Evolution of aquatic life-forms in Alismatidae: Phylogenetic estimation from chloroplast rbcL gene sequence data

The relationship of Photorhabdus isolates that were cultured from human clinical specimens in Australia to Photorhabdus asymbiotica isolates from human clinical specimens in the USA and to species of the genus Photorhabdus that are associated symbiotically with entomopathogenic nematodes was evaluated. A polyphasic approach that involved DNA–DNA hybridization, phylogenetic analyses of 16S rRNA and gyrB gene sequences and phenotypic characterization was adopted. These investigations showed that gyrB gene sequence data correlated well with DNA–DNA hybridization and phenotypic data, but that 16S rRNA gene sequence data were not suitable for defining species within the genus Photorhabdus. Australian clinical isolates proved to be related most closely to clinical isolates from the USA, but the two groups were distinct. A novel subspecies, Photorhabdus asymbiotica subsp. australis subsp. nov. (type strain, 9802892T=CIP 108025T=ACM 5210T), is proposed, with the concomitant creation of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. Analysis of gyrB sequences, coupled with previously published data on DNA–DNA hybridization and PCR-RFLP analysis of the 16S rRNA gene, indicated that there are more than the three subspecies of Photorhabdus luminescens that have been described and confirmed the validity of the previously proposed subdivision of Photorhabdus temperata. Although a non-luminescent, symbiotic isolate clustered consistently with P. asymbiotica in gyrB phylogenetic analyses, DNA–DNA hybridization indicated that this isolate does not belong to the species P. asymbiotica and that there is a clear distinction between symbiotic and clinical species of Photorhabdus.

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Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02821-0 ◽

2004 ◽

Vol 54 (2) ◽

pp. 493-497 ◽

Cited By ~ 60

Author(s):

Brian J. Henson ◽

Sharon M. Hesselbrock ◽

Linda E. Watson ◽

Susan R. Barnum

Keyword(s):

Phylogenetic Analysis ◽

Gene Sequence ◽

Sequence Data ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Cellular Division ◽

Heterocystous Cyanobacteria ◽

Nitrogen Fixation Gene ◽

True Branching ◽

Gene Sequence Data

The heterocystous cyanobacteria are currently placed in subsections IV and V, which are distinguished by cellular division in one plane (false branching) and in more than one plane (true branching), respectively. Published phylogenies of 16S rRNA gene sequence data support the monophyly of the heterocystous cyanobacteria, with members of subsection V embedded within subsection IV. It has been postulated that members of subsection V arose from within subsection IV. Therefore, phylogenetic analysis of nucleotide sequences of the nitrogen-fixation gene nifD from representatives of subsections IV and V was performed by using maximum-likelihood criteria. The heterocystous cyanobacteria are supported as being monophyletic, with the non-heterocystous cyanobacteria as their closest relative. However, neither subsection IV nor subsection V is monophyletic, with representatives of both subsections intermixed in two sister clades. Analysis of nifD does not support recognition of two distinct subsections.

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The Use of rRNA Gene Sequence Data in the Classification and Identification of Prokaryotes

Methods in Microbiology - Taxonomy of Prokaryotes ◽

10.1016/b978-0-12-387730-7.00016-4 ◽

2011 ◽

pp. 349-384 ◽

Cited By ~ 4

Author(s):

Wolfgang Ludwig ◽

Frank Oliver Glöckner ◽

Pelin Yilmaz

Keyword(s):

Gene Sequence ◽

Sequence Data ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequence Data

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A new species of Pestalotiopsis from leaf spots of Licuala grandis from Hainan, China

Phytotaxa ◽

10.11646/phytotaxa.88.3.2 ◽

2013 ◽

Vol 88 (3) ◽

pp. 49 ◽

Cited By ~ 3

Author(s):

KUN GENG ◽

BIN ZHANG ◽

YU SONG ◽

KEVIN D. HYDE ◽

JI-CHUAN KANG ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Molecular Phylogeny ◽

Gene Sequence ◽

Sequence Data ◽

Leaf Spots ◽

A New Species ◽

Type Sequence ◽

Gene Sequence Data ◽

Β Tubulin

A new species, Pestalotiopsis licualacola, was isolated from grey leafspots of Licuala grandis (ruffled fan palm). It is morphologically distinct in having relatively small, greyish brown conidia (16–20 × 3–5 μm), and 1–3 short apical appendages without knobs. Phylogenetic analysis based on combination of ITS, β-tubulin and tef1 gene sequence data clearly distinguishes P. licualacola from other species in this genus, with ex-type sequence data in GenBank. Based on morphology and molecular phylogeny we describe it as a new species.

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Two new species of the Phimochirus holthuisi complex from the Gulf of Mexico, supported by morphology, color, and genetics (Crustacea: Anomura: Paguridae)

Zootaxa ◽

10.11646/zootaxa.4683.4.4 ◽

2019 ◽

Vol 4683 (4) ◽

pp. 531-551

Author(s):

DARRYL L. FELDER ◽

RAFAEL LEMAITRE ◽

CATHERINE CRAIG

Keyword(s):

New Species ◽

Gulf Of Mexico ◽

Continental Shelf ◽

Gene Sequence ◽

Sequence Data ◽

Phylogenetic Analyses ◽

The Other ◽

Two New Species ◽

Molecular Phylogenetic ◽

Gene Sequence Data

Coloration, gene-sequence data (H3, 12s, 16s), and subtle features in morphology support the description of two new species, both formerly regarded to represent accepted variants of Phimochirus holthuisi s.l. While color in life consistently separates these species from P. holthuisi s.s. and from each other, morphological distinctions are subtle and less than absolute in small specimens, being based on ventral spine counts of walking leg dactyls and relative development of the superior crest on the major chela. Molecular phylogenetic analyses clearly support the separation of sister clades, representing two new species, from P. holthuisi s.s. as well as other congeners available for analysis. Both of the new species are presently known to occur widely throughout the northern Gulf of Mexico, though one occurs more commonly in the northeastern and southeastern Gulf, and may range as far south as Suriname. The other has been taken primarily in the northwestern Gulf, and is not known from outside Gulf waters. While both of the new species appear restricted to relatively deep subtidal waters of the continental shelf, Phimochirus holthuisi s.s. is instead more commonly found in shallow nearshore tropical waters on or near coral reefs. Previous literature reports of P. holthuisi usually represent, at least in part, one or both of these two new species.

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