D1–D2 domains of nuclear rDNA of two pentasetacid mites, P. araucariae (MK903025 and MK898944) and P. novozelandicus n. sp. (MK903024 and MK898943) are provided. Molecular phylogenetic analyses of full-length D1–D2 eriophyoid sequences, including GenBank sequences and newly generated sequences of pentasetacids, confirmed the monophyly of Pentasetacidae but failed to resolve the basal phylogeny of Eriophyoidea. This may be because the D1–D2 domains of 28S are hypervariable in Eriophyoidea. Moreover, in pentasetacids D1–D2 sequences are about 20% shorter than in other eriophyoids, and thus harder to align. Two types of anal lobes are described in Eriophyoidea: (1) Eriophyidae s.l. and Phytoptidae s.l. have bilaterally symmetric lobes; (2) pentasetacids have non-divided lobes. The presence of an anal secretory apparatus, comprising internal structures that have previously been described in Eriophyidae s.l. and Phytoptidae s.l., is confirmed in pentasetacid genera. The phylogeny of pentasetacids is also discussed in the context of the paleobiography of Araucariaceae.

Two new phyllocoptine species and new records of eriophyoid mites (Eriophyidae, Phyllocoptinae) from Crimea, with evaluation of the phylogenetic position of the new taxa using GenBank data

2019 ◽  
Vol 24 (5) ◽  
pp. 882
Author(s):  
Philipp Chetverikov ◽  
Pavel Klimov ◽  
Viktoria Yu. Letukhova ◽  
Géza Ripka ◽  
Sarah Zukoff
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Mite Species ◽  
New Combination ◽  
Phylogenetic Position ◽  
Endemic Plant ◽  
Plant Host ◽  
Mitochondrial Coi ◽  
Rdna Sequences ◽  
Eriophyoid Mites

We describe two new species and report new occurrences for six species of eriophyid mites (Eriophyoidea: Eriophyidae) in Crimea: Abacarus denticulifer n. sp. from Agropyron cristatum (L.) Gaertn. (Poaceae), Aceria aculiformis Sukhareva 1986 from Melica ciliata L. (Poaceae), Aceria peucedani (Canestrini 1891) from Seseli tortuosum L. (Apiaceae), Anthocoptes recki (Bagdasarian 1972) n. comb. (from Tegonotus) from Pistacia atlantica subsp. mutica (Fisch. & C.A. Mey.) (Anacardiaceae), Epitrimerus inulae Farkas 1963 from Inula germanica L. (Asteraceae), Phyllocoptes sanctus n. sp. from Potentilla recta subsp. obscura (Willd.) (Rosaceae), Phyllocoptes bilobospinosus Chetverikov 2019 (in Chetverikov et al. 2019) from Tamarix spp. (Tamaricaceae), Tegoprionus dentatus (Nalepa 1891) from Galium verum L. (Rubiaceae). For an Indian phyllocoptine mite species associated with Apluda mutica L. (Poaceae), a new combination was proposed: Abacarus muticus (Sur & Chakrabarti 2017) n. comb. (from Mesalox). Mitochondrial COI and D2 28S rDNA sequences of three phyllocoptine species from Crimea were obtained: A. denticulifer n. sp. (GenBank accession numbers MK415989 and MK408623), P. bilobospinosus (MK408624), and P. sanctus n. sp. (MK415988 and MK408622). Comparison of all COI and D2 28S sequences of Eriophyoidea from GenBank showed that sequences JF920111 and JF920110 Aceria tulipae are identical to JF920101 Aceria tosichella, and D2 28S sequence KP297379 Tegolophus sp. is identical to KM111079 Shevtchenkella sp., which indicates either one or more misidentifications or sample contamination. Molecular phylogenetic analyses (a) confirmed the morphology-based assignment of A. denticulifer n. sp. to the Abacarus hystrix s.l. species complex, (b) supported the monophyly of Abacarus hystrix s.l., (c) revealed that the genera Phyllocoptes, Epitrimerus, and Calepitrimerus are paraphyletic, and (d) indicated that Phyllocoptini (including P. sanctus n. sp.), which are associated with Rosaceae and Caprifoliaceae, are monophyletic. The position of P. bilobospinosus was uncertain in all analyses. Based on the results of our study, it is recommended that descriptions of new species in large, putatively paraphyletic genera of Eriophyoidea include comparisons with mite species associated with the same plant family. Our work also provides new evidence that a species in a large complex of cryptic species could have evolved a distinct morphology if it is associated with an endemic plant host restricted to a geographically isolated area.

scholarly journals New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

2019 ◽  
Vol 36 (4) ◽  
pp. 757-765 ◽  
Author(s):  
Jürgen F H Strassert ◽  
Mahwash Jamy ◽  
Alexander P Mylnikov ◽  
Denis V Tikhonenkov ◽  
Fabien Burki
Keyword(s):  
Phylogenetic Signal ◽  
Evolutionary Origin ◽  
Phylogenetic Position ◽  
Aquatic Environments ◽  
Phylogenomic Analysis ◽  
Data Sets ◽  
Transcriptome Data ◽  
Phylogenetic Reconstructions ◽  
Phylogenomic Analyses ◽  
Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

scholarly journals Solution to the phylogenetic enigma of Tetraplatia , a worm-shaped cnidarian

2005 ◽  
Vol 2 (1) ◽  
pp. 120-124 ◽  
Author(s):  
Allen G Collins ◽  
Bastian Bentlage ◽  
George I Matsumoto ◽  
Steven H.D Haddock ◽  
Karen J Osborn ◽  
...  
Keyword(s):  
Body Plan ◽  
Phylogenetic Position ◽  
Recent Origin ◽  
Phylogenetic Affinities

Tetraplatia is a genus containing two species of pelagic cnidarians of curious morphology. Their vermiform shape and four swimming flaps are difficult to relate to the features of other cnidarians, thus obscuring their phylogenetic affinities. Since their discovery in the mid-1800s, a number of prominent cnidarian workers have weighed in on this conundrum, some arguing that they are aberrant hydrozoans and others concluding that they are unusual scyphozoans. Current taxonomic practice conforms to the latter view. However, data presented here from the large and small subunits of the nuclear ribosome leave little doubt that Tetraplatia is in fact a hydrozoan genus. Indeed, its precise phylogenetic position is within Narcomedusae, as some authors had previously deduced based on structural characters. The distinctive body plan of Tetraplatia is remarkable because it appears to have a recent origin, in contrast to the prevailing pattern of metazoan history.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Oomycete metabarcoding reveals the presence of Lagenidium spp. in phytotelmata

2019 ◽  
Author(s):  
Paula Leoro-Garzon ◽  
Andrew J Gonedes ◽  
Isabel E Olivera ◽  
Aurelien Tartar
Keyword(s):  
Single Molecule ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Microbial Detection ◽  
Animal Pathogens ◽  
Culture Independent ◽  
Mosquito Breeding ◽  
Phylogenetic Affinities ◽  
Detection Strategies

The oomycete genus Lagenidium, which includes the mosquito biocontrol agent L. giganteum, is composed of animal pathogens, yet is phylogenetically closely related to the well characterized plant pathogens Phytophthora and Pythium spp. These phylogenetic affinities were further supported by the identification of canonical oomycete effectors in the L. giganteum transcriptome, and suggested, mirroring the endophytic abilities demonstrated in entomopathogenic fungi, that L. giganteum may have similarly retained capacities to establish interactions with plant tissues. To test this hypothesis, culture-independent, metabarcoding analyses aimed at detecting L. giganteum in bromeliad phytotelmata (a proven mosquito breeding ground) microbiomes were performed. Two independent and complementary microbial detection strategies based on the amplification of cox1 DNA barcodes were used and produced globally concordant outcomes revealing that two distinct Lagenidium phylotypes are present in phytotelmata. A total of 23,869 high quality reads were generated from four phytotelmata, with 52%, and 11.5%, corresponding to oomycetes, and Lagenidium spp., barcodes, respectively. Newly-designed Lagenidium-specific cox1 primers combined with cloning/Sanger sequencing produced only Lagenidium spp. barcodes, with a majority of sequences clustering with L. giganteum. High throughput sequencing based on a Single Molecule Real Time (SMRT) approach combined with broad range cox1 oomycete primers confirmed the presence of L. giganteum in phytotelmata, but indicated that a potentially novel Lagenidium phylotype (closely related to L. humanum) may represent one of the most prevalent oomycetes in these environments (along with Pythium spp.). Phylogenetic analyses demonstrated that all detected Lagenidium phylotype cox1 sequences clustered in a strongly-supported, monophyletic clade that included both L. giganteum and L. humanum. Therefore, Lagenidium spp. are present in phytotelmata microbiomes. This observation provides a basis to investigate potential relationships between Lagenidium spp. and phytotelma-forming plants, especially in the absence of water and/or invertebrate hosts, and reveals phytotelmata as sources for the identification of novel Lagenidium isolates with potential as biocontrol agents against vector mosquitoes.

scholarly journals Conservation of a gene cluster reveals novel cercosporin biosynthetic mechanisms and extends production to the genus Colletotrichum

2017 ◽  
Author(s):  
Ronnie de Jonge ◽  
Malaika K. Ebert ◽  
Callie R. Huitt-Roehl ◽  
Paramita Pal ◽  
Jeffrey C. Suttle ◽  
...  
Keyword(s):  
Sugar Beet ◽  
Gene Cluster ◽  
Fungal Pathogens ◽  
Plant Pathogens ◽  
Pathogenic Fungi ◽  
Gene Clusters ◽  
Phylogenomic Analysis ◽  
First Case ◽  
Horizontal Transfers ◽  
Fungal Genus

AbstractSpecies in the genus Cercospora cause economically devastating diseases in sugar beet, maize, rice, soy bean and other major food crops. Here we sequenced the genome of the sugar beet pathogen C. beticola and found it encodes 63 putative secondary metabolite gene clusters, including the cercosporin toxin biosynthesis (CTB) cluster. We show that the CTB gene cluster has experienced multiple duplications and horizontal transfers across a spectrum of plant pathogenic fungi, including the wide host range Colletotrichum genus as well as the rice pathogen Magnaporthe oryzae. Although cercosporin biosynthesis has been thought to-date to rely on an eight gene CTB cluster, our phylogenomic analysis revealed gene collinearity adjacent to the established cluster in all CTB cluster-harboring species. We demonstrate that the CTB cluster is larger than previously recognized and includes cercosporin facilitator protein (CFP) previously shown to be involved with cercosporin auto-resistance, and four additional genes required for cercosporin biosynthesis including the final pathway enzymes that install the unusual cercosporin methylenedioxy bridge. Finally, we demonstrate production of cercosporin by Colletotrichum fioriniae, the first known cercosporin producer within this agriculturally important genus. Thus, our results provide new insight into the intricate evolution and biology of a toxin critical to agriculture and broaden the production of cercosporin to another fungal genus containing many plant pathogens of important crops worldwide.Significance StatementSpecies in the fungal genus Cercospora cause diseases in many important crops worldwide. Their success as pathogens is largely due to the secretion of cercosporin during infection. We report that the cercosporin toxin biosynthesis (CTB) cluster is ancient and was horizontally transferred to diverse fungal pathogens on an unprecedented scale. Since these analyses revealed genes adjacent to the established CTB cluster, we evaluated their role in C. beticola to show that four are necessary for cercosporin biosynthesis. Finally, we confirmed that the apple pathogen Colletotrichum fioriniae produces cercosporin, the first case outside the family Mycosphaerellaceae. Other Colletotrichum plant pathogens also harbor the CTB cluster, which points to a wider concern that this toxin may play in virulence and human health.

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