Sequence characterization and phylogenetic analysis of the 5S ribosomal DNA in species of the family Batrachoididae

5S ribosomal DNA (rDNA) sequences were analyzed in four species belonging to different genera of the fish family Batrachoididae. Several 5S rDNA variants differing in their non-transcribed spacers (NTSs) were found and were grouped into two main types. Two species showed both types of 5S rDNA, whereas the other two species showed only one type. One type of NTS of Amphichthys cryptocentrus showed a high polymorphism due to several deletions and insertions, and phylogenetic analysis showed a between-species clustering of this type of NTS in Amphichthys cryptocentrus. These results suggest a clear differentiation in the model of 5S rDNA evolution of these four species of Batrachoididae, which appear to have been subject to processes of concerted evolution and birth-and-death evolution with purifying selection.

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Phylogeny of dracunculoid nematodes (Chromadorea: Rhabditida: Spirurina: Dracunculoidea) from some Eurasian freshwater fishes

Zootaxa ◽

10.11646/zootaxa.4858.4.3 ◽

2020 ◽

Vol 4858 (4) ◽

pp. 521-541

Author(s):

SERGEY G. SOKOLOV ◽

ALEXANDER P. KALMYKOV ◽

SVETLANA V. MALYSHEVA

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationship ◽

Ribosomal Dna ◽

Phylogenetic Relationships ◽

Type Species ◽

Freshwater Fishes ◽

Ssu Rdna ◽

Lsu Rdna ◽

Rdna Sequences ◽

The Family

Sets of small ribosomal DNA (SSU rDNA) and large ribosomal DNA (LSU rDNA) sequences were obtained for Philometroides moraveci Vismanis & Yunchis, 1994, Philometra kotlani (Molnár, 1969), Philometra rischta Skrjabin, 1923, Philometra cf. obturans (Prenant, 1886) (Philometridae), Sinoichthyonema amuri (Garkavi, 1972), Agrachanus scardinii (Molnár, 1966), Kalmanmolnaria intestinalis (Dogiel & Bychowsky, 1934) and Skrjabillanus tincae Shigin & Shigina, 1958 (Skrjabillanidae). Phylogenetic analysis of SSU rDNA data shows that dracunculoid nematodes are divided into two well-supported clades designated as Clade I and Clade II, respectively. Clade I includes the type species of the genus Philonema Kuitunen-Ekbaum, 1933, some species from the family Daniconematidae Moravec & Køie, 1987 and two subfamilies of skrjabillanids, Skrjabillaninae Shigin & Shigina, 1958 and Esocineminae Moravec, 2006. Clade II unites species from the families Dracunculidae Stiles, 1907, Micropleuridae Baylis & Daubney, 1926 and Philometridae Baylis & Daubney, 1926. Within the Philometridae, there are several well-supported groups of species, one of which unites freshwater Philometra spp. from the Palearctic cyprinids, identified as P. kotlani, P rischta, P. ovata (Zeder, 1803) and P. cyprinirutili (Creplin, 1825). However, the phylogenetic relationships of most philometrids are unresolved. An analysis of partial SSU and LSU rDNA sequences indicates that there is no direct phylogenetic relationship between Agrachanus Tikhomirova, 1971 (type species Skrjabillanus scardinii Molnár, 1966) and Skrjabillanus Shigin & Shigina, 1958 (type species Sk. tincae), which means that the genus Agrachanus can be resurrected. Our study confirms that Philonematinae Ivashkin, Sobolev & Khromova, 1971 should be elevated to the family rank. We formally establish the family Philonematidae Ivashkin, Sobolev & Khromova, 1971 stat. nov. We also suggest combining the superfamilies Dracunculoidea Stiles, 1907 and Camallanoidea Railliet & Henry, 1915 into the infraorder Camallanomorpha Roberts, Janovy & Nadler, 2013.

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New Data Define the Molecular Phylogeny and Taxonomy of Four Freshwater Suctorian Ciliates With Redefinition of Two Families Heliophryidae and Cyclophryidae (Ciliophora, Phyllopharyngea, Suctoria)

Frontiers in Microbiology ◽

10.3389/fmicb.2021.768724 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mingzhen Ma ◽

Yuqing Li ◽

Qingxiang Yuan ◽

Xuetong Zhao ◽

Khaled A. S. Al-Rasheid ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Molecular Phylogeny ◽

Phylogenetic Analyses ◽

Ssu Rdna ◽

Freshwater Lake ◽

The Other ◽

Sufficient Evidence ◽

Rdna Sequences ◽

The Family ◽

Molecular Phylogenetic

Four suctorian ciliates, Cyclophrya magna Gönnert, 1935, Peridiscophrya florea (Kormos & Kormos, 1958) Dovgal, 2002, Heliophrya rotunda (Hentschel, 1916) Matthes, 1954 and Dendrosoma radians Ehrenberg, 1838, were collected from a freshwater lake in Ningbo, China. The morphological redescription and molecular phylogenetic analyses of these ciliates were investigated. Phylogenetic analyses inferred from SSU rDNA sequences show that all three suctorian orders, Endogenida, Evaginogenida, and Exogenida, are monophyletic and that the latter two clusters as sister clades. The newly sequenced P. florea forms sister branches with C. magna, while sequences of D. radians group with those from H. rotunda within Endogenida. The family Heliophryidae, which is comprised of only two genera, Heliophrya and Cyclophrya, was previously assigned to Evaginogenida. There is now sufficient evidence, however, that the type genus Heliophrya reproduces by endogenous budding, which corresponds to the definitive feature of Endogenida. In line with this and with the support of molecular phylogenetic analyses, we therefore transfer the family Heliophryidae with the type genus Heliophrya to Endogenida. The other genus, Cyclophrya, still remains in Evaginogenida because of its evaginative budding. Therefore, combined with morphological and phylogenetic analysis, Cyclophyidae are reactivated, and it belongs to Evaginogenida.

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A phylogeny inferred from large-subunit (26S) ribosomal DNA sequences suggests that the family Dasypogonaceae is closely aligned with the Restionaceae allies

Australian Systematic Botany ◽

10.1071/sb02006 ◽

2002 ◽

Vol 15 (6) ◽

pp. 749 ◽

Cited By ~ 6

Author(s):

Ray Neyland

Keyword(s):

Phylogenetic Analysis ◽

Ribosomal Dna ◽

Dna Sequences ◽

Large Subunit ◽

Monophyletic Group ◽

26S Rdna ◽

Rdna Sequences ◽

Australian Family ◽

The Family

The Dasypogonaceae is a small Australian family composed of four genera. Previous systematic studies have failed to place the Dasypogonaceae with confidence. The present phylogenetic analysis, inferred from large-subunit (26S) rDNA sequences, strongly suggests that the Dasypogonaceae form a monophyletic group with the taxa referred to as the Restionaceae allies (i.e. Anarthriaceae, Centrolepidaceae, Ecdeiocoleaceae).

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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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The 5S rRNA gene units in ancestral two-rowed barley (Hordeum spontaneum C. Koch) and bulbous barley (H. bulbosum L.): sequence analysis and phylogenetic relationships with the 5S rDNA units of cultivated barley (H. vulgare L.)

Genome ◽

10.1139/g96-019 ◽

1996 ◽

Vol 39 (1) ◽

pp. 140-149 ◽

Cited By ~ 36

Author(s):

Bernard R. Baum ◽

Douglas A. Johnson

Keyword(s):

Phylogenetic Analysis ◽

5S Rdna ◽

Hordeum Spontaneum ◽

Wild Relatives ◽

5S Rrna ◽

Rrna Genes ◽

Rrna Gene ◽

Sequence Comparisons ◽

Rdna Sequences ◽

Cultivated Barley

5S rRNA genes from several accessions of Hordeum spontaneum and Hordeum bulbosum, wild relatives of cultivated barley, Hordeum vulgare, have been amplified by the polymerase chain reaction, cloned, and sequenced. Evaluation of aligned sequences along with principal coordinate analysis demonstrates that the two classes of 5S rDNA sequences found in cultivated barley, and subclasses (groups) of these sequences, can also be found in its closest wild relatives. The two classes of units, formerly categorized as containing short or long 5S rDNA repeats, are distinguishable by the presence or absence of a TAG repeating unit. Sequence comparisons of individual clones (units) isolated from different species have allowed us to confirm that orthology exists for several groups. This demonstration of orthologous groups suggests that the 5S rDNA sequence may be useful for further phylogenetic analysis in the genus Hordeum and possibly in the Triticeae. Key words : 5S rDNA, barley, sequence diversity, phylogenetic analysis.

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Deniquelata barringtoniae gen. et sp. nov., associated with leaf spots of Barringtonia asiatica

Phytotaxa ◽

10.11646/phytotaxa.105.1.2 ◽

2013 ◽

Vol 105 (1) ◽

pp. 11 ◽

Cited By ~ 20

Author(s):

HIRAN A. ARIYAWANSA ◽

SAJEEWA S.N. MAHARACHCHIKUMBURA ◽

SAMANTHA C.KARUNARATHNE ◽

EKACHAI CHUKEATIROTE ◽

ALI H. BAHKALI ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Genus ◽

Sequence Data ◽

Molecular Data ◽

The Other ◽

New Genus And Species ◽

Leaf Spots ◽

The Family ◽

Pathogenicity Testing

Deniquelata barringtoniae gen. et sp. nov. (Montagnulaceae) forms numerous ascomata on distinct zonate leaf spots of Barringtonia asiatica (Lecythidaceae). We isolated this taxon and sequenced the 18S and 28S nrDNA. The result of phylogenetic analysis based on 18S and 28S nrDNA sequence data indicate that the genus belongs in the family Montagnulaceae, Dothideomycetes, Ascomycota. The ascomata are immersed, dark brown to black, with bitunicate asci and brown, muriform ascospores. Deniquelata is distinguished from the other genera in Montagnulaceae based on its short, broad, furcate and pedicellate asci, verruculose ascospores with short narrow pseudoparaphyses with parasitic naturee and this is also supported by molecular data. A new genus and species is therefore introduced to accommodate this taxon. We used isolates of this species to show via pathogenicity testing that the taxon is able to cause leaf spots when leaves are pin pricked.

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The Complete Plastid Genomes of Seven Sargassaceae Species and Their Phylogenetic Analysis

Frontiers in Plant Science ◽

10.3389/fpls.2021.747036 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ruoran Li ◽

Xuli Jia ◽

Jing Zhang ◽

Shangang Jia ◽

Tao Liu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Brown Algae ◽

Linear Analysis ◽

The Other ◽

Genomic Evolution ◽

Protein Coding ◽

Protein Coding Genes ◽

Plastid Genomes ◽

The Family ◽

Generation Sequencing

Sargassum is one of the most important genera of the family Sargassaceae in brown algae and is used to produce carrageenan, mannitol, iodine, and other economic substances. Here, seven complete plastid genomes of Sargassum ilicifolium var. conduplicatum, S. graminifolium, S. phyllocystum, S. muticum, S. feldmannii, S. mcclurei, and S. henslowianum were assembled using next-generation sequencing. The sizes of the seven circular genomes ranged from 124,258 to 124,563 bp, with two inverted regions and the same set of plastid genes, including 139 protein-coding genes (PCGs), 28 transfer (t)RNAs, and 6 ribosomal (r)RNAs. Compared with the other five available plastid genomes of Fucales, 136 PCGs were conserved, with two common ones shared with Coccophora langsdorfii, and one with S. fusiforme and S. horneri. The co-linear analysis identified two inversions of trnC(gca) and trnN(gtt) in ten Sargassum species, against S. horneri and C. langsdorfii. The phylogenetic analysis based on the plastid genomes of 55 brown algae (Phaeophyceae) showed four clades, whose ancient ancestor lived around 201.42 million years ago (Mya), and the internal evolutionary branches in Fucales started to be formed 92.52 Mya, while Sargassum species were divided into two subclades 14.33 Mya. Our novel plastid genomes provided evidence for the speciation of brown algae and plastid genomic evolution events.

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A new phylogenetic analysis of the Sphaerotheriida (Diplopoda) with a revision of the Australian giant pill-millipedes

Invertebrate Systematics ◽

10.1071/is13048 ◽

2014 ◽

Vol 28 (2) ◽

pp. 196 ◽

Cited By ~ 5

Author(s):

Thomas Wesener

Keyword(s):

Phylogenetic Analysis ◽

South African ◽

Type Species ◽

Morphological Characters ◽

The Other ◽

Current Position ◽

The South ◽

Sem Images ◽

New Family ◽

The Family

Cyliosoma Pocock, 1895, the oldest available genus name for Australian giant pill-millipedes, is revised with a redescription of its type species, Sphaerotherium angulatum Butler, 1878. All 16 species of Epicyliosoma Silvestri, 1917 are transferred to Cyliosoma, together with two species, Sphaerotherium fraternum Butler, 1872 and S. marginepunctatum Karsch, 1881, which are redescribed here. A new phylogenetic analysis of the Sphaerotheriida was conducted using 100 morphological characters and including two Cyliosoma species and four recently described or redescribed species of the family Zephroniidae. Most character states are illustrated for Cyliosoma, including the first SEM images of a member of the genus. Cyliosoma is neither closely related to the South African Sphaerotherium, nor to the other Australian genus, Procyliosoma, and is here placed in a new family, Cyliosomatidae. The monotypic Australian genus Cynotelopus Jeekel, 1986 is also referred to the Cyliosomatidae. The current position of the Cyliosomatidae is in a trichotomy including the South African Sphaerotheriidae and the Malagasy–Indian Arthrosphaeridae.

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Evolutionary Dynamics of 5S rDNA and Recurrent Association of Transposable Elements in Electric Fish of the Family Gymnotidae (Gymnotiformes): The Case of Gymnotus mamiraua

Cytogenetic and Genome Research ◽

10.1159/000449431 ◽

2016 ◽

Vol 149 (4) ◽

pp. 297-303 ◽

Cited By ~ 12

Author(s):

Maelin da Silva ◽

Patricia Barbosa ◽

Roberto F. Artoni ◽

Eliana Feldberg

Keyword(s):

Electric Fish ◽

Evolutionary Dynamics ◽

Chromosomal Location ◽

Molecular Mapping ◽

5S Rdna ◽

Mapping Data ◽

Rdna Sequences ◽

Rdna Sites ◽

The Family

Gymnotidae is a family of electric fish endemic to the Neotropics consisting of 2 genera: Electrophorus and Gymnotus. The genus Gymnotus is widely distributed and is found in all of the major Brazilian river systems. Physical and molecular mapping data for the ribosomal DNA (rDNA) in this genus are still scarce, with its chromosomal location known in only 11 species. As other species of Gymnotus with 2n = 54 chromosomes from the Paraná-Paraguay basin, G. mamiraua was found to have a large number of 5S rDNA sites. Isolation and cloning of the 5S rDNA sequences from G. mamiraua identified a fragment of a transposable element similar to the Tc1/mariner transposon associated with a non-transcribed spacer. Double fluorescence in situ hybridization analysis of this element and the 5S rDNA showed that they were colocalized on several chromosomes, in addition to acting as nonsyntenic markers on others. Our data show the association between these sequences and suggest that the Tc1 retrotransposon may be the agent that drives the spread of these 5S rDNA-like sequences in the G. mamiraua genome.

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Phylogeny of the Anomura (Decapoda, Crustacea): Spermatozoa and spermatophore morphological evidence

Contributions to Zoology ◽

10.1163/18759866-06702002 ◽

1997 ◽

Vol 67 (2) ◽

pp. 125-141 ◽

Cited By ~ 37

Author(s):

Christopher C. Tudge

Keyword(s):

Phylogenetic Analysis ◽

Decapod Crustacean ◽

Sister Group ◽

Morphological Characters ◽

The Other ◽

Monophyletic Group ◽

Morphological Evidence ◽

Monophyletic Clade ◽

The Family ◽

Single Clade

A phylogenetic analysis of selected anomuran, thalassinidean, and other decapod crustacean taxa, based on spermatozoal ultrastructural characters and spermatophore morphological characters, was performed and the following relationships of the taxa are elucidated from the trees produced. The Anomura are not a monophyletic assemblage, with the lomoid Lomis being exclusive of the remainder of the anomuran taxa, and the thalassinid Thalassina included in the anomuran clade. The synapomorphy joining the majority of the conventional anomuran taxa (Lomis excluded) is the cytoplasmic origin of the microtubular arms. When the palinurid and thalassinoid representatives are separately designated as outgroups, the Astacidea and Brachyura jointly formed a sister group to the Anomura. The superfamilies Thalassinoidea, Paguroidea, and Galatheoidea are not monophyletic groups. In all analyses the anomuran families Coenobitidae and Porcellanidae each form a monophyletic group. The paguroid family Diogenidae is paraphyletic, with the genera Clibanarius and Cancellus separate from a single clade containing the remaining diogenid genera. The families Paguridae and Parapaguridae form a monophyletic clade with the exception of Porcellanopagurus. The two representatives of the family Chirostylidae (Eumunida and Uroptychus) fail to associate with the other species in the Galatheoidea. The taxa in the family Galatheidae are not a monophyletic assemblage. The only investigated hippoid Hippa is portrayed as the sister group to the remainder of the anomuran taxa (with the exception of Lomis).

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