scholarly journals Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 138 ◽  
Author(s):  
Dennis Knierim ◽  
Quentin Barrière ◽  
Ioana Grigoras ◽  
Stephan Winter ◽  
Heinrich-Josef Vetten ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Plant Virus ◽  
Type Species ◽  
Subterranean Clover ◽  
Genome Composition ◽  
Single Stranded Dna ◽  
Typical Member ◽  
Subterranean Clover Stunt Virus ◽  
The Family

Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plants to verify its genome composition and found the missing genome components. These results indicated that SCSV also has eight genome components and is a typical member of the genus Nanovirus.

scholarly journals Actibacterium mucosum gen. nov., sp. nov., a marine alphaproteobacterium from Mediterranean seawater

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2858-2864 ◽  
Author(s):  
Teresa Lucena ◽  
María A. Ruvira ◽  
Esperanza Garay ◽  
M. Carmen Macián ◽  
David R. Arahal ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Cellular Fatty Acid ◽  
Major Cellular Fatty Acid ◽  
Content Type ◽  
Separate Branch ◽  
The Family ◽  
Novel Genus And Species

Strain R46T, a marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. It is an aerobic chemo-organotrophic, mesophilic and slightly halophilic organism, with complex ionic requirements. Phylogenetic analyses based on the 16S rRNA and gyrB gene sequences showed that strain R46T formed a separate branch within the family Rhodobacteraceae , bearing similarities below 94.7 and 80.3 %, respectively, to any other recognized species. It contained Q10 as the predominant isoprenoid quinone and C18 : 1ω7c/C18 : 1ω6c as the major cellular fatty acid. Phosphatidylglycerol was the only identified polar lipid, although other lipids were also detected. The DNA G+C content of the genomic DNA was 61.3 mol%. On the basis of extensive phenotypic and phylogenetic comparative analysis, it is concluded that the strain represents a novel genus and species, for which the name Actibacterium mucosum gen. nov., sp. nov. is proposed. The type strain of the type species is Actibacterium mucosum R46T ( = CECT 7668T = KCTC 23349T).

Molecular phylogeny of the freshwater prawn genus Macrobrachium (Decapoda, Palaemonidae), with emphasis on the relationships among selected American species

2010 ◽  
Vol 24 (2) ◽  
pp. 194 ◽  
Author(s):  
Leonardo G. Pileggi ◽  
Fernando L. Mantelatto
Keyword(s):  
Phylogenetic Analysis ◽  
Larval Development ◽  
Dna Sequences ◽  
Type Species ◽  
Species Complex ◽  
Taxonomic Status ◽  
Freshwater Prawn ◽  
The Family ◽  
Different Types ◽  
History Of

The genus Macrobrachium Bate, 1868 is one of the best examples of widespread crustacean genera distributed globally throughout tropical and subtropical waters. Previous investigators have noted the systematic complexity of the group, and have suggested rearrangements within the family Palaemonidae. Our phylogenetic analysis of new mitochondrial DNA sequences of 58 species of Macrobrachium distributed mainly in America support the hypothesis of monophyly of this genus, if Cryphiops Dana, 1852 is accepted as a generic synonym. We concluded that the independent evolution of different types of life cycle (abbreviated larval development – ALD and extended larval development – ELD) must have occurred more than once in the history of the group. Similarly, we also concluded that the current type species of the genus, Macrobrachium americanum Bate, 1868, should not be considered valid, as previously proposed. The synonymy of two members of the ‘olfersi’ species complex (M. birai Lobão, Melo & Fernandes, 1986 and M. holthuisi Genofre & Lobão, 1978) with M. olfersi (Wiegmann, 1836) was confirmed. Similar results were found in comparing M. petronioi Melo, Lobão & Fernandes, 1986 and M. potiuna (Müller, 1880), in which the genetic divergence placed M. petronioi within the level of intraspecific variation of M. potiuna. The taxonomic status of the genus Cryphiops, as well as theories on the origin of Macrobrachium, is also called into question.

Unity in diversity: phylogenetics and taxonomy of Rhabdoweisiaceae (Dicranales, Bryophyta)

2020 ◽  
Author(s):  
Vladimir E Fedosov ◽  
Alina V Fedorova ◽  
Juan Larraín ◽  
Marina B Santos ◽  
Michael Stech ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Divergent Evolution ◽  
New Genera ◽  
Morphological Heterogeneity ◽  
Phylogenetic Reconstructions ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Unity In Diversity

Abstract Molecular phylogenetic reconstructions of Rhabdoweisiaceae based on plastid (trnS-rps4 and trnL-F) and mitochondrial (nad5) DNA sequences and a comprehensive taxon sampling were performed, including 15 out of 16 genera currently attributed to the family, taxa recently found belonging to Rhabdoweisiaceae and expanded outgroups from related families of Dicranidae. The suggested revised delimitation of the family comprises Camptodontium (previously referred to Dicranaceae), three subaquatic species currently classified in Blindia (Seligeriaceae), and Glyphomitrium (previously referred to Ptychomitriaceae, Erpodiaceae or its own family) and Eucamptodon perichaetialis (the type species of the genus, previously referred to Dicnemonaceae). The emended delimitation of Rhabdoweisiaceae thus adds to the already high morphological heterogeneity resulting from the divergent evolution of specialized traits in different lineages of epiphytes and saxicolous hygrophytes. Taxonomic inferences from the phylogenetic analyses include segregation of three new genera, Pseudoblindia (for species currently recognized as Kiaeria falcata, Blindia robusta, B. lewinskyae and B. inundata), Ripariella (for Kiaeria riparia) and Brideliella (for Oncophorus wahlenbergii, O. demetrii and Symblepharis lindigii). Hollia is reinstated for the dicnemonoid Australasian species previously classified in Eucamptodon. Additionally, we propose to merge (1) Oreoweisia, Pocsiella and Pseudohyophila with Cynodontium, and (2) Kiaeria s.s. with Arctoa. Furthermore, we propose to limit Oncophorus to O. virens and O. integerrimus and expand the circumscription of Symblepharis to accommodate O. crispifolius, O. dendrophilus, O. elongatus and O. raui. The generic status and inclusion in Rhabdoweisiaceae are confirmed for Cnestrum and the recently described Notocynodontium, and the exclusion of Amphidium, Dichodontium, Holodontium and Hymenoloma from the family is supported.

Three new species, two new genera, and new family Biphragmosagittidae (Сhaetognatha) from Southwest Pacific Ocean

2011 ◽  
Vol 20 (1) ◽  
pp. 161-173
Author(s):  
A.P. Kassatkina
Keyword(s):  
New Species ◽  
Type Species ◽  
Morphological Characters ◽  
The Body ◽  
New Order ◽  
New Genera ◽  
New Family ◽  
The Family ◽  
Three New Species

Resuming published and own data, a revision of classification of Chaetognatha is presented. The family Sagittidae Claus & Grobben, 1905 is given a rank of subclass, Sagittiones, characterised, in particular, by the presence of two pairs of sac-like gelatinous structures or two pairs of fins. Besides the order Aphragmophora Tokioka, 1965, it contains the new order Biphragmosagittiformes ord. nov., which is a unique group of Chaetognatha with an unusual combination of morphological characters: the transverse muscles present in both the trunk and the tail sections of the body; the seminal vesicles simple, without internal complex compartments; the presence of two pairs of lateral fins. The only family assigned to the new order, Biphragmosagittidae fam. nov., contains two genera. Diagnoses of the two new genera, Biphragmosagitta gen. nov. (type species B. tarasovi sp. nov. and B. angusticephala sp. nov.) and Biphragmofastigata gen. nov. (type species B. fastigata sp. nov.), detailed descriptions and pictures of the three new species are presented.

scholarly journals Characterization of squalene synthase gene from Gymnema sylvestre R. Br.

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Competitive Inhibition ◽  
Sequence Data ◽  
Homology Model ◽  
Squalene Synthase ◽  
Gymnema Sylvestre ◽  
Gardenia Jasminoides ◽  
Ramachandran Plots ◽  
Flanking Regions

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.

Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽  
2010 ◽  
Vol 53 (10) ◽  
pp. 769-777 ◽  
Author(s):  
Melanie Mehes-Smith ◽  
Paul Michael ◽  
Kabwe Nkongolo
Keyword(s):  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Pinus Monticola ◽  
The Family ◽  
Species Specific ◽  
Rapd And Issr ◽  
Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

Rapid Amplification of Uncharacterized Transposon-tagged DNA Sequences from Genomic DNA

Yeast ◽  
1997 ◽  
Vol 13 (3) ◽  
pp. 233-240 ◽  
Author(s):  
KRISTIN T. CHUN ◽  
HOWARD J. EDENBERG ◽  
MARK R. KELLEY ◽  
MARK G. GOEBL
Keyword(s):  
Dna Sequences ◽  
Genomic Dna ◽  
Rapid Amplification

Three new cribrimorph bryozoans (order Cheilostomatida) from the early Miocene of Argentina, with a discussion on spinocystal shield morphologies

2021 ◽  
pp. 1-15
Author(s):  
Juan López-Gappa ◽  
Leandro M. Pérez ◽  
Ana C.S. Almeida ◽  
Débora Iturra ◽  
Dennis P. Gordon ◽  
...  
Keyword(s):  
Type Species ◽  
Systematic Position ◽  
Early Miocene ◽  
Morphological Data ◽  
Fossil Species ◽  
Extant Species ◽  
The Family ◽  
Subjective Synonym

Abstract Bryozoans with calcified frontal shields formed by the fusion of costae, collectively constituting a spinocyst, are traditionally assigned to the family Cribrilinidae. Today, this family is regarded as nonmonophyletic. In the Argentine Cenozoic, cribrilinids were until recently represented by only two fossil species from the Paleocene of Patagonia. This study describes the first fossil representatives of Jolietina and Parafigularia: J. victoria n. sp. and P. pigafettai n. sp., respectively. A fossil species of Figularia, F. elcanoi n. sp., is also described. The material comes from the early Miocene of the Monte León and Chenque formations (Patagonia, Argentina). For comparison, we also provide redescriptions of the remaining extant species of Jolietina: J. latimarginata (Busk, 1884) and J. pulchra Canu and Bassler, 1928a. The systematic position of some species previously assigned to Figularia is here discussed. Costafigularia n. gen. is erected, with Figularia pulcherrima Tilbrook, Hayward, and Gordon, 2001 as type species. Two species previously assigned to Figularia are here transferred to Costafigularia, resulting in C. jucunda n. comb. and C. tahitiensis n. comb. One species of Figularia is reassigned to Vitrimurella, resulting in V. ampla n. comb. The family Vitrimurellidae is here reassigned to the superfamily Cribrilinoidea. The subgenus Juxtacribrilina is elevated to genus rank. Inferusia is regarded as a subjective synonym of Parafigularia. Parafigularia darwini Moyano, 2011 is synonymized with I. taylori Kuklinski and Barnes, 2009, resulting in Parafigularia taylori n. comb. Morphological data suggest that these genera comprise different lineages, and a discussion on the disparities among cribrilinid (sensu lato) spinocysts is provided. UUID: http://zoobank.org/215957d3-064b-47e2-9090-d0309f6c9cd8

Early Paleozoic Hyolitha from North America: reexamination of Walcott's and Resser's type specimens

1988 ◽  
Vol 62 (2) ◽  
pp. 218-233 ◽  
Author(s):  
John Mark Malinky
Keyword(s):  
North America ◽  
Lower Cambrian ◽  
Type Species ◽  
New Genus ◽  
Early Paleozoic ◽  
Type Specimens ◽  
Middle Cambrian ◽  
Upper Cambrian ◽  
New Family ◽  
The Family

Concepts of the family Hyolithidae Nicholson fide Fisher and the genera Hyolithes Eichwald and Orthotheca Novak have been expanded through time to encompass a variety of morphologically dissimilar shells. The Hyolithidae is here considered to include only those hyolithid species which have a rounded (convex) dorsum; slopes on the dorsum are inflated, and the venter may be flat or slightly inflated. Hyolithes encompasses species which possess a low dorsum and a prominent longitudinal sulcus along each edge of the dorsum; the ligula is short and the apertural rim is flared. The emended concept of Orthotheca includes only those species of orthothecid hyoliths which have a subtriangular transverse outline and longitudinal lirae covering the shell on both dorsum and venter.Eighteen species of Hyolithes and one species of Orthotheca from the Appalachian region and Western Interior were reexamined in light of more modern taxonomic concepts and standards of quality for type material. Reexamination of type specimens of H. similis Walcott from the Lower Cambrian of Newfoundland, H. whitei Resser from the Lower Cambrian of Nevada, H. billingsi Walcott from the Lower Cambrian of Nevada, H. gallatinensis Resser from the Upper Cambrian of Wyoming, and H. partitus Resser from the Middle Cambrian of Alabama indicates that none of these species represents Hyolithes. Hyolithes similis is here included under the new genus Similotheca, in the new family Similothecidae. Hyolithes whitei is designated as the type species of the new genus Nevadotheca, to which H. billingsi may also belong. Hyolithes gallatinensis is referred to Burithes Missarzhevsky with question, and H. partitus may represent Joachimilites Marek. The type or types of H. attenuatus Walcott, H. cecrops Walcott, H. comptus Howell, H. cowanensis Resser, H. curticei Resser, H. idahoensis Resser, H. prolixus Resser, H. resseri Howell, H. shaleri Walcott, H. terranovicus Walcott, and H. wanneri Resser and Howell lack shells and/or other taxonomically important features such as a complete aperture, rendering the diagnoses of these species incomplete. Their names should only be used for the type specimens until better preserved topotypes become available for study. Morphology of the types of H.? corrugatus Walcott and “Orthotheca” sola Resser does not support placement in the Hyolitha; the affinities of these species are uncertain.

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