Molecular and morphological systematics of a new, reef forming, cupped oyster from the northern Arabian Gulf: Talonostrea salpinx new species

The rocky northern shores of Kuwait and those of the western, inner shores of Kuwait Bay are dominated by a small, densely encrusting oyster. The identity of this oyster has never been confirmed and was mistaken previously for a small Saccostrea. The shell morphology suggests that this species belongs to the subfamily Crassostreinae, but within that subfamily, the presence of marginal erect trumpet-shaped projections is so far unique. Phylogenetic analyses based on mitochondrial DNA sequence data confirmed that this species belongs to the Crassostreinae and has a sister position to the clade including Talonostrea talonata and T. zhanjiangensis. Genetic distance between this species and Talonostrea species is remarkably high, being ~20% for the cytochrome oxidase I gene and ~7% for the 16S rRNA gene. Based on morphological and molecular analyses, this oyster is therefore described here as Talonostrea salpinx Oliver, Salvi & Al-Kandari, sp. nov. Shell morphology is shown to be variable, and the different forms encountered are described. The wider distribution and origins of this species, whether native or introduced, are discussed.

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Desulfitibacter alkalitolerans gen. nov., sp. nov., an anaerobic, alkalitolerant, sulfite-reducing bacterium isolated from a district heating plant

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64356-0 ◽

2006 ◽

Vol 56 (12) ◽

pp. 2831-2836 ◽

Cited By ~ 29

Author(s):

Marie Bank Nielsen ◽

Kasper Urup Kjeldsen ◽

Kjeld Ingvorsen

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

District Heating ◽

Rrna Gene ◽

Corrosion Monitoring ◽

Optimum Growth ◽

Genes Encoding ◽

Nitrate And Nitrite ◽

The 16S Rrna Gene ◽

Heating Plant

A novel alkalitolerant, anaerobic bacterium, designated strain sk.kt5T, was isolated from a metal coupon retrieved from a corrosion-monitoring reactor of a Danish district heating plant (Skanderborg, Jutland). The cells of strain sk.kt5T were motile, rod-shaped (0.4–0.6×2.5–9.6 μm), stained Gram-positive and formed endospores. Strain sk.kt5T grew at pH 7.6–10.5 (with optimum growth at pH 8.0–9.5), at temperatures in the range 23–44 °C (with optimum growth at 35–37 °C), at NaCl concentrations in the range 0–5 % (w/v) (with optimum growth at 0–0.5 %) and required yeast extract for growth. Only a limited number of substrates were utilized as electron donors, including betaine, formate, lactate, methanol, choline and pyruvate. Elemental sulfur, sulfite, thiosulfate, nitrate and nitrite, but not sulfate or Fe(III) citrate, were used as electron acceptors. The G+C content of the DNA was 41.6 mol%. Phylogenetic analyses of the sequence data for the dsrAB genes [encoding the major subunits of dissimilatory (bi)sulfite reductase] and the 16S rRNA gene placed strain sk.kt5T within a novel lineage in the class Clostridia of the phylum Firmicutes. Taken together, the physiological and genotypic data suggest that strain sk.kt5T represents a novel species within a novel genus, for which the name Desulfitibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain of Desulfitibacter alkalitolerans is sk.kt5T (=JCM 12761T=DSM 16504T).

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Cymbidium yunnanensis: a new orchid species (Orchidaceae; Epidendroideae) from China based on morphological and molecular evidence

Phytotaxa ◽

10.11646/phytotaxa.387.2.7 ◽

2019 ◽

Vol 387 (2) ◽

pp. 149-157 ◽

Cited By ~ 5

Author(s):

GUO-QIANG ZHANG ◽

GUI-ZHEN CHEN ◽

LI-JUN CHEN ◽

SI-REN LAN

Keyword(s):

New Species ◽

Dna Sequence ◽

Yunnan Province ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Evidence ◽

Orchid Species ◽

Molecular Analyses ◽

Dna Sequence Data ◽

A New Species

A new orchid species, Cymbidium yunnanensis (Orchidaceae; Epidendroideae; Cymbidieae), from Yunnan Province, China, is described and illustrated. Based on morphological and molecular analyses, we demonstrate that this new species is similar to C. floribundum, but it differs in its smaller size, leaves 5–15 cm, shorter scape, white flowers with pale purplish markings on its sepals and petals, lip with purplish red blotch, petals narrowly falcate oblong and lip midlobe nearly round with column foot 1.5–2.0 mm long. Phylogenetic analyses based on nuclear ribosomal ITS and plastid (matK, rbcL) DNA sequence data support C. yunnanensis as a new species.

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Discovery of Novel Rickettsiella spp. in Ixodid Ticks from Western Canada

Applied and Environmental Microbiology ◽

10.1128/aem.03564-13 ◽

2013 ◽

Vol 80 (4) ◽

pp. 1403-1410 ◽

Cited By ~ 6

Author(s):

Clare A. Anstead ◽

Neil B. Chilton

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sequence Type ◽

Ixodid Ticks ◽

Rrna Gene ◽

Western Canada ◽

Content Type ◽

The 16S Rrna Gene

ABSTRACTThe genomic DNA from four species of ixodid ticks in western Canada was tested for the presence ofRickettsiellaby PCR analyses targeting the 16S rRNA gene. Eighty-eight percent of theIxodes angustus(n= 270), 43% of theI. sculptus(n= 61), and 4% of theI. kingi(n= 93) individuals examined were PCR positive forRickettsiella, whereas there was no evidence for the presence ofRickettsiellainDermacentor andersoni(n= 45). Three different single-strand conformation polymorphism profiles of the 16S rRNA gene were detected among amplicons derived fromRickettsiella-positive ticks, each corresponding to a different sequence type. Furthermore, each sequence type was associated with a different tick species. Phylogenetic analyses of sequence data of the 16S rRNA gene and three other genes (rpsA,gidA, andsucB) revealed that all three sequence types were placed in a clade that contained species and pathotypes of the genusRickettsiella. The bacterium inI. kingirepresented the sister taxon to theRickettsiellainI. sculptus, and both formed a clade withRickettsiellagryllifrom crickets (Gryllus bimaculatus) and “R. ixodidis” fromI. woodi. In contrast, theRickettsiellainI. angustuswas not a member of this clade but was placed external to the clade comprising the pathotypes ofR. popilliae. The results indicate the existence of at least two new species ofRickettsiella: one inI. angustusand another inI. kingiandI. sculptus. However, theRickettsiellastrains inI. kingiandI. sculptusmay also represent different species because each had unique sequences for all four genes.

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Cymbidium shidianense (Orchidaceae: Epidendroideae), a new species from China: evidence from morphology and molecular data

Phytotaxa ◽

10.11646/phytotaxa.399.1.10 ◽

2019 ◽

Vol 399 (1) ◽

pp. 100 ◽

Cited By ~ 5

Author(s):

GUI-ZHEN CHEN ◽

GUO-QIANG ZHANG ◽

JIE HUANG ◽

MENG WANG ◽

WEN-HUI RAO ◽

...

Keyword(s):

New Species ◽

Yunnan Province ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Orchid Species ◽

Molecular Analyses ◽

Dna Sequence Data ◽

Pale Green ◽

A New Species

A new orchid species, Cymbidium shidianense (Orchidaceae; Cymbidieae), from Yunnan Province, China, is described and illustrated based on morphological and molecular analyses. This new species is similar in morphology to C. cyperifolium, but it differs in its larger pseudobulbs, rigid leaves, broader pale green sepals, petals with darkly coloured veins and set of V-shaped blotches on the lip midlobe. A phylogenetic analyses based on nuclear ribosomal ITS and plastid (matK, rbcL) DNA sequence data support C. shidianense as related to C. cyperifolium.

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Reclassification of Mesoplasma pleciae as Acholeplasma pleciae comb. nov. on the basis of 16S rRNA and gyrB gene sequence data

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02904-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 1951-1952 ◽

Cited By ~ 14

Author(s):

Thomas F. Knight

Keyword(s):

16S Rrna ◽

Genomic Dna ◽

Gene Sequence ◽

Sequence Data ◽

Rrna Gene ◽

Dna Sequence Data ◽

Gyrb Gene Sequence ◽

Genomic Dna Sequence ◽

The 16S Rrna Gene ◽

Gene Sequence Data

Genomic DNA sequence data for the 16S rRNA gene and the gyrB gene of Mesoplasma pleciae PS-1T (=ATCC 49582T=NBRC 100476T) demonstrate a much closer relationship to Acholeplasma laidlawii and Acholeplasma oculi than to other species in the order Entomoplasmatales. In addition, the preferred use of UGG rather than UGA as the codon for tryptophan in the gyrB sequence probably places the organism outside the order Entomoplasmatales. It is proposed that M. pleciae be reclassified in the genus Acholeplasma, as Acholeplasma pleciae comb. nov.

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Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

Microorganisms ◽

10.3390/microorganisms9030666 ◽

2021 ◽

Vol 9 (3) ◽

pp. 666

Author(s):

Niccolò Forin ◽

Alfredo Vizzini ◽

Federico Fainelli ◽

Enrico Ercole ◽

Barbara Baldan

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

Botanical Garden ◽

Molecular Study ◽

Its2 Sequence ◽

Type Specimens ◽

Its1 Sequence ◽

Dna Sequence Data ◽

Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

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Biological and Phylogenetic Analyses Suggest that Two Cryphonectria spp. Cause Cankers of Eucalyptus in Africa

Plant Disease ◽

10.1094/pdis.2003.87.11.1329 ◽

2003 ◽

Vol 87 (11) ◽

pp. 1329-1332 ◽

Cited By ~ 18

Author(s):

J. Roux ◽

H. Myburg ◽

B. D. Wingfield ◽

M. J. Wingfield

Keyword(s):

South Africa ◽

South America ◽

South African ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Eucalyptus Grandis ◽

Its Region ◽

South African Isolate ◽

Dna Sequence Data ◽

The Republic

Cryphonectria cubensis is an economically important pathogen of commercial Eucalyptus spp. Differences have been reported for disease symptoms associated with Cryphonectria canker in South Africa and other parts of the world, and recent DNA-based comparisons have confirmed that the fungus in South Africa is different from that in South America and Australasia. During a disease survey in the Republic of Congo, Cryphonectria canker was identified as an important disease on Eucalyptus grandis and E. urophylla. In this study, we compared Congolese and South African isolates of C. cubensis using DNA sequence data and pathogenicity under greenhouse conditions. The β-tubulin and internal transcribed spacer (ITS) region sequences show that C. cubensis in Congo is different from the fungus in South Africa and that Congolese isolates group most closely with South American isolates. Furthermore, pathogenicity tests showed that a South African isolate was more aggressive than two Congolese isolates. We conclude that two distinct Cryphonectria spp. occur in Africa and hypothesize that the fungus in the Congo probably was introduced into Africa from South America. Both fungi are important pathogens causing disease and death of economically important plantation trees. However, they apparently have different origins and must be treated separately in terms of disease management and quarantine considerations.

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Contrasting the population genetic structure of two velvet worm taxa (Onychophora : Peripatopsidae : Peripatopsis) in forest fragments along the south-eastern Cape, South Africa

Invertebrate Systematics ◽

10.1071/is16085 ◽

2017 ◽

Vol 31 (6) ◽

pp. 781 ◽

Cited By ~ 4

Author(s):

Savel R. Daniels ◽

Megan Dreyer ◽

Prashant P. Sharma

Keyword(s):

South Africa ◽

Population Genetic ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Forest Fragments ◽

Eastern Cape ◽

Dna Sequence Data ◽

Mtdna Coi ◽

Haplotype Networks ◽

Velvet Worm

During the present study, we examined the phylogeography and systematics of two species of velvet worm (Peripatopsis Pocock, 1894) in the forested region of the southern Cape of South Africa. A total of 89 P. moseleyi (Wood-Mason, 1879) and 65 P. sedgwicki (Purcell, 1899) specimens were collected and sequenced for the cytochrome c oxidase subunit I mtDNA (COI). In addition, a single P. sedgwicki specimen per sample locality was sequenced for the 18S rRNA locus. Furthermore, morphological variation among P. sedgwicki sample localities were explored using traditional alpha taxonomic characters. DNA sequence data were subjected to phylogenetic analyses using Bayesian inference and population genetic analyses using haplotype networks and analyses of molecular variance (AMOVAs). Phylogenetic results revealed the presence of four and three clades within P. moseleyi and P. sedgwicki respectively. Haplotype networks were characterised by the absence of shared haplotypes between clades, suggesting genetic isolation, a result corroborated by the AMOVA and highly significant FST values. Specimens from Fort Fordyce Nature Reserve were both genetically and morphologically distinct from the two remaining P. sedgwicki clades. The latter result suggests the presence of a novel lineage nested within P. sedgwicki and suggests that species boundaries within this taxon require re-examination.

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A new species of trypanosome, Trypanosoma desterrensis sp. n., isolated from South American bats

Parasitology ◽

10.1017/s0031182003003536 ◽

2003 ◽

Vol 127 (3) ◽

pp. 265-271 ◽

Cited By ~ 17

Author(s):

E. C. GRISARD ◽

N. R. STURM ◽

D. A. CAMPBELL

Keyword(s):

New Species ◽

Dna Sequence ◽

Sequence Data ◽

Rrna Gene ◽

South American ◽

Sequence Variability ◽

Dna Sequence Data ◽

Hybridization Probes ◽

5S Rrna Gene ◽

A New Species

Trypanosomes isolated from South American bats include the human pathogen Trypanosoma cruzi. Other Trypanosoma spp. that have been found exclusively in bats are not well characterized at the DNA sequence level and we have therefore used the SL RNA gene to differentiate and characterize kinetoplastids isolated from bats in South America. A Trypanosoma sp. isolated from bats in southern Brazil was compared with the geographically diverse isolates T. cruzi marinkellei, T. vespertilionis, and T. dionisii. Analysis of the SL RNA gene repeats revealed size and sequence variability among these bat trypanosomes. We have developed hybridization probes to separate these bat isolates and have analysed the DNA sequence data to estimate their relatedness. A new species, Trypanosoma desterrensis sp. n., is proposed, for which a 5S rRNA gene was also found within the SL RNA repeat.

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A new species of Puddle Frog, genus Phrynobatrachus (Amphibia: Anura: Phrynobatrachidae) from Ghana

Zootaxa ◽

10.11646/zootaxa.4374.4.6 ◽

2018 ◽

Vol 4374 (4) ◽

pp. 565 ◽

Cited By ~ 1

Author(s):

CALEB OFORI-BOATENG ◽

ADAM D. LEACHÉ ◽

BRIGHT OBENG-KANKAM ◽

N’GORAN GERMAIN KOUAMÉ ◽

ANNIKA HILLERS ◽

...

Keyword(s):

Genetic Diversity ◽

New Species ◽

Sequence Data ◽

Face Mask ◽

West African ◽

Rrna Gene ◽

Forest Region ◽

Mtdna Sequence ◽

A New Species ◽

The 16S Rrna Gene

We describe a new species of Phrynobatrachus from the eastern part of the Upper Guinea forest region, Ghana, West Africa. Morphologically, the new species can be distinguished from all of its congeners by the combination of a slender body, short and pointed snout, a relatively warty dorsum, a black-spotted throat in both sexes, a gular flap in males, a dark spotted chest, a white-greyish venter with occasional blackish spots, rudimentary pedal webbing, none to slightly dilated finger tips and strongly delated toe tips, presence of both inner and outer metatarsal tubercles and absence of a dark face mask, eyelid tubercles and longer dorsal ridges. We collected mitochondrial DNA (mtDNA) sequence data from the 16S rRNA gene to measure the genetic diversity of the new species, and to estimate phylogenetic relationships. The new species is a distinct and monophyletic evolutionary lineage most closely related to Phrynobatrachus gutturosus, P. fraterculus and P. maculiventris. The discovery of this new species highlights that the biodiversity of West African forests is still incompletely known and that the few remaining forests need urgent protection.

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