scholarly journals Molecular diversity within the genus Laeonereis (Annelida, Nereididae) along the west Atlantic coast: paving the way for integrative taxonomy

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11364
Author(s):  
Bruno R. Sampieri ◽  
Pedro E. Vieira ◽  
Marcos A. L. Teixeira ◽  
Victor C. Seixas ◽  
Paulo R. Pagliosa ◽  
...  
Keyword(s):  
16S Rrna ◽  
Molecular Diversity ◽  
Sequence Data ◽  
Atlantic Coast ◽  
Rrna Genes ◽  
Southeastern Brazil ◽  
28S Rrna ◽  
Morphological Examination ◽  
Separate Species ◽  
The Way

The polychaete genus Laeonereis (Annelida, Nereididae) occurs over a broad geographic range and extends nearly across the entire Atlantic coast of America, from the USA to Uruguay. Despite the research efforts to clarify its diversity and systematics, mostly by morphological and ecological evidence, there is still uncertainty, mainly concerning the species Laeonereis culveri, which constitutes an old and notorious case of taxonomic ambiguity. Here, we revised the molecular diversity and distribution of Laeonereis species based on a multi-locus approach, including DNA sequence analyses of partial segments of the cytochrome c oxidase subunit I (COI), 16S rRNA, and 28S rRNA genes. We examined Laeonereis specimens collected from 26 sites along the American Atlantic coast from Massachusetts (USA) to Mar del Plata (Argentina). Although no comprehensive morphological examination was performed between different populations, the COI barcodes revealed seven highly divergent MOTUs, with a mean K2P genetic distance of 16.9% (from 6.8% to 21.9%), which was confirmed through four clustering algorithms. All MOTUs were geographically segregated, except for MOTUs 6 and 7 from southeastern Brazil, which presented partially overlapping ranges between Rio de Janeiro and São Paulo coast. Sequence data obtained from 16S rRNA and 28S rRNA markers supported the same MOTU delimitation and geographic segregation as those of COI, providing further evidence for the existence of seven deeply divergent lineages within the genus. The extent of genetic divergence between MOTUs observed in our study fits comfortably within the range reported for species of polychaetes, including Nereididae, thus providing a strong indication that they might constitute separate species. These results may therefore pave the way for integrative taxonomic studies, aiming to clarify the taxonomic status of the Laeonereis MOTUs herein reported.

scholarly journals Multilocus sequence analysis of Ensifer and related taxa

2007 ◽  
Vol 57 (3) ◽  
pp. 489-503 ◽  
Author(s):  
Miet Martens ◽  
Manuel Delaere ◽  
Renata Coopman ◽  
Paul De Vos ◽  
Monique Gillis ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
New Combination ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Separate Species

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

A new amphibious species of the genus Scolopendra Linnaeus, 1758 (Scolopendromorpha, Scolopendridae) from the Ryukyu Archipelago and Taiwan

Zootaxa ◽  
2021 ◽  
Vol 4952 (3) ◽  
pp. 465-494
Author(s):  
SHO TSUKAMOTO ◽  
SHIMPEI F. HIRUTA ◽  
KATSUYUKI EGUCHI ◽  
JHIH-RONG LIAO ◽  
SATOSHI SHIMANO
Keyword(s):  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Valid Species ◽  
28S Rrna ◽  
Ryukyu Archipelago ◽  
Morphological Examination ◽  
Mitochondrial Coi ◽  
Molecular Phylogenetic ◽  
East And Southeast Asia ◽  
18S Rrna Genes

In Japan and Taiwan, five valid species of the genus Scolopendra Linnaeus, 1758 have been described: S. morsitans Linnaeus, 1758, S. subspinipes Leach, 1816, S. mutilans Koch, 1878, S. japonica Koch, 1878, and S. multidens Newport, 1844. Recently, an undetermined species was found in the Ryukyu Archipelago and Taiwan. Using molecular phylogenetic analyses with mitochondrial COI and 16S rRNA and nuclear 28S rRNA and 18S rRNA genes as well as conventional morphological examination, we successfully discriminated this sixth species as an independent lineage from S. subspinipes, S. mutilans, and other named congeners from East and Southeast Asia. Therefore, the species was described as S. alcyona Tsukamoto & Shimano, sp. nov. Several situational evidences suggest that this species prefers streamside environments and exhibits amphibious behavior. 

scholarly journals Revision of the genus Emphylica Turner, 1913 based on morphology and molecular data (Lepidoptera, Crambidae, Pyraustinae)

ZooKeys ◽  
2019 ◽  
Vol 836 ◽  
pp. 113-133 ◽  
Author(s):  
Kai Chen ◽  
Qingming Liu ◽  
Jianhua Jin ◽  
Dandan Zhang
Keyword(s):  
New Species ◽  
16S Rrna ◽  
Sequence Data ◽  
Southern China ◽  
Molecular Data ◽  
28S Rrna ◽  
New Combinations ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
A New Species

Moths of the genus Emphylica Turner, 1913 resemble species of Achyra Guenée, 1849, Loxostege Hübner, 1825 and Sitochroa Hübner, 1825 in having a conical frons. In order to examine the monophyly of Emphylica, and its relationship to other genera with a conical frons, a molecular phylogenetic framework is reconstructed based on sequence data of COI, 16S rRNA, 28S rRNA, EF-1α and Wg gene regions. The results robustly support the monophyly of Emphylica. Achyra + (Loxostege + Sitochroa) is in a sister position to Emphylica. A new species, E.crassihamatasp. n., is described from Southern China and two new combinations, E.diaphana (Caradja & Meyrick, 1934), comb. n. and E.cruoralis (Warren, 1895), comb. n., are proposed. An identification key based on males is provided for all Emphylica species. The adult habitus and genitalia of all species are figured.

scholarly journals Revision of the genus Epiparbattia Caradja, 1925 (Lepidoptera, Crambidae, Pyraustinae), based on morphology and molecular data

ZooKeys ◽  
2020 ◽  
Vol 960 ◽  
pp. 143-155
Author(s):  
Dandan Zhang ◽  
Kai Chen ◽  
Lanbin Xiang
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
16S Rrna ◽  
Sequence Data ◽  
Molecular Data ◽  
28S Rrna ◽  
A New Species ◽  
General Appearance

The genus Epiparbattia Caradja, 1925 is revised based on general appearance, including genitalia. A new species, Epiparbattia multispinalis Zhang & Chen, sp. nov. is described. The external characters and genitalia morphology of all species are figured. The phylogeny of Epiparbattia species is investigated using molecular data. Monophyly of the genus is well supported by phylogenetic analysis based on sequence data of COI, 16S rRNA, EF-1α and 28S rRNA gene regions.

scholarly journals Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group

2016 ◽  
Vol 54 (11) ◽  
pp. 2749-2756 ◽  
Author(s):  
Janetta R. Hakovirta ◽  
Samantha Prezioso ◽  
David Hodge ◽  
Segaran P. Pillai ◽  
Linda M. Weigel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacillus Cereus ◽  
Sequence Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Single Nucleotide ◽  
Content Type

Analysis of 16S rRNA genes is important for phylogenetic classification of known and novel bacterial genera and species and for detection of uncultivable bacteria. PCR amplification of 16S rRNA genes with universal primers produces a mixture of amplicons from all rRNA operons in the genome, and the sequence data generally yield a consensus sequence. Here we describe valuable data that are missing from consensus sequences, variable effects on sequence data generated from nonidentical 16S rRNA amplicons, and the appearance of data displayed by different software programs. These effects are illustrated by analysis of 16S rRNA genes from 50 strains of theBacillus cereusgroup, i.e.,Bacillus anthracis,Bacillus cereus,Bacillus mycoides, andBacillus thuringiensis. These species have 11 to 14 rRNA operons, and sequence variability occurs among the multiple 16S rRNA genes. A single nucleotide polymorphism (SNP) previously reported to be specific toB. anthraciswas detected in someB. cereusstrains. However, a different SNP, at position 1139, was identified as being specific toB. anthracis, which is a biothreat agent with high mortality rates. Compared with visual analysis of the electropherograms, basecaller software frequently missed gene sequence variations or could not identify variant bases due to overlapping basecalls. Accurate detection of 16S rRNA gene sequences that include intragenomic variations can improve discrimination among closely related species, improve the utility of 16S rRNA databases, and facilitate rapid bacterial identification by targeted DNA sequence analysis or by whole-genome sequencing performed by clinical or reference laboratories.

scholarly journals Discordant 16S and 23S rRNA Gene Phylogenies for the Genus Helicobacter: Implications for Phylogenetic Inference and Systematics

2005 ◽  
Vol 187 (17) ◽  
pp. 6106-6118 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Zeli Shen ◽  
Michael S. Scimeca ◽  
Lauren N. Stokes ◽  
Tahani Boumenna ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Data ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
23S Rrna Gene ◽  
23S Rrna Genes

ABSTRACT Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

Phylogeny of bethylid wasps (Hymenoptera: Bethylidae) inferred from 28S and 16S rRNA genes

2010 ◽  
Vol 41 (1) ◽  
pp. 55-73 ◽  
Author(s):  
Martin Carr ◽  
Peter Mayhew ◽  
J. Peter Young
Keyword(s):  
16S Rrna ◽  
Strong Support ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Monophyletic Clade ◽  
Outgroup Species ◽  
Molecular Studies ◽  
Mitochondrial 16S Rrna Gene

AbstractWe conduct the first molecular studies of the higher level phylogeny of bethylid wasps (Hymenoptera: Bethylidae). Sequences of the 500-bp D2/D3 expansion regions of the nuclear 28S rRNA gene are obtained for 33 bethylid species in 18 genera covering all four commonly recognized subfamilies, and an additional 13 outgroup species. A 450-bp sequence of the mitochondrial 16S rRNA gene is obtained for a smaller subset of those species. Strong support is found for the monophyly of Bethylidae, and for Bethylinae as the sister to the other bethylid subfamilies. Pristocerinae are supported as monophyletic. A species of Mesitiinae clusters with the Sclerodermini (sensu lato), these two strongly supported as a monophyletic clade. The Epyrini are supported as monophyletic, but our data do not demonstrate whether Pristocerinae or the Mesitiinae+Sclerodermini clade are their closest relatives. Kishino–Hasegawa tests reject the monophyly of the Epyrinae. Our results are consistent with Kieffer's original five major subtaxa of Bethylidae.

scholarly journals Molecular and Histological Characterization of Primary (Betaproteobacteria) and Secondary (Gammaproteobacteria) Endosymbionts of Three Mealybug Species

2011 ◽  
Vol 78 (4) ◽  
pp. 1187-1197 ◽  
Author(s):  
Laurence N. Gatehouse ◽  
Paul Sutherland ◽  
Shaun A. Forgie ◽  
Ryohei Kaji ◽  
John T. Christeller
Keyword(s):  
16S Rrna ◽  
Protein Interactions ◽  
Sequence Data ◽  
Virus Transmission ◽  
Amino Acid Sequences ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Pseudococcus Longispinus

ABSTRACTMicroscopic localization of endosymbiotic bacteria in three species of mealybug (Pseudococcus longispinus, the long-tailed mealybug;Pseudococcus calceolariae, the citrophilus mealybug; andPseudococcus viburni, the obscure mealybug) showed these organisms were confined to bacteriocyte cells within a bacteriome centrally located within the hemocoel. Two species of bacteria were present, with the secondary endosymbiont, in all cases, living within the primary endosymbiont. DNA from the dissected bacteriomes of all three species of mealybug was extracted for analysis. Sequence data from selected 16S rRNA genes confirmed identification of the primary endosymbiont as “CandidatusTremblaya princeps,” a betaproteobacterium, and the secondary endosymbionts as gammaproteobacteria closely related toSodalis glossinidius. A single 16S rRNA sequence of the primary endosymbiont was found in all individuals of each mealybug species. In contrast, the presence of multiple divergent strains of secondary endosymbionts in each individual mealybug suggests different evolutionary and transmission histories of the two endosymbionts. Mealybugs are known vectors of the plant pathogenGrapevine leafroll-associated virus 3. To examine the possible role of either endosymbiont in virus transmission, an extension of the model for interaction of proteins with bacterial chaperonins, i.e., GroEL protein homologs, based on mobile-loop amino acid sequences of their GroES homologs, was developed and used for analyses of viral coat protein interactions. The data from this model are consistent with a role for the primary endosymbiont in mealybug transmission ofGrapevine leafroll-associated virus 3.

scholarly journals Three Cases of Anaerobiospirillum succiniciproducens Bacteremia Confirmed by 16S rRNA Gene Sequencing

1998 ◽  
Vol 36 (5) ◽  
pp. 1209-1213 ◽  
Author(s):  
Wee Tee ◽  
Tony M. Korman ◽  
Mary Jo Waters ◽  
Andrew Macphee ◽  
Adam Jenney ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Data ◽  
Infected Individual ◽  
The Other ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Anaerobiospirillum Succiniciproducens

We describe three cases of Anaerobiospirillum succiniciproducens bacteremia from Australia. We believe one of these cases represents the first report of A. succiniciproducens bacteremia in a human immunodeficiency virus (HIV)-infected individual. The other two patients had an underlying disorder (one patient had bleeding esophageal varices complicating alcohol liver disease and one patient had non-Hodgkin’s lymphoma). A motile, gram-negative, spiral anaerobe was isolated by culturing blood from all patients. Electron microscopy showed a curved bacterium with bipolar tufts of flagella resembling Anaerobiospirillumspp. Sequencing of the 16S rRNA genes of the isolates revealed no close relatives (organisms likely to be in the same genus) in the sequence databases, nor were any sequence data available for A. succiniciproducens. This report presents for the first time the 16S rRNA gene sequence of the type strain of A. succiniciproducens, strain ATCC 29305. Two of the three clinical isolates have sequences identical to that of the type strain, while the sequence of the other strain differs from that of the type strain at 4 nucleotides.

scholarly journals Molecular Evolution of Mycoplasma capricolum subsp. capripneumoniae Strains, Based on Polymorphisms in the 16S rRNA Genes

1998 ◽  
Vol 180 (9) ◽  
pp. 2350-2358 ◽  
Author(s):  
Bertil Pettersson ◽  
Göran Bölske ◽  
François Thiaucourt ◽  
Mathias Uhlén ◽  
Karl-Erik Johansson
Keyword(s):  
16S Rrna ◽  
Sequence Data ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequence Length ◽  
Nucleotide Substitution Rate ◽  
16S Rrna Sequence ◽  
Mycoplasma Capricolum ◽  
Mycoplasma Mycoides ◽  
Lines Of Descent

ABSTRACT Mycoplasma capricolum subsp.capripneumoniae belongs to the so-called Mycoplasma mycoides cluster and is the causal agent of contagious caprine pleuropneumonia (CCPP). All members of the M. mycoidescluster have two rRNA operons. The sequences of the 16S rRNA genes of both rRNA operons from 20 strains of M. capricolum subsp.capripneumoniae of different geographical origins in Africa and Asia were determined. Nucleotide differences which were present in only one of the two operons (polymorphisms) were detected in 24 positions. The polymorphisms were not randomly distributed in the 16S rRNA genes, and some of them were found in regions of low evolutionary variability. Interestingly, 11 polymorphisms were found in all theM. capricolum subsp. capripneumoniae strains, thus defining a putative ancestor. A sequence length difference between the 16S rRNA genes in a poly(A) region and 12 additional polymorphisms were found in only one or some of the strains. A phylogenetic tree was constructed by comparative analysis of the polymorphisms, and this tree revealed two distinct lines of descent. The nucleotide substitution rate of strains within line II was up to 50% higher than within line I. A tree was also constructed from individual operonal 16S rRNA sequences, and the sequences of the two operons were found to form two distinct clades. The topologies of both clades were strikingly similar, which supports the use of 16S rRNA sequence data from homologous operons for phylogenetic studies. The strain-specific polymorphism patterns of the 16S rRNA genes of M. capricolum subsp.capripneumoniae may be used as epidemiological markers for CCPP.

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