scholarly journals A Phylogenetic Analysis of Greek Isolates ofAspergillusSpecies Based on Morphology and Nuclear and Mitochondrial Gene Sequences

2013 ◽  
Vol 2013 ◽  
pp. 1-18 ◽  
Author(s):  
Antonios Krimitzas ◽  
Ioanna Pyrri ◽  
Vassili N. Kouvelis ◽  
Evangelia Kapsanaki-Gotsi ◽  
Milton A. Typas
Keyword(s):  
Rna Polymerase Ii ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Morphological Characters ◽  
Nuclear Genes ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Combined Use

Aspergillusspecies originating from Greece were examined by morphological and molecular criteria to explore the diversity of this genus. The phylogenetic relationships of these species were determined using sequences from the ITS and IGS region of the nuclear rRNA gene complex, two nuclear genes (β-tubulin (benA) and RNA polymerase II second largest subunit (rpb2)) and two mitochondrial genes (small rRNA subunit (rns) and cytochrome oxidase subunit I (cox1)) and, where available, related sequences from databases. The morphological characters of the anamorphs and teleomorphs, and the single gene phylogenetic trees, differentiated and placed the species examined in the well-supported sections ofAenei,Aspergillus,Bispori,Candidi,Circumdati,Clavati,Cremei,Flavi,Flavipedes,Fumigati,Nidulantes,Nigri,Restricti,Terrei,Usti, andZonati, with few uncertainties. The combined use of the three commonly employed nuclear genes (benA,rpb2, and ITS), the IGS region, and two less often used mitochondrial gene sequences (rnsandcox1) as a single unit resolved several taxonomic ambiguities. A phylogenetic tree was inferred using Neighbour-Joining, Maximum Parsimony, and Bayesian methods. The strains examined formed seven well-supported clades within the genusAspergillus. Altogether, the concatenated nuclear and mitochondrial sequences offer additional tools for an improved understanding of phylogenetic relationships within this genus.

Phylogenetic analysis of the Prionini (Coleoptera: Cerambycidae: Prioninae) from China based on mitochondrial ribosomal RNA genes and Cytochrome oxidase I gene

Zootaxa ◽  
2010 ◽  
Vol 2487 (1) ◽  
pp. 1 ◽  
Author(s):  
BO FENG ◽  
LI CHEN ◽  
YAN-LI E ◽  
KAI-DI ZHENG
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Mitochondrial Gene ◽  
Single Gene ◽  
Divergence Time ◽  
Mitochondrial Genes ◽  
12S Rrna ◽  
Molecular Systematic ◽  
Close Relationship

This is the first molecular systematic treatment of the Prionini. Here, three mitochondrial genes were partially sequenced from the Chinese Prionini to analyze phylogenetic relationships. Nucleotide compositions of three mitochondrial genes in the Chinese Prionini are biased toward A and T as in other insects. Ratios of transition vs. transversion (Ts/Tv) in 12S rRNA decrease with divergence time. However, ratios in 16S rRNA first increase with divergence time but decrease when divergence time is prolonged. Some nodes have poor bootstrap values or Bayesian posterior probabilities in phylogenetic trees reconstructed from single mitochondrial gene. In addition, some conflicting clades are found among phylogenetic trees based on a different gene. Therefore, a single mitochondrial gene provides limited phylogenetic signal and phylogenetic relationships based on a single gene sequence may be questionable. The Chinese Prionini is a monophyletic group. However, the genus Dorysthenes is paraphyletic. Dorysthenes fossatus should be transferred from Dorysthenes but the true status of D. fossatus is currently unknown. Species of Dorysthenes (excluding D. fossatus) constitute a monophyletic clade and there is close relationship between Dorysthenes paradoxus and Dorysthenes zivetta.

Descriptions of Trichodorus lownsberyi sp. n., Nanidorus minor (Colbran, 1956) Siddiqi, 1974 (Nematoda: Trichodoridae) and Longidorus quercus sp. n. (Nematoda: Longidoridae) from Mexico

Nematology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Ignacio Cid del Prado Vera ◽  
Sergei A. Subbotin ◽  
Wilfrida Decraemer
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
The Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Sequences ◽  
28S Rrna Gene ◽  
Buxus Sempervirens ◽  
Stubby Root Nematode

Summary A new species of stubby root nematode, Trichodorus lownsberyi sp. n., collected from soil around Buxus sempervirens at Montecillo Campus, Colegio de Postgraduados, Mexico, is described and illustrated. Trichodorus lownsberyi sp. n. is characterised by the abundant males with a characteristic spicule shape, the narrower part about mid-blade having visible bristles in most specimens, and the presence and position of the three ventromedian cervical papillae, which are all anterior to the secretory-excretory pore. Females possess a rhomboid-shaped vagina and oval to rounded triangular vaginal sclerotised pieces with a pore-like vulva. The phylogenetic relationships of T. lownsberyi sp. n. with related species were constructed using the ITS2 rRNA and the D2-D3 expansion segments of 28S rRNA gene sequences. Trichodorus lownsberyi sp. n. was a sister species to T. viruliferus in the phylogenetic trees. A Mexican population of Nanidorus minor from a peach orchard is also described and illustrated. The new needle nematode, Longidorus quercus sp. n., was recovered from soil around roots of oak, Quercus crassipes, from Cerro Jusda ‘El Diablo’ in Mexico State. Longidorus quercus sp. n. females are characterised by the C-shaped posterior end of the body after fixation, L = 4.9 (3.9-5.6) mm, a = 71 (60.8-93.2), lip region rounded, sometimes slightly flattened, marked by depression, odontostylet 170 (144-206) μm long, hemispherical to bluntly conoid tail and no males. The new species was characterised using the D2-D3 of 28S rRNA and COI gene sequences. The phylogenetic relationships of L. quercus sp. n. with other Longidorus species were reconstructed using the D2-D3 of 28S rRNA gene sequences.

Morphology, molecules and fritillaries: approaching a stable phylogeny for Argynnini (Lepidoptera: Nymphalidae)

2006 ◽  
Vol 37 (4) ◽  
pp. 405-418 ◽  
Author(s):  
Andrew Brower ◽  
Niklas Wahlberg ◽  
Thomas Simonsen ◽  
Rienk de Jong
Keyword(s):  
Phylogenetic Relationships ◽  
Mitochondrial Gene ◽  
Morphological Characters ◽  
Nuclear Genes ◽  
Total Evidence ◽  
Monophyletic Clade ◽  
Gene Coi ◽  
Phylogenetic Hypotheses ◽  
The Stability

AbstractWe examine the phylogenetic relationships among 29 species of Argynnini based on 141 previously published morphological characters and new data from the mitochondrial gene COI and the two nuclear genes EF-1a and wingless. We investigate the stability and robustness of the resulting phylogenetic hypotheses through various combinations of the 4 functionally separate datasets. Increasing the number of datasets in combined analyses led to increased support for clades, sometimes substantially. We find that the tribe Argynnini is a well-supported, robust, monophyletic clade with the following internal subtribal structure: (Euptoietina (Yrameina (Boloriina Argynnina))). Our analyses support the classification of argynnine species into six robust and stable genera: Euptoieta, Yramea, Boloria, Issoria, Brenthis and Argynnis. We suggest that for moderate amounts of data, a total evidence approach is always best.

scholarly journals Distribution and recombination of Wolbachia endosymbionts in Korean coleopteran insects

2019 ◽  
Vol 43 (1) ◽  
Author(s):  
Gilsang Jeong ◽  
Taeman Han ◽  
Haechul Park ◽  
Soyeon Park ◽  
Pureum Noh
Keyword(s):  
16S Rrna ◽  
Phylogenetic Trees ◽  
Surface Protein ◽  
Rrna Gene ◽  
Infection Frequency ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Endosymbiotic Bacteria ◽  
Molecular Machinery ◽  
Broad Scale

Abstract Background Wolbachia are among the most prevalent endosymbiotic bacteria and induce reproductive anomalies in various invertebrate taxa. The bacterium has huge impacts on host reproductive biology, immunity, evolution, and molecular machinery. However, broad-scale surveys of Wolbachia infections at the order scale, including the order Coleoptera, are limited. In this study, we investigated the Wolbachia infection frequency in 201 Coleopteran insects collected in Korea. Results A total of 26 species (12.8%) belonging to 11 families harbored Wolbachia. The phylogenetic trees of based on partial 16S rRNA gene sequences and partial Wolbachia surface protein (wsp) gene sequences were largely incongruent to that of their hosts. This result confirms that Wolbachia evolved independently from their hosts, Conclusion Phylogenetic trees suggest that complex horizontal gene transfer and recombination events occurred within and between divergent Wolbachia subgroups.

scholarly journals Phylogenetic relationships within the family Halobacteriaceae inferred from rpoB′ gene and protein sequences

2007 ◽  
Vol 57 (10) ◽  
pp. 2289-2295 ◽  
Author(s):  
Madalin Enache ◽  
Takashi Itoh ◽  
Tadamasa Fukushima ◽  
Ron Usami ◽  
Lucia Dumitru ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Marker ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Rpob Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
The Family

In order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16S rRNA gene sequences, the DNA-dependent RNA polymerase subunit B′ gene (rpoB′) was used as a complementary molecular marker. Partial sequences of the gene were determined from 16 strains of the family Halobacteriaceae. Comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16S rRNA gene sequences suggested that species of the genera Natrialba, Natronococcus, Halobiforma, Natronobacterium, Natronorubrum, Natrinema/Haloterrigena and Natronolimnobius formed a monophyletic group in all trees. In the RpoB′ protein tree, the alkaliphilic species Natrialba chahannaoensis, Natrialba hulunbeirensis and Natrialba magadii formed a tight group, while the neutrophilic species Natrialba asiatica formed a separate group with species of the genera Natronorubrum and Natronolimnobius. Species of the genus Natronorubrum were split into two groups in both the rpoB′ gene and protein trees. The most important advantage of the use of the rpoB′ gene over the 16S rRNA gene is that sequences of the former are highly conserved amongst species of the family Halobacteriaceae. All sequences determined so far can be aligned unambiguously without any gaps. On the other hand, gaps are necessary at 49 positions in the inner part of the alignment of 16S rRNA gene sequences. The rpoB′ gene and protein sequences can be used as an excellent alternative molecular marker in phylogenetic analysis of the Halobacteriaceae.

Phylogenetic Relationships among the Species of the Genus Testudo (Testudines: Testudinidae) Inferred from Mitochondrial 12S rRNA Gene Sequences

2002 ◽  
Vol 22 (2) ◽  
pp. 174-183 ◽  
Author(s):  
Antoinette C. van der Kuyl ◽  
Donato L. Ph. Ballasina ◽  
John T. Dekker ◽  
Jolanda Maas ◽  
Ronald E. Willemsen ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
12S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
12S Rrna Gene ◽  
Mitochondrial 12S Rrna

scholarly journals Variovorax gossypii sp. nov., isolated from Gossypium hirsutum

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4335-4340 ◽  
Author(s):  
Peter Kämpfer ◽  
Hans-Jürgen Busse ◽  
John A. McInroy ◽  
Stefanie P. Glaeser
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gossypium Hirsutum ◽  
Dna Hybridization ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
The 16S Rrna Gene

A beige-pigmented bacterial strain (JM-310T), isolated from the healthy internal root tissue of 4-week-old cotton (Gossypium hirsutum, cultivar ‘DES-119’) in Tallassee (Macon county), Alabama, USA, was studied taxonomically. The isolate produced small rod-shaped cells, which showed a Gram-negative staining behaviour. A comparison of the 16S rRNA gene sequence of the isolate revealed 99.2, 98.8, 98.7, 98.7, 98.1 and 97.6 % similarity to the 16S rRNA gene sequences of the type strains of Variovorax paradoxus, Variovorax boronicumulans, Variovorax ginsengisoli, Variovorax soli, Variovorax defluvii and Variovorax dokdonensis, respectively. In phylogenetic trees based on 16S rRNA gene sequences, strain JM-301T was placed within the monophyletic cluster of Variovorax species. The fatty acid profile of strain JM-310T consisted mainly of the major fatty acids C16 : 0, C10 : 0 3-OH and summed feature 4 (iso-C15 : 0 2-OH/C16 : 1ω7c/t). The quinone system of strain JM-310T contained predominantly ubiquinone Q-8 and lesser amounts of Q-7 and Q-9. The major polyamine was putrescine and the diagnostic polyamine 2-hydroxyputrescine was detected as well. The polar lipid profile consisted of the major lipids phosphatidylethanolamine, phosphatidylglycerol, diphospatidylglycerol and several unidentified lipids. DNA–DNA hybridization experiments with V. paradoxus LMG 1797T, V. boronicumulans 1.22T, V. soli KACC 11579T and V. ginsengisoli 3165T gave levels of relatedness of < 70 %. These DNA–DNA hybridization results in addition to differential biochemical properties indicate clearly that strain JM-310T is a member of a novel species, for which the name Variovorax gossypii sp. nov. is proposed. The type strain is JM-310T ( = LMG 28869T = CIP 110912T = CCM 8614T).

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

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