Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes

The phylogenetic relationships of all known species of the genus Aeromonas, and especially Aeromonas bestiarum and Aeromonas salmonicida, were investigated on 70 strains using the rpoD sequence, which encodes the σ 70 factor. This analysis was complemented with the sequence of gyrB, which has already proven useful for determining the phylogenetic relationships in the genus. Nucleotide sequences of rpoD and gyrB showed that both genes had similar substitution rates (<2 %) and a similar number of variable positions (34 % for rpoD versus 32 % for gyrB). Strain groupings by analysis of rpoD, gyrB and a combination of both genes were consistent with the taxonomic organization of all Aeromonas species described to date. However, the simultaneous analysis of both clocks improved the reliability and the power to differentiate, in particular, closely related taxa. At the inter-species level, gyrB showed a better resolution for differentiating Aeromonas sp. HG11/Aeromonas encheleia and Aeromonas veronii/Aeromonas culicicola/Aeromonas allosaccharophila, while rpoD more clearly differentiated A. salmonicida from A. bestiarum. The analysis of rpoD provided initial evidence for clear phylogenetic divergence between the latter two species.

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Periconia citlaltepetlensis sp. nov. (Periconiaceae, Pleosporales): a psychrotolerant fungus from high elevation volcanic glacier (Mexico)

Phytotaxa ◽

10.11646/phytotaxa.459.3.5 ◽

2020 ◽

Vol 459 (3) ◽

pp. 235-247

Author(s):

ROSA P. CALVILLO-MEDINA ◽

AURORA COBOS-VILLAGRÁN ◽

TANIA RAYMUNDO

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

First Record ◽

High Elevation ◽

Nucleotide Sequences ◽

Species Level ◽

Rdna Analysis

Periconia citlaltepetlensis sp. nov. is the first record of a fungus identified to species level from high elevation volcanic glacier in Mexico. It is a novel dothideomycete species supported by morphological, cultural characters and phylogenetic analysis (nucleotide sequences data rDNA analysis). The new species is characterized by conidiophores often with 2–4 enteroblastic, percurrent proliferations, large, globose, golden brown or reddish brown conidia that are borne singly or in basipetal chains, verrucose to irregular lobate crests, born singly or in basipetal chains of two conidia; acropetally proliferating; conidiogenesis holoblastic. The morphology of P. citlaltepetlensis is compared to other Periconia species and a detailed description and morphological illustrations are provided.

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Systematics of New World Curtonotum Macquart (Diptera: Curtonotidae)

Zootaxa ◽

10.11646/zootaxa.3079.1.1 ◽

2011 ◽

Vol 3079 (1) ◽

pp. 1 ◽

Cited By ~ 3

Author(s):

JOHN KLYMKO ◽

STEPHEN A. MARSHALL

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Species Complex ◽

New World ◽

Species Level ◽

Junior Synonym ◽

World Species ◽

Species Complexes

The New World species of the curtonotid genus Curtonotum Macquart are reviewed, and all species outside the vulpinum and murinum species complexes (as defined below) are revised. Descriptions and illustrations are provided for 24 species, including 13 newly described species: C. adusticrus sp. n., C. atlanticum sp. n., C. bivittatum sp. n., C. brunneum sp. n., C. curtispinum sp. n., C. desperatum sp. n., C. papillatum sp. n., C. gracile sp. n., C. hunkingi sp. n., C. flavisetum sp. n., C. floridense sp. n., C. nigrum sp. n., and C. scambum sp. n. Curtonotum nigripalpe Hendel is proposed as a new junior synonym of C. hendelianum (Enderlein). A key to these New World species is presented and the phylogenetic relationships between them are discussed. Lectotypes are designated for C. tumidum Enderlein, C. bathmedum Hendel, C. taeniatum Hendel, C. trypetipenne Hendel, C. impunctatum Hendel, 1913, nec impunctatum Hendel, 1932 and C. apicale Hendel. Curtonotum perplexum nom. n., is given as the replacement name for C. impunctatum Hendel, 1932 nec impunctatum Hendel, 1913. Two species complexes are left untreated at the species level (the C. murinum species complex, including C. murinum Hendel, C. coriaceum Hendel, C. perplexum nom. n., and C. decumanum Bezzi; and the C. vulpinum species complex including C. vulpinum Hendel and C. fumipenne Hendel). Both complexes are included in the phylogenetic analysis and key.

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Phylogenetic Analysis of the Incidence of lux Gene Horizontal Transfer in Vibrionaceae

Journal of Bacteriology ◽

10.1128/jb.00101-08 ◽

2008 ◽

Vol 190 (10) ◽

pp. 3494-3504 ◽

Cited By ~ 42

Author(s):

Henryk Urbanczyk ◽

Jennifer C. Ast ◽

Allison J. Kaeding ◽

James D. Oliver ◽

Paul V. Dunlap

Keyword(s):

Phylogenetic Analysis ◽

Horizontal Transfer ◽

Vibrio Vulnificus ◽

Housekeeping Genes ◽

Housekeeping Gene ◽

Vibrio Splendidus ◽

Photobacterium Leiognathi ◽

Photobacterium Damselae ◽

Phylogenetic Divergence ◽

Distinctive Phenotype

ABSTRACT Horizontal gene transfer (HGT) is thought to occur frequently in bacteria in nature and to play an important role in bacterial evolution, contributing to the formation of new species. To gain insight into the frequency of HGT in Vibrionaceae and its possible impact on speciation, we assessed the incidence of interspecies transfer of the lux genes (luxCDABEG), which encode proteins involved in luminescence, a distinctive phenotype. Three hundred three luminous strains, most of which were recently isolated from nature and which represent 11 Aliivibrio, Photobacterium, and Vibrio species, were screened for incongruence of phylogenies based on a representative housekeeping gene (gyrB or pyrH) and a representative lux gene (luxA). Strains exhibiting incongruence were then subjected to detailed phylogenetic analysis of horizontal transfer by using multiple housekeeping genes (gyrB, recA, and pyrH) and multiple lux genes (luxCDABEG). In nearly all cases, housekeeping gene and lux gene phylogenies were congruent, and there was no instance in which the lux genes of one luminous species had replaced the lux genes of another luminous species. Therefore, the lux genes are predominantly vertically inherited in Vibrionaceae. The few exceptions to this pattern of congruence were as follows: (i) the lux genes of the only known luminous strain of Vibrio vulnificus, VVL1 (ATCC 43382), were evolutionarily closely related to the lux genes of Vibrio harveyi; (ii) the lux genes of two luminous strains of Vibrio chagasii, 21N-12 and SB-52, were closely related to those of V. harveyi and Vibrio splendidus, respectively; (iii) the lux genes of a luminous strain of Photobacterium damselae, BT-6, were closely related to the lux genes of the lux-rib 2 operon of Photobacterium leiognathi; and (iv) a strain of the luminous bacterium Photobacterium mandapamensis was found to be merodiploid for the lux genes, and the second set of lux genes was closely related to the lux genes of the lux-rib 2 operon of P. leiognathi. In none of these cases of apparent HGT, however, did acquisition of the lux genes correlate with phylogenetic divergence of the recipient strain from other members of its species. The results indicate that horizontal transfer of the lux genes in nature is rare and that horizontal acquisition of the lux genes apparently has not contributed to speciation in recipient taxa.

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Section Mimadenia: its phylogenetic relationships within the genus Mimosa (Leguminosae, Mimosoideae) using plastid trnL - F sequence data

Australian Systematic Botany ◽

10.1071/sb10022 ◽

2011 ◽

Vol 24 (2) ◽

pp. 104 ◽

Cited By ~ 8

Author(s):

C. Bessega ◽

R. H. Fortunato

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Intergenic Spacer ◽

Nucleotide Sequences ◽

Trnl Intron ◽

Infrageneric Classification ◽

Morphological Group ◽

Evolutionary Hypothesis

Mimosa L. includes more than 530 species and is subdivided into five sections, including Mimadenia Barneby, Batocaulon DC., Habbasia DC., Calothamnos Barneby and Mimosa. It has previously been proposed that Mimosa is derived from piptadenioid ancestors and that section Mimadenia is a morphological group intermediate between the piptadenoid ancestor and the remaining species from Mimosa. The main goals of the present study were to assess the monophyly of the genus Mimosa as it is currently described, including representatives of all five sections, test the previous evolutionary hypothesis that section Mimadenia is primitive within Mimosa and discuss the infrageneric classification from a phylogenetic view. We report a phylogenetic analysis of chloroplast nucleotide sequences of the trnL intron and the trnL–trnF intergenic spacer from 36 species of Mimosa, and six related genera. Our analysis indicated that genus Mimosa is monophyletic, and the species of section Mimadenia constitute a clade sister to the rest of the genus. Although section Mimadenia, as described by Barneby (1991), seems to be monophyletic, the remaining sections Barneby (1991) proposed are not resolved as monophyletic. An effort needs to be made towards a new infrageneric classification of Mimosa that considers the phylogenetic evidence.

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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Diversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan

Scientific Reports ◽

10.1038/s41598-020-80690-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Hongru Su ◽

Eri Onoda ◽

Hitoshi Tai ◽

Hiromi Fujita ◽

Shigetoshi Sakabe ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Core Genome ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Housekeeping Genes ◽

Pcr Screening ◽

Taxonomic Profiling ◽

Quantitative Characteristics

AbstractEhrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1–V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.

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Comparative analysis and phylogenetic investigation of Hong Kong Ilex chloroplast genomes

Scientific Reports ◽

10.1038/s41598-021-84705-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Bobby Lim-Ho Kong ◽

Hyun-Seung Park ◽

Tai-Wai David Lau ◽

Zhixiu Lin ◽

Tae-Jin Yang ◽

...

Keyword(s):

Hong Kong ◽

Comparative Analysis ◽

Phylogenetic Relationships ◽

Species Level ◽

The Other ◽

Trna Genes ◽

Protein Coding ◽

Chloroplast Genomes ◽

Plant Group ◽

Ilex Rotunda

AbstractIlex is a monogeneric plant group (containing approximately 600 species) in the Aquifoliaceae family and one of the most commonly used medicinal herbs. However, its taxonomy and phylogenetic relationships at the species level are debatable. Herein, we obtained the complete chloroplast genomes of all 19 Ilex types that are native to Hong Kong. The genomes are conserved in structure, gene content and arrangement. The chloroplast genomes range in size from 157,119 bp in Ilex graciliflora to 158,020 bp in Ilex kwangtungensis. All these genomes contain 125 genes, of which 88 are protein-coding and 37 are tRNA genes. Four highly varied sequences (rps16-trnQ, rpl32-trnL, ndhD-psaC and ycf1) were found. The number of repeats in the Ilex genomes is mostly conserved, but the number of repeating motifs varies. The phylogenetic relationship among the 19 Ilex genomes, together with eight other available genomes in other studies, was investigated. Most of the species could be correctly assigned to the section or even series level, consistent with previous taxonomy, except Ilex rotunda var. microcarpa, Ilex asprella var. tapuensis and Ilex chapaensis. These species were reclassified; I. rotunda was placed in the section Micrococca, while the other two were grouped with the section Pseudoaquifolium. These studies provide a better understanding of Ilex phylogeny and refine its classification.

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Mechanism of Metronidazole Resistance inHelicobacter pylori: Comparison of the rdxA Gene Sequences in 30 Strains

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.44.8.2207-2210.2000 ◽

2000 ◽

Vol 44 (8) ◽

pp. 2207-2210 ◽

Cited By ~ 26

Author(s):

Nadia Maggi Solcà ◽

Marco Valerio Bernasconi ◽

Jean-Claude Piffaretti

Keyword(s):

Phylogenetic Analysis ◽

Helicobacter Pylori ◽

Amino Acid ◽

Resistant Strain ◽

Point Mutations ◽

Housekeeping Genes ◽

Amino Acid Substitutions ◽

Metronidazole Resistance ◽

Nucleotide Mutation ◽

Nucleotide Insertion

ABSTRACT The rdxA gene of 30 independently isolatedHelicobacter pylori strains was sequenced. A comparison of the rdxA sequences revealed a higher percentage of amino acid substitutions in the corresponding protein than in other housekeeping genes. Out of 122 point mutations, 41 were missense and 4 were nonsense. A resistant strain with a nucleotide insertion in therdxA sequence was also found. With the exception of the point mutations and the insertion generating a stop signal, no particular nucleotide mutation or amino acid substitution could be associated to metronidazole resistance. Moreover, phylogenetic analysis of the 30 nucleotide sequences did not demonstrate specific clusters associated with the resistance phenotype.

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Phylogeny accurately predicts behaviour in Indian Ocean Clitaetra spiders (Araneae:Nephilidae)

Invertebrate Systematics ◽

10.1071/is09002 ◽

2009 ◽

Vol 23 (3) ◽

pp. 193 ◽

Cited By ~ 18

Author(s):

Matjaž Kuntner ◽

Ingi Agnarsson

Keyword(s):

South Africa ◽

Phylogenetic Analysis ◽

Indian Ocean ◽

Species Level ◽

Web Architecture ◽

Evolutionarily Conserved ◽

The Family ◽

Behavioural Biology

Phylogenies are underutilised, powerful predictors of traits in unstudied species. We tested phylogenetic predictions of web-related behaviour in Clitaetra Simon, 1889, an Afro-Indian spider genus of the family Nephilidae. Clitaetra is phylogenetically sister to all other nephilids and thus important for understanding ancestral traits. Behavioural information on Clitaetra has been limited to only C. irenae Kuntner, 2006 from South Africa which constructs ladder webs. A resolved species-level phylogeny unambiguously optimised Clitaetra behavioural biology and predicted web traits in five unstudied species and a uniform intrageneric nephilid web biology. We tested these predictions by studying the ecology and web biology of C. perroti Simon, 1894 on Madagascar and C. episinoides Simon, 1889 on Mayotte. We confirm predicted arboricolous web architecture in these species. The expected ontogenetic allometric transition from orbs in juveniles to elongate ladder webs in adults was statistically significant in C. perroti, whereas marginally not significant in C. episinoides. We demonstrate the persistence of the temporary spiral in finished Clitaetra webs. A morphological and behavioural phylogenetic analysis resulted in unchanged topology and persisting unambiguous behavioural synapomorphies. Our results support the homology of Clitaetra hub reinforcement with the nephilid hub-cup. In Clitaetra, behaviour was highly predictable and remained consistent with new observations. Our results confirm that nephilid web biology is evolutionarily conserved within genera.

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Phylogenetic analysis of the subfamily Hylodinae (Anura, Leptodactylidae) based on morphological characters

Amphibia-Reptilia ◽

10.1163/1568538054253456 ◽

2005 ◽

Vol 26 (2) ◽

pp. 139-147 ◽

Cited By ~ 6

Author(s):

Francisca do Val ◽

Paulo Nuin

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Maximum Parsimony ◽

Morphological Characters ◽

The Other ◽

The Family

AbstractThe systematics and phylogenetic relationships of the family Leptodactylidae are controversial as is the intrafamilial phylogeny of the leptodactylids. Here we analyze the relationships of the leptodactylid subfamily Hylodinae. This subfamily has been considered to be monophyletic and composed of three genera, Hylodes, Crossodactylus and Megaelosia. In the present study 49 characters were used, based on different studies on Leptodactylidae phylogeny. Maximum parsimony methods with unweighted and successively weighted characters were used to estimate the phylogeny of the Hylodinae. Upon analysis, the data provided further evidence of the monophyletic status of the three genera, with Megaelosia being the basal genus and the other two genera being sister taxa. The analysis with successive weighting results in a more resolved topology of the species subgroups of the genus Hylodes and separates this genus from Crossodactylus and confirms that the hylodines are monophyletic.

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