scholarly journals First finding of free-living representatives of Prokinetoplastina and their nuclear and mitochondrial genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Denis V. Tikhonenkov ◽  
Ryan M. R. Gawryluk ◽  
Alexander P. Mylnikov ◽  
Patrick J. Keeling
Keyword(s):  
New Species ◽  
Mitochondrial Genomes ◽  
Molecular Characteristics ◽  
Ancestral State ◽  
Metabolic Potential ◽  
Free Living ◽  
Polycistronic Mrna ◽  
First Finding ◽  
Ancestral States ◽  
Environmental Sequences

AbstractKinetoplastids are heterotrophic flagellated protists, including important parasites of humans and animals (trypanosomatids), and ecologically important free-living bacterial consumers (bodonids). Phylogenies have shown that the earliest-branching kinetoplastids are all parasites or obligate endosymbionts, whose highly-derived state makes reconstructing the ancestral state of the group challenging. We have isolated new strains of unusual free-living flagellates that molecular phylogeny shows to be most closely related to endosymbiotic and parasitic Perkinsela and Ichthyobodo species that, together with unidentified environmental sequences, form the clade at the base of kinetoplastids. These strains are therefore the first described free-living prokinetoplastids, and potentially very informative in understanding the evolution and ancestral states of morphological and molecular characteristics described in other kinetoplastids. Overall, we find that these organisms morphologically and ultrastructurally resemble some free-living bodonids and diplonemids, and possess nuclear genomes with few introns, polycistronic mRNA expression, high coding density, and derived traits shared with other kinetoplastids. Their genetic repertoires are more diverse than the best-studied free-living kinetoplastids, which is likely a reflection of their higher metabolic potential. Mitochondrial RNAs of these new species undergo the most extensive U insertion/deletion editing reported so far, and limited deaminative C-to-U and A-to-I editing, but we find no evidence for mitochondrial trans-splicing.

scholarly journals Metabolic Diversity and Evolutionary History of the Archaeal Phylum “Candidatus Micrarchaeota” Uncovered from a Freshwater Lake Metagenome

2020 ◽  
Vol 86 (23) ◽  
Author(s):  
Vitaly V. Kadnikov ◽  
Alexander S. Savvichev ◽  
Andrey V. Mardanov ◽  
Alexey V. Beletsky ◽  
Artem V. Chupakov ◽  
...  
Keyword(s):  
Metabolic Pathways ◽  
Mine Drainage ◽  
De Novo ◽  
Group Analysis ◽  
Freshwater Lake ◽  
Ancestral State ◽  
Metabolic Potential ◽  
Free Living ◽  
Nucleotide Biosynthesis ◽  
Generation Mechanisms

ABSTRACT Acidophilic archaea of the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group from the uncultured candidate phylum “Candidatus Micrarchaeota” have small genomes and cell sizes and are known to be metabolically dependent and physically associated with their Thermoplasmatales hosts. However, phylogenetically diverse “Ca. Micrarchaeota” are widely distributed in various nonacidic environments, and it remains uncertain because of the lack of complete genomes whether they are also devoted to a partner-dependent lifestyle. Here, we obtained nine metagenome-assembled genomes of “Ca. Micrarchaeota” from the sediments of a meromictic freshwater lake, including a complete, closed 1.2 Mbp genome of “Ca. Micrarchaeota” Sv326, an archaeon phylogenetically distant from the ARMAN lineage. Genome analysis revealed that, contrary to ARMAN “Ca. Micrarchaeota,” the Sv326 archaeon has complete glycolytic pathways and ATP generation mechanisms in substrate phosphorylation reactions, the capacities to utilize some sugars and amino acids as substrates, and pathways for de novo nucleotide biosynthesis but lacked an aerobic respiratory chain. We suppose that Sv326 is a free-living scavenger rather than an obligate parasite/symbiont. Comparative analysis of “Ca. Micrarchaeota” genomes representing different order-level divisions indicated that evolution of the “Ca. Micrarchaeota” from a free-living “Candidatus Diapherotrites”-like ancestor involved losses of important metabolic pathways in different lineages and gains of specific functions in the course of adaptation to a partner-dependent lifestyle and specific environmental conditions. The ARMAN group represents the most pronounced case of genome reduction and gene loss, while the Sv326 lineage appeared to be rather close to the ancestral state of the “Ca. Micrarchaeota” in terms of metabolic potential. IMPORTANCE The recently described superphylum DPANN includes several phyla of uncultivated archaea with small cell sizes, reduced genomes, and limited metabolic capabilities. One of these phyla, “Ca. Micrarchaeota,” comprises an enigmatic group of archaea found in acid mine drainage environments, the archaeal Richmond Mine acidophilic nanoorganisms (ARMAN) group. Analysis of their reduced genomes revealed the absence of key metabolic pathways consistent with their partner-associated lifestyle, and physical associations of ARMAN cells with their hosts were documented. However, “Ca. Micrarchaeota” include several lineages besides the ARMAN group found in nonacidic environments, and none of them have been characterized. Here, we report a complete genome of “Ca. Micrarchaeota” from a non-ARMAN lineage. Analysis of this genome revealed the presence of metabolic capacities lost in ARMAN genomes that could enable a free-living lifestyle. These results expand our understanding of genetic diversity, lifestyle, and evolution of “Ca. Micrarchaeota.”

scholarly journals Predatory colponemids are the sister group to all other alveolates

2020 ◽  
Author(s):  
Denis V. Tikhonenkov ◽  
Jürgen F. H. Strassert ◽  
Jan Janouškovec ◽  
Alexander P. Mylnikov ◽  
Vladimir V. Aleoshin ◽  
...  
Keyword(s):  
Sister Group ◽  
List Type ◽  
Ancestral State ◽  
Free Living ◽  
Protein Coding ◽  
Freshwater Habitats ◽  
Ancestral States ◽  
Phylogenomic Analyses ◽  
Diverse Groups

AbstractAlveolates are a major supergroup of eukaryotes encompassing more than ten thousand free-living and parasitic species, including medically, ecologically, and economically important apicomplexans, dinoflagellates, and ciliates. These three groups are among the most widespread eukaryotes on Earth, and their environmental success can be linked to unique innovations that emerged early in each group. Understanding the emergence of these well-studied and diverse groups and their innovations has relied heavily on the discovery and characterization of early-branching relatives, which allow ancestral states to be inferred with much greater confidence. Here we report the phylogenomic analyses of 313 eukaryote protein-coding genes from transcriptomes of three members of one such group, the colponemids (Colponemidia), which unambiguously support their monophyly and position as the sister lineage to all other alveolates. Colponemid-related sequences from environmental surveys and our microscopical observations show that colponemids are not common in nature, but diverse and widespread in freshwater habitats around the world. Studied colponemids possess two types of extrusive organelles (trichocysts or toxicysts) for active hunting of other unicellular eukaryotes and potentially play an important role in microbial food webs. Colponemids have generally plesiomorphic morphology and illustrate the ancestral state of Alveolata. We further discuss their importance in understanding the evolution of alveolates as well as origin of myzocytosis and plastids.HighlightsPhylogenomics resolves Colponemidia as a sister group to all other alveolatesThe ancestor of all alveolates was a biflagellate predator feeding by phagocytosisColponemids may illuminate the ancestral states of apicomplexans, dinoflagellates, and ciliatesColponemids are geographically widespread in freshwater habitats

Perspiria boucheri sp. nov. (Nematoda, Desmodorida) from the East China Sea

Zootaxa ◽  
2019 ◽  
Vol 4695 (2) ◽  
pp. 195-200
Author(s):  
JING SUN ◽  
HONGXIU ZHAI ◽  
YONG HUANG
Keyword(s):  
New Species ◽  
East China Sea ◽  
Buccal Cavity ◽  
Nematode Species ◽  
East China ◽  
Similar Species ◽  
Marine Nematode ◽  
The East China Sea ◽  
Free Living ◽  
China Sea

A new free-living marine nematode species from marine sediments in the East China Sea, is described here as Perspiria boucheri sp. nov. The new species is characterized by amphideal fovea surrounded partially by body annulations; four cephalic setae stout; conical buccal cavity with a minute dorsal tooth and two ventrosublateral teeth; pharynx with a pyriform terminal bulb; tail elongated, conical with 3/4 posterior cylindrical portion which having distinct coarse annulations; spicules strongly curved with narrow ventral velum, handle-shaped proximally; gubernaculum canoe-shaped, without apophysis. The new species differs from the most similar species Perspiria striaticaudata (Timm, 1962) by strongly curved spicules with handle-shaped proximal end, gubernaculum without dorsal apophysis and relatively shorter tail. Updated key to all species of Perspiria is provided. 

scholarly journals A new lineage of mazaediate fungi in the Eurotiomycetes: Cryptocaliciomycetidae subclass. nov., based on the new species Cryptocalicium blascoi and the revision of the ascoma evolution

2021 ◽  
Vol 20 (7) ◽  
pp. 889-904
Author(s):  
M. Prieto ◽  
Javier Etayo ◽  
I. Olariaga
Keyword(s):  
New Species ◽  
Common Ancestor ◽  
External Surface ◽  
Evolutionary Relationships ◽  
New Order ◽  
Ancestral State ◽  
Multigene Phylogeny ◽  
State Reconstruction ◽  
Distinct Structure ◽  
Dark Violet

AbstractThe class Eurotiomycetes (Ascomycota, Pezizomycotina) comprises important fungi used for medical, agricultural, industrial and scientific purposes. Eurotiomycetes is a morphologically and ecologically diverse monophyletic group. Within the Eurotiomycetes, different ascoma morphologies are found including cleistothecia and perithecia but also apothecia or stromatic forms. Mazaediate representatives (with a distinct structure in which loose masses of ascospores accumulate to be passively disseminated) have evolved independently several times. Here we describe a new mazaediate species belonging to the Eurotiomycetes. The multigene phylogeny produced (7 gene regions: nuLSU, nuSSU, 5.8S nuITS, mtSSU, RPB1, RPB2 and MCM7) placed the new species in a lineage sister to Eurotiomycetidae. Based on the evolutionary relationships and morphology, a new subclass, a new order, family and genus are described to place the new species: Cryptocalicium blascoi. This calicioid species occurs on the inner side of loose bark strips of Cupressaceae (Cupressus, Juniperus). Morphologically, C. blascoi is characterized by having minute apothecioid stalked ascomata producing mazaedia, clavate bitunicate asci with hemiamyloid reaction, presence of hamathecium and an apothecial external surface with dark violet granules that becomes turquoise green in KOH. The ancestral state reconstruction analyses support a common ancestor with open ascomata for all deep nodes in Eurotiomycetes and the evolution of closed ascomata (cleistothecioid in Eurotiomycetidae and perithecioid in Chaetothyriomycetidae) from apothecioid ancestors. The appropriateness of the description of a new subclass for this fungus is also discussed.

scholarly journals Investigation of ancestral alleles in the Bovinae subfamily

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Maulana M. Naji ◽  
Yuri T. Utsunomiya ◽  
Johann Sölkner ◽  
Benjamin D. Rosen ◽  
Gábor Mészáros
Keyword(s):  
Extreme Points ◽  
Genetic Mutation ◽  
Zebu Cattle ◽  
Ancestral State ◽  
Initial State ◽  
High Count ◽  
Environmental Pressures ◽  
Ancestral States ◽  
Productive Traits ◽  
Species Specific

Abstract Background In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. Results Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. Conclusions Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

A new species of free-living marine nematode, Diplolaimella ariakensis n. sp. (Nematoda: Monhysteridae) from the Ariake Sea, Japan

Nematology ◽  
2021 ◽  
pp. 1-11
Author(s):  
Daisuke Shimada ◽  
Toshiki Komiya ◽  
Toyoshi Yoshiga
Keyword(s):  
New Species ◽  
Buccal Cavity ◽  
Marine Nematode ◽  
Ariake Sea ◽  
Free Living ◽  
Long Tail ◽  
Dichotomous Key ◽  
Anterior Position ◽  
Close Relationship ◽  
A New Species

Summary A new species of free-living marine nematode, Diplolaimella ariakensis n. sp., is described from a muddy tidal flat of the Ariake Sea, southern Japan. Diplolaimella ariakensis n. sp. differs from its congeners by the following: presence of ocelli, absence of denticles in the buccal cavity, a long tail (11-14 cloacal body diam., c = 3.2-4.0 in male, 17-21 anal body diam., c = 2.9-3.4 in female), spicules as long as 1.4-1.8 cloacal body diam., gubernaculum 0.4-0.5 cloacal body diam. long with a dorsocaudal apophysis 0.5-0.7 cloacal body diam. long, presence of a precloacal supplement, absence of postcloacal papillae, presence of seven pairs of body pores in male, and the anterior position of the vulva (V = 43-46). A dichotomous key to Diplolaimella species is provided. Almost full-length 18S rRNA and partial cytochrome c oxidase subunit I gene sequences were determined for D. ariakensis n. sp. A maximum likelihood tree of 18S sequences supported a close relationship between D. ariakensis n. sp. and D. dievengatensis.

scholarly journals Phylogeny, evidence for a cryptic plastid, and distribution of Chytriodinium parasites (Dinophyceae) infecting copepods

2018 ◽  
Author(s):  
Jürgen F. H. Strassert ◽  
Elisabeth Hehenberger ◽  
Javier del Campo ◽  
Noriko Okamoto ◽  
Martin Kolisko ◽  
...  
Keyword(s):  
Phylogenetic Position ◽  
Rrna Gene ◽  
Ancestral State ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Free Living ◽  
Surface Ocean ◽  
Lsu Rrna Gene ◽  
Important Host ◽  
Copepod Eggs

ABSTRACTSpores of the dinoflagellate Chytriodinium are known to infest copepod eggs causing their lethality. Despite the potential to control the population of such an ecologically important host, knowledge about Chytriodinium parasites is limited: we know little about phylogeny, parasitism, abundance, or geographical distribution. We carried out genome sequence surveys on four manually isolated sporocytes from the same sporangium to analyse the phylogenetic position of Chytriodinium based on SSU and concatenated SSU/LSU rRNA gene sequences, and also characterize two genes related to the plastidial heme pathway, hemL and hemY. The results suggest the presence of a cryptic plastid in Chytriodinium and a photosynthetic ancestral state of the parasitic Chytriodinium/Dissodinium clade. Finally, by mapping Tara Oceans V9 SSU amplicon data to the recovered SSU rRNA gene sequences from the sporocytes, we show that globally, Chytriodinium parasites are most abundant within the pico/nano- and mesoplankton of the surface ocean and almost absent within microplankton, a distribution indicating that they generally exist either as free-living spores or host-associated sporangia.

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