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The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.

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The large mitochondrial genome of Symbiodinium minutum reveals conserved non-coding sequences between dinoflagellates and apicomplexans.
Genome Biol Evol. 2015 Jul 20;
Authors: Shoguchi E, Shinzato …

Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.

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Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii.

Stand Genomic Sci. 2015;10:17

Authors: Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M, Klenk HP

Abstract
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.

PMID: 26203330 [PubMed]

Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.

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Diversity of Heterotrophic Protists from Extremely Hypersaline Habitats.

Protist. 2015 Jun 18;166(4):422-437

Authors: Park JS, Simpson AG

Abstract
Heterotrophic protists (protozoa) are a diverse but understudied component of the biota of extremely hypersaline environments, with few data on molecular diversity within halophile ‘species’, and almost nothing known of their biogeographic distribution. We have garnered SSU rRNA gene sequences for several clades of halophilic protozoa from enrichments from waters of >12.5% salinity from Australia, North America, and Europe (6 geographic sites, 25 distinct samples). The small stramenopile Halocafeteria was found at all sites, but phylogenies did not show clear geographic clustering. The ciliate Trimyema was recorded from 6 non-European samples. Phylogenies confirmed a monophyletic halophilic Trimyema group that included possible south-eastern Australian, Western Australian and North American clusters. Several halophilic Heterolobosea were detected, demonstrating that Pleurostomum contains at least three relatively distinct clades, and increasing known continental ranges for Tulamoeba peronaphora and Euplaesiobystra hypersalinica. The unclassified flagellate Palustrimonas, found in one Australian sample, proves to be a novel deep-branching alveolate. These results are consistent with a global distribution of halophilic protozoa groups (∼morphospecies), but the Trimyema case suggests that is worth testing whether larger forms exhibit biogeographic phylogenetic substructure. The molecular detection/characterization of halophilic protozoa is still far from complete at the clade level, let alone the ‘species level’.

PMID: 26202993 [PubMed – as supplied by publisher]

Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.

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Hammondia hammondi harbors functional orthologs of the host-modulating effectors GRA15 and ROP16 but is distinguished from Toxoplasma gondii by a unique transcriptional profile.

Eukaryot Cell. 2014 Dec;13(12):1507-18

Authors: Walzer KA, Wier GM, Dam RA, Srinivasan AR, Borges AL, English ED, Herrmann DC, Schares G, Dubey JP, Boyle JP

Abstract
Toxoplasma gondii and its nearest extant relative, Hammondia hammondi, are phenotypically distinct despite their remarkable similarity in gene content, synteny, and functionality. To begin to identify genetic differences that might drive distinct infection phenotypes of T. gondii and H. hammondi, in the present study we (i) determined whether two known host-interacting proteins, dense granule protein 15 (GRA15) and rhoptry protein 16 (ROP16), were functionally conserved in H. hammondi and (ii) performed the first comparative transcriptional analysis of H. hammondi and T. gondii sporulated oocysts. We found that GRA15 and ROP16 from H. hammondi (HhGRA15 and HhROP16) modulate the host NF-κB and STAT6 pathways, respectively, when expressed heterologously in T. gondii. We also found the transcriptomes of H. hammondi and T. gondii to be highly distinct. Consistent with the spontaneous conversion of H. hammondi tachyzoites into bradyzoites both in vitro and in vivo, H. hammondi high-abundance transcripts are enriched for genes that are of greater abundance in T. gondii bradyzoites. We also identified genes that are of high transcript abundance in H. hammondi but are poorly expressed in multiple T. gondii life stages, suggesting that these genes are uniquely expressed in H. hammondi. Taken together, these data confirm the functional conservation of known T. gondii virulence effectors in H. hammondi and point to transcriptional differences as a potential source of the phenotypic differences between these species.

PMID: 25280815 [PubMed – indexed for MEDLINE]

Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.

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Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities.

BMC Genomics. 2015;16:526

Authors: Wong DH, Beiko RG

Abstract
BACKGROUND: Lateral gene transfer (LGT) is an important evolutionary process in microbial evolution. In sewage treatment plants, LGT of antibiotic resistance and xenobiotic degradation-related proteins has been suggested, but the role of LGT outside these processes is unknown. Microbial communities involved in Enhanced Biological Phosphorus Removal (EBPR) have been used to treat wastewater in the last 50 years and may provide insights into adaptation to an engineered environment. We introduce two different types of analysis to identify LGT in EBPR sewage communities, based on identifying assembled sequences with more than one strong taxonomic match, and on unusual phylogenetic patterns. We applied these methods to investigate the role of LGT in six energy-related metabolic pathways.
RESULTS: The analyses identified overlapping but non-identical sets of transferred enzymes. All of these were homologous with sequences from known mobile genetic elements, and many were also in close proximity to transposases and integrases in the EBPR data set. The taxonomic method had higher sensitivity than the phylogenetic method, identifying more potential LGTs. Both analyses identified the putative transfer of five enzymes within an Australian community, two in a Danish community, and none in a US-derived culture.
CONCLUSIONS: Our methods were able to identify sequences with unusual phylogenetic or compositional properties as candidate LGT events. The association of these candidates with known mobile elements supports the hypothesis of transfer. The results of our analysis strongly suggest that LGT has influenced the development of functionally important energy-related pathways in EBPR systems, but transfers may be unique to each community due to different operating conditions or taxonomic composition.

PMID: 26173980 [PubMed – in process]

Genomic analysis of the causative agents of coccidiosis in domestic chickens.

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Genomic analysis of the causative agents of coccidiosis in domestic chickens.
Genome Res. 2014 Oct;24(10):1676-85
Authors: Reid AJ, Blake DP, Ansari HR, Billington K, Browne HP, Bryant J, Dunn M,…

The genome of Eimeria falciformis–reduction and specialization in a single host apicomplexan parasite.

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The genome of Eimeria falciformis–reduction and specialization in a single host apicomplexan parasite.

BMC Genomics. 2014;15:696

Authors: Heitlinger E, Spork S, Lucius R, Dieterich C

Abstract
BACKGROUND: The phylum Apicomplexa comprises important unicellular human parasites such as Toxoplasma and Plasmodium. Eimeria is the largest and most diverse genus of apicomplexan parasites and some species of the genus are the causative agent of coccidiosis, a disease economically devastating in poultry. We report a complete genome sequence of the mouse parasite Eimeria falciformis. We assembled and annotated the genome sequence to study host-parasite interactions in this understudied genus in a model organism host.
RESULTS: The genome of E. falciformis is 44 Mb in size and contains 5,879 predicted protein coding genes. Comparative analysis of E. falciformis with Toxoplasma gondii shows an emergence and diversification of gene families associated with motility and invasion mainly at the level of the Coccidia. Many rhoptry kinases, among them important virulence factors in T. gondii, are absent from the E. falciformis genome. Surface antigens are divergent between Eimeria species. Comparisons with T. gondii showed differences between genes involved in metabolism, N-glycan and GPI-anchor synthesis. E. falciformis possesses a reduced set of transmembrane transporters and we suggest an altered mode of iron uptake in the genus Eimeria.
CONCLUSIONS: Reduced diversity of genes required for host-parasite interaction and transmembrane transport allow hypotheses on host adaptation and specialization of a single host parasite. The E. falciformis genome sequence sheds light on the evolution of the Coccidia and helps to identify determinants of host-parasite interaction critical for drug and vaccine development.

PMID: 25142335 [PubMed – indexed for MEDLINE]

Ancient homology of the mitochondrial contact site and cristae organizing system points to an endosymbiotic origin of mitochondrial cristae.

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Ancient homology of the mitochondrial contact site and cristae organizing system points to an endosymbiotic origin of mitochondrial cristae.

Curr Biol. 2015 Jun 1;25(11):1489-95

Authors: Muñoz-Gómez SA, Slamovits CH, Dacks JB, Baier KA, Spencer KD, Wideman JG

Abstract
Mitochondria are eukaryotic organelles that originated from an endosymbiotic α-proteobacterium. As an adaptation to maximize ATP production through oxidative phosphorylation, mitochondria contain inner membrane invaginations called cristae. Recent work has characterized a multi-protein complex in yeast and animal mitochondria called MICOS (mitochondrial contact site and cristae organizing system), responsible for the determination and maintenance of cristae [1-4]. However, the origin and evolution of these characteristic mitochondrial features remain obscure. We therefore conducted a comprehensive search for MICOS components across the major groups that encompass eukaryotic diversity to determine the extent of conservation of this complex. We detected homologs for the majority of MICOS components among opisthokonts (the group containing animals and fungi), but only Mic60 and Mic10 were consistently identified outside this group. The conservation of Mic60 and Mic10 in eukaryotes is consistent with their central role in MICOS function [5-7], indicating that the basic mechanism for cristae determination arose early in evolution and has remained relatively unchanged. We found that eukaryotes with ultrastructurally simplified anaerobic mitochondria that lack cristae have also lost MICOS. We then searched for a prokaryotic MICOS and identified a homolog of Mic60 present only in α-proteobacteria, providing evidence for the endosymbiotic origin of mitochondrial cristae. Our study clarifies the origins of mitochondrial cristae and their subsequent evolutionary history, provides evidence for a general mechanism of cristae formation and maintenance in eukaryotes, and points to a new potential factor involved in membrane differentiation in prokaryotes.

PMID: 26004762 [PubMed – in process]

Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes.

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Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes.
Genome Biol Evol. 2015;7(6):1728-42
Authors: Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM
Abstr…

Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.

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Gene fusion, fission, lateral transfer, and loss: Not-so-rare events in the evolution of eukaryotic ATP citrate lyase.
Mol Phylogenet Evol. 2015 May 27;91:12-16
Authors: Gawryluk RM, Eme L, Roger A…