When molecules support morphology: Phylogenetic reconstruction of the family Onuphidae (Eunicida, Annelida) based on 16S rDNA and 18S rDNA

Partial sequences of the 18S nuclear and 16S mitochondrial ribosomal genes were obtained for 14�species of thalassinidean shrimp (families Callianassidae, Laomediidae, Strahlaxiidae, Thalassinidae and Upogebiidae) and a further six species in related decapod infraorders (families Aeglidae, Astacidae, Lithodidae, Palinuridae, Raninidae and Scyllaridae). Maximum-likelihood and Bayesian analyses show equivocal support for the monophyly of the Thalassinidea, but show strong support for division of the infraorder into two major clades. This dichotomy separates representatives in the Upogebiidae, Laomediidae and Thalassinidae from those in the Strahlaxiidae and Callianassidae. The Laomediidae is shown to be paraphyletic, with the thalassinid species, Thalassina squamifera, being placed on a branch between Axianassa and a clade comprising Jaxea and Laomedia, the three current laomediid genera. For a monophyletic Laomediidae, the family Axianassidae should be resurrected for the genus Axianassa.

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Comparative Cytogenetics in Four Leptodactylus Species (Amphibia, Anura, Leptodactylidae): Evidence of Inner Chromosomal Diversification in Highly Conserved Karyotypes

Cytogenetic and Genome Research ◽

10.1159/000515831 ◽

2021 ◽

pp. 1-11

Author(s):

David S. da Silva ◽

Heriberto F. da Silva Filho ◽

Marcelo B. Cioffi ◽

Edivaldo H.C. de Oliveira ◽

Anderson J.B. Gomes

Keyword(s):

18S Rdna ◽

Repetitive Sequences ◽

Molecular Cytogenetics ◽

Comparative Cytogenetics ◽

The Family ◽

Agnor Staining ◽

Dna Elements ◽

Conventional Cytogenetics ◽

Species Specific ◽

Repetitive Dna Elements

With 82 species currently described, the genus Leptodactylus is the most diverse and representative one in the family Leptodactylidae. Concerning chromosomal organization, this genus represents an interesting and underexplored group since data from molecular cytogenetics are incipient, and little is known about the organization and distribution of repetitive DNA elements in the karyotypes. In this sense, this study aimed at providing a comparative analysis in 4 Leptodactylus species (L. macrosternum, L. pentadactylus, L. fuscus, and Leptodactylus cf. podicipinus), combining conventional cytogenetics (Giemsa staining, C-banding, and AgNOR staining) and mapping of molecular markers (18S rDNA, telomeric and microsatellite probes), to investigate mechanisms underlying their karyotype differentiation process. The results showed that all species had karyotypes with 2n = 22 and FN = 44, except for Leptodactylus cf. podicipinus which presented FN = 36. The 18S rDNA was observed in pair 8 of all analyzed species (corresponding to pair 4 in L. pentadactylus), coinciding with the secondary constrictions and AgNOR staining. FISH with microsatellite DNA probes demonstrated species-specific patterns, as well as an association of these repetitive sequences with constitutive heterochromatin blocks and ribosomal DNA clusters, revealing the dynamics of microsatellites in the genome of the analyzed species. In summary, our data demonstrate an ongoing process of genomic divergence inside species with almost similar karyotype, driven most likely by a series of pericentric inversions, followed by differential accumulation of repetitive sequences.

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Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

Applied and Environmental Microbiology ◽

10.1128/aem.01177-14 ◽

2014 ◽

Vol 80 (17) ◽

pp. 5503-5514 ◽

Cited By ~ 40

Author(s):

Christophe Habib ◽

Armel Houel ◽

Aurélie Lunazzi ◽

Jean-François Bernardet ◽

Anne Berit Olsen ◽

...

Keyword(s):

Sequence Analysis ◽

Parallel Evolution ◽

Phylogenetic Reconstruction ◽

Multilocus Sequence Analysis ◽

Fish Pathogens ◽

Long Distance ◽

Marine Aquaculture ◽

Content Type ◽

The Family ◽

Cohesive Group

ABSTRACTThe genusTenacibaculum, a member of the familyFlavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogenTenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the speciesT. maritimumconstitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoringTenacibaculuminfections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related toT. dicentrarchi, a recently described species.

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New morphological data and molecular diagnostic of Henneguya friderici (Myxozoa: Myxobolidae), a parasite of Leporinus friderici (Osteichthyes: Anostomidae) from southeastern Brazil

Revista Brasileira de Parasitologia Veterinária ◽

10.1590/s1984-29612017010 ◽

2017 ◽

Vol 26 (1) ◽

pp. 81-88 ◽

Cited By ~ 2

Author(s):

Letícia Poblete Vidal ◽

José Luis Luque

Keyword(s):

Body Length ◽

18S Rdna ◽

Genetic Similarity ◽

Morphological Data ◽

Southeastern Brazil ◽

Molecular Diagnostic ◽

Similarity Analysis ◽

Rdna Sequencing ◽

The Family ◽

Gill Filaments

Abstract The myxozoan Henneguya friderici is a parasite of the gills, intestine, kidney and liver of Leporinus friderici, a characiform fish belonging to the family Anostomidae. Forty-two specimens of L. friderici that had been caught in the Mogi Guaçú River, state of São Paulo, were studied. Elongated white plasmodia were found in the gill filaments of 10 host specimens (24%). The mature spores had an ellipsoidal body with polar capsules of equal size and caudal length greater than body length. This study also described 18S rDNA sequencing of H. friderici infecting the gill filaments. This produced a sequence of 1050 bp that demonstrated significant genetic differences with previously described species of Henneguya. Similarity analysis using sequences from species that clustered closest to those produced by this study showed that the species with greatest genetic similarity to H. friderici was H. leporinicola, with 94% similarity.

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Inference about Monophyly of the Family Oedipodidae and the Classification of Subfamilies Based on 16S rDNA Sequences

International Journal of Biotechnology for Wellness Industries ◽

10.6000/1927-3037.2014.03.03.4 ◽

2014 ◽

Vol 3 (3) ◽

pp. 102-110

Author(s):

Guo-Fang Jiang ◽

Dian-Feng Liu

Keyword(s):

16S Rdna ◽

Rdna Sequences ◽

16S Rdna Sequences ◽

The Family

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Stigmatic surface in the Vochysiaceae: reproductive and taxonomic implications

Acta Botanica Brasilica ◽

10.1590/s0102-33062009000300018 ◽

2009 ◽

Vol 23 (3) ◽

pp. 780-785 ◽

Cited By ~ 6

Author(s):

Renata Carmo-Oliveira ◽

Berta Lange de Morretes

Keyword(s):

Histological Analysis ◽

Developmental Stages ◽

Phylogenetic Reconstruction ◽

Breeding Systems ◽

Stigmatic Surface ◽

Central Brazil ◽

Fresh Material ◽

The Family ◽

Taxonomic Implications ◽

Trees And Shrubs

The Vochysiaceae are Neotropical trees and shrubs, common in the savanna areas in Central Brazil (Cerrados). The family has been traditionally divided into two tribes: Erismeae, with three genera, and Vochysieae, with five genera. We investigated the stigmatic surface of six Vochysiaceae species, belonging to four genera of Vochysieae: Vochysia, Salvertia, Callisthene and Qualea. Flowers and buds at different developmental stages were collected. Morphological features were observed on fresh material and stigmatic receptivity was inferred based on esterasic activity. Pistils were fixed and embedded in paraplast and sectioned on a rotary microtome; the sections were stained before histological analysis. Stigmas of open flowers were also observed by scanning electron microscopy. Stigmas of all species were wet and showed esterasic activity at pre-anthesis and anthesis stages. Stigmatic surface was continuous with transmitting tissue of glandular nature. Vochysia and Salvertia stigmatic surfaces were formed by multicelular uniseriate hairs, and species of the remaining genera showed papillate surface. The exudate over mature stigmas in all species flowed without rupture of stigmatic surface and pollen tubes grew down between hairs or papillae. Differences on the stigmatic surface agreed with a phylogenetic reconstruction that separated two clades and indicated that Vochysieae is not monophyletic. Stigmatic features could not be associated with pollination and breeding systems.

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Phylogenetic relationships among the clownfish-hosting sea anemones

10.1101/560045 ◽

2019 ◽

Author(s):

Benjamin M. Titus ◽

Charlotte Benedict ◽

Robert Laroche ◽

Luciana C. Gusmão ◽

Vanessa Van Deusen ◽

...

Keyword(s):

Phylogenetic Reconstruction ◽

Taxonomic Revision ◽

Sea Anemone ◽

Coral Triangle ◽

Sea Anemones ◽

Ecological Processes ◽

Holistic Understanding ◽

The Family ◽

Genus 2 ◽

Insight Into

AbstractThe clownfish-sea anemone symbiosis has been a model system for understanding fundamental evolutionary and ecological processes. However, our evolutionary understanding of this symbiosis comes entirely from studies of clownfishes. A holistic understanding of a model mutualism requires systematic, biogeographic, and phylogenetic insight into both partners. Here, we conduct the largest phylogenetic analysis of sea anemones (Order Actiniaria) to date, with a focus on expanding the biogeographic and taxonomic sampling of the 10 nominal clownfish-hosting species. Using a combination of mtDNA and nuDNA loci we test 1) the monophyly of each clownfish-hosting family and genus, 2) the current anemone taxonomy that suggests symbioses with clownfishes evolved multiple times within Actiniaria, and 3) whether, like the clownfishes, there is evidence that host anemones have a Coral Triangle biogeographic origin. Our phylogenetic reconstruction demonstrates widespread poly-and para-phyly at the family and genus level, particularly within the family Stichodactylidae and genus Sticodactyla, and suggests that symbioses with clownfishes evolved minimally three times within sea anemones. We further recover evidence for a Tethyan biogeographic origin for some clades. Our data provide the first evidence that clownfish and some sea anemone hosts have different biogeographic origins, and that there may be cryptic species of host anemones. Finally, our findings reflect the need for a major taxonomic revision of the clownfish-hosting sea anemones.

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Phylogeny of the family Pasteurellaceae based on rpoB sequences

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.03043-0 ◽

2004 ◽

Vol 54 (4) ◽

pp. 1393-1399 ◽

Cited By ~ 153

Author(s):

Bożena Korczak ◽

Henrik Christensen ◽

Stefan Emler ◽

Joachim Frey ◽

Peter Kuhnert

Keyword(s):

16S Rdna ◽

Dna Hybridization ◽

Gene Encoding ◽

Phylogenetic Studies ◽

Study Selection ◽

Gene Sequence Analysis ◽

Rdna Sequencing ◽

The Family ◽

Type Strains ◽

Selection Of

Sequences of the gene encoding the β-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA–DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.

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16S rRNA and Multilocus Phylogenetic Analysis of the Iron Oxidizing Acidophiles of the Acidiferrobacteraceae Family

Solid State Phenomena ◽

10.4028/www.scientific.net/ssp.262.339 ◽

2017 ◽

Vol 262 ◽

pp. 339-343 ◽

Cited By ~ 1

Author(s):

Francisco Issotta ◽

Paulo C. Covarrubias ◽

Ana Moya-Beltrán ◽

Sören Bellenberg ◽

Christian Thyssen ◽

...

Keyword(s):

Draft Genome ◽

Phylogenetic Reconstruction ◽

Taxonomic Status ◽

Genomic Diversity ◽

Evolutionary Information ◽

Comparative Genomic ◽

The Family ◽

Sulfur Oxidizer ◽

Acid Waters ◽

Type Strains

The family Acidiferrobacteraceae (order Acidiferrobacterales) currently contains three genera of chemolithoautotrophs: Sulfuricaulis (2016), Sulfurifustis (2015) and Acidiferrobacter (2011). While the two former are neutrophilic sulfur oxidizers isolated from lake sediments in Japan, the latter is an extremely acidophilic, moderately osmophilic, thermotolerant iron/sulfur oxidizer known to occur in macroscopic streamers in Rio Tinto, Spain and in acid waters worldwide. The type strains of both Sulfuricaulis limnicola (HA5T) and Sulfurifustis variabilis (skN76T) have been sequenced, and the draft genome of the ZJ isolate of Acidiferrobacter thiooxydans (MDCF01) has recently been deposited in public databases. Despite this fact, little evidence on the genomic diversity and evolution of this group has been presented so far. Using comparative genomic analyses and phylogenetic reconstruction strategies, we explored the evolutionary information contained in the available genome sequences to shed light on the taxonomic status of a novel isolate of the genus Acidiferrobacter (SP-III/3; DSM 27195).

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