Thraustochytrids are chromists, not Fungi: 18s rRNA signatures of Heterokonta

1994 ◽  
Vol 346 (1318) ◽  
pp. 387-397 ◽  
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Rrna Genes ◽  
Evolutionary Relationships ◽  
Signature Sequences ◽  
A Cell ◽  
Chromophyte Algae ◽  
Marine Protists ◽  
18S Rrna Genes ◽  
Rrna Sequences

Thraustochytrids are a neglected group of non-photosynthetic marine protists characterized by the presence of a sagenogenetosome, an ectoplasmic net and a cell wall composed of non-cellulosic scales. Though originally classified as fungi, they are ultrastructurally closest to the labyrinthulids, which have often been treated as protozoa, but are now usually considered to be more closely related to the heterokont algae. In order to clarify their controversial taxonomic position and evolutionary relationships, we have cloned and sequenced the 18s rRNA genes of the thraustochytrids Thraustochytrium kinnei and Ulkenia profunda . Phylogenetic analysis by several methods confirms earlier suggestions based on ultrastructure that thraustochytrids constitute a deeply divergent branch of the phylum Heterokonta, which is currently classified in the kingdom Chromista. The phylum Heterokonta also includes numerous chromophyte algae (e.g. brown algae and diatoms) as well as the oomycetes. Heterokont 18s rRNA sequences can be distinguished from those of all other eukaryotes by having an AU not a UA base pair at the very base of helix 47 in the V9 region. We also tabulate signature sequences that can be used to characterize 18s rRNA sequences from each of the major heterokont taxa.

Molecular identification and phylogenetic characterisation of Thelohanellus kitauei — short communication

2013 ◽  
Vol 61 (1) ◽  
pp. 30-35 ◽  
Author(s):  
Sang Shin ◽  
Ji Kim ◽  
Casiano Choresca ◽  
Jee Han ◽  
Jin Jun ◽  
...  
Keyword(s):  
18S Rrna ◽  
Short Communication ◽  
Genetic Relationships ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Pcr Product ◽  
Cyprinus Carpio Haematopterus ◽  
18S Rrna Genes ◽  
Rrna Sequences

Thelohanellus kitauei was isolated from the koi Cyprinus carpio haematopterus, and the 18S rRNA gene of T. kitauei was amplified by optimised nested-PCR. The PCR product was sequenced and compared with other 18S rRNA genes of Thelohanellus species to investigate the relationships between their host specificities and infection sites. Based on the 18S rRNA sequences, T. kitauei is most closely related to T. hovorkai (which can infect the intestine). Phylogenetic analysis revealed that T. kitauei was clustered with other Thelohanellus spp. infecting Cyprininae. The present study suggests that the infection site and the host specificity (subfamily level) are reflected in the genetic relationships among Thelohanellus species.

Phylogenetic analysis using rDNA reveals polyphyly of Oplophoridae (Decapoda:Caridea)

2010 ◽  
Vol 24 (2) ◽  
pp. 172 ◽  
Author(s):  
Tin-Yam Chan ◽  
Ho Chee Lei ◽  
Chi Pang Li ◽  
Ka Hou Chu
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Morphological Characters ◽  
The Other ◽  
Rrna Genes ◽  
Deep Channel ◽  
The Family ◽  
Molecular Phylogenetic ◽  
18S Rrna Genes ◽  
Molar Process

Molecular phylogenetic analysis on nine of the ten genera in the caridean family Oplophoridae Dana, 1852, as well as 14 other caridean families using mitochondrial 16S and nuclear 18S rRNA genes, does not support the monophyletic status of Oplophoridae. Two disparate groups of oplophorids are revealed, with different morphological characters and ecology. It is proposed that the family Oplophoridae is restricted to the three genera Oplophorus, Systellaspis and Janicella. These three genera tend to be distributed in shallower water than the other oplophorid genera, and can also be distinguished from them by certain morphological characters. They have a thicker integument, superficial cuticular photophores and larger eyes, and the molar process of their mandibles is greatly reduced or bears a deep channel. The family Acanthephyridae Bate, 1888 is resurrected for the other seven genera, which are generally distributed in deeper water and are characterised by red soft integument, no cuticular photophores, smaller eyes and well-developed molar process of the mandibles without a deep channel. The relationships between these two families and other caridean families could not be clearly resolved in this study.

scholarly journals Molecular Biological Detection of Anaerobic Gut Fungi (Neocallimastigales) from Landfill Sites

2006 ◽  
Vol 72 (8) ◽  
pp. 5659-5661 ◽  
Author(s):  
Robert J. Lockhart ◽  
Michele I. Van Dyke ◽  
Ian R. Beadle ◽  
Paul Humphreys ◽  
Alan J. McCarthy
Keyword(s):  
Phylogenetic Analysis ◽  
Nested Pcr ◽  
18S Rrna ◽  
Cellulose Degradation ◽  
Rrna Genes ◽  
Anaerobic Fungi ◽  
Biological Detection ◽  
Oligonucleotide Primers ◽  
Landfill Sites ◽  
18S Rrna Genes

ABSTRACT Oligonucleotide primers were designed for the 18S rRNA genes of members of the Neocallimastigales and used in a nested PCR protocol to amplify 787-bp fragments of DNA from landfill site samples. The specificities of the primers were confirmed by phylogenetic analysis of the environmental clone sequences, and this method can therefore now be used to investigate the ecology of the obligately anaerobic fungi. To our knowledge, this is the first demonstration of the occurrence of members of the Neocallimastigales outside the mammalian gut, and their distribution across the landfill samples examined here suggests that they are actively involved in cellulose degradation.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

scholarly journals Eucaryotic Diversity in a Hypersaline Microbial Mat

2007 ◽  
Vol 74 (1) ◽  
pp. 329-332 ◽  
Author(s):  
Leah M. Feazel ◽  
John R. Spear ◽  
Alicia B. Berger ◽  
J. Kirk Harris ◽  
Daniel N. Frank ◽  
...  
Keyword(s):  
18S Rrna ◽  
Microbial Mat ◽  
Rrna Genes ◽  
Clone Libraries ◽  
18S Rrna Genes

ABSTRACT To determine the eucaryotic diversity of the hypersaline Guerrero Negro microbial mat, we amplified 18S rRNA genes from DNA extracted from this mat and constructed and analyzed clone libraries. The extent of eucaryotic diversity detected was remarkably low, only 15 species among 890 clones analyzed. Six eucaryotic kingdoms were represented, as well as a novel cluster of sequences. Nematode sequences dominated the clone libraries.

scholarly journals Crenosoma striatum in lungs of European hedgehogs (Erinaceus europeus) from Portugal

2020 ◽  
Vol 57 (2) ◽  
pp. 179-184
Author(s):  
P. F. Barradas ◽  
A. R. Flores ◽  
T. L. Mateus ◽  
F. Carvalho ◽  
F. Gärtner ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
18S Rrna ◽  
Population Sample ◽  
Genetic Data ◽  
Rrna Genes ◽  
12S Rrna ◽  
Rrna Gene ◽  
Mitochondrial 12S Rrna ◽  
18S Rrna Genes

SummaryCrenosoma striatum is a host-specifi c metastrongiloid nematode causing respiratory tract disease in hedgehogs (Erinaceus europaeus). Since few studies have reported C. striatum in hedgehogs and little genetic data is available concerning this lungworm, this study aimed to determine the occurrence of C. striatum in a population sample of hedgehogs from Portugal, additionally providing morphological, histological and molecular data. From 2017 to 2018 a survey of infection was carried out in 11 necropsied hedgehogs. Worms were extracted from fresh lung tissues and microscopically evaluated. Molecular characterization of partial mitochondrial (12S rRNA) and nuclear (18S rRNA) genes was performed. The presence of lungworms in pulmonary tissues of five hedgehogs (45.5%) was detected. Morphological and histopathological analyses evidenced adult forms of nematodes consistent with C. striatum. Molecular characterization of 18S rRNA genes confirmed the classifi cation as C. striatum. Also, novel genetic data characterizing the mitochondrial (12S rRNA) gene of C. striatum is presented.This is the first report of C. striatum infection in hedgehogs of Portugal. The findings here reported provide new insights regarding the geographic distribution and the molecular identification of this lungworm species.

scholarly journals Molecular identification and phylogenetic analysis of suaeda maritima from parangipettai coastal areas, southeast coast of india

2020 ◽  
Vol 7 (1) ◽  
pp. 28-34
Author(s):  
Anbarasi G ◽  
Vishnupriya B
Keyword(s):  
18S Rrna ◽  
Spinacia Oleracea ◽  
Genetic Material ◽  
Rrna Genes ◽  
Atriplex Canescens ◽  
Salt Marsh Plant ◽  
Suaeda Maritima ◽  
Atriplex Torreyi ◽  
18S Rrna Genes ◽  
Study Species

Conventional taxonomy is limited with delineating species and controversies arise with DNA barcoding based identifications. Hence, an alternative supporting approach is very much needed to identify species and differentiate them within the species based on the genetic material. 18S rRNA genes have been particularly helpful in analyzing phylogeny at the species level. In addition, bioinformatics which represents a new, growing area of science uses computational approaches to answer biological questions. Salt tolerant costal salt marsh plant of Suaeda maritima was selected for 18s rRNA sequencing to solve the ambiguity in itsspecies level identification. Similarity search of study species shared 99% similarity with 5 species of Atriplex canescens clone s128, Atriplex torreyi var. griffithsii clone p508, Spinacia oleracea, Oenothera laciniata clone,Beta vulgaris. Phylogenetic tree infer that S.maritima is closely related to Spinacia oleracea and Oenothera laciniata. Atriplex canescens (fourwing saltbush), Atriplex torreyi and Phaulothamnus spinescens, Celosia argentea found to be closely related and are in one group. Hence, this study result clearly shows thus study species evaluated from angiosperm and provides key step in understanding the evolution of salt tolerance in angiosperm.

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