Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis

Rotterová, Johana; Salomaki, Eric D.; Pánek, Tomáš; Bourland, William A.; Žihala, David; Táborský, Petr; Edgcomb, Virginia P.; Beinart, Roxanne A.; Kolísko, Martin; Čepička, Ivan

doi:10.1016/j.cub.2020.03.064

Cited by 61 publications

(75 citation statements)

References 94 publications

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“…Still, as more data are needed for this group, most of the ciliate classification systems considered cariacotricheans as incertae sedis clustering somewhere in SAL (Adl et al 2019). Two other newly established lineages in the vicinity of Armophrea are Parablepharismea and Muranotrichea (Rotterová et al 2020). In our trees, all three lineages -Cariacotrichea, Parablepharismea, and Muranotricheaalways grouped together creating a sister clade to Armophorea as in Rotterová et al (2020).…”

Section: Constrained Monophyly Of Ciliate Lineagesmentioning

confidence: 67%

“…Two other newly established lineages in the vicinity of Armophrea are Parablepharismea and Muranotrichea (Rotterová et al 2020). In our trees, all three lineages -Cariacotrichea, Parablepharismea, and Muranotricheaalways grouped together creating a sister clade to Armophorea as in Rotterová et al (2020). For simplicity, we decided to label all these clades as Armophorea in our reference trees, which corresponds to the APM clade defined in Rotterová et al (2020).…”

Section: Constrained Monophyly Of Ciliate Lineagesmentioning

confidence: 99%

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Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Rajter¹,

Dunthorn²

2021

MBMG

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Although ciliates are one of the most dominant microbial eukaryotic groups in many environments, there is a lack of updated global ciliate alignments and reference trees that can be used for phylogenetic placement methods to analyze environmental metabarcoding data. Here we fill this gap by providing reference alignments and trees for those ciliates taxa with available SSU-rDNA sequences derived from identified species. Each alignment contains 478 ciliate and six outgroup taxa, and they were made using different masking strategies for alignment positions (unmasked, masked and masked except the hypervariable V4 region). We constrained the monophyly of the major ciliate groups based on the recently updated classification of protists and based on phylogenomic data. Taxa of uncertain phylogenetic position were kept unconstrained, except for Mesodinium species that we constrained to form a clade with the Litostomatea. These ciliate reference alignments and trees can be used to perform taxonomic assignments of metabarcoding data, discover novel ciliate clades, estimate species richness, and overlay measured ecological parameters onto the phylogenetic placements.

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Section: Constrained Monophyly Of Ciliate Lineagesmentioning

confidence: 67%

Section: Constrained Monophyly Of Ciliate Lineagesmentioning

confidence: 99%

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Rajter¹,

Dunthorn²

2021

MBMG

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“…2,28,[30][31][32]44,48,60 For anerobic metabolic proteins, the PDH complex, ETC complex I, and MICOS proteins, that are not found apicomplexans or chromerids, BLASTp searches were conducted using ciliate and stramenopile queries. 40,48,73,74 The resulting hits were manually parsed to retain top hits from apicomplexans and chromerids, as well as dinoflagellates, ciliates and stramenopiles. The parsed hits were then aligned with MAFFT v. 7.212.…”

Section: Declaration Of Interestsmentioning

confidence: 99%

Parallel functional reduction in the mitochondria of apicomplexan parasites

2021

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“…Extreme forms of these interspecies H 2 -transfer are the methanogenic endo-and ecto-symbionts of rumen protozoa (Embley and Finlay, 1994). The close association seen between rumen ciliates and methanogens (Vogels et al, 1980) seems a more general feature of anaerobic ciliates, aimed at boosting their metabolic rate (Rotterová et al, 2020). Although AF are not known to have methanogenic endo-or ecto-symbionts, they do contain modified mitochondria known as hydrogenosomes (van der Giezen, 2009), and there is in vitro based evidence of crossfeeding (syntrophy) between hydrogenic AF and methanogenic archaea in the herbivore gut ecosystem (Yarlett et al, 1986).…”

Section: Role Of Anaerobic Fungi In Methanogenesismentioning

confidence: 99%

Anaerobic Fungi: Past, Present, and Future

et al. 2020

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Anaerobic fungi (AF) play an essential role in feed conversion due to their potent fiber degrading enzymes and invasive growth. Much has been learned about this unusual fungal phylum since the paradigm shifting work of Colin Orpin in the 1970s, when he characterized the first AF. Molecular approaches targeting specific phylogenetic marker genes have facilitated taxonomic classification of AF, which had been previously been complicated by the complex life cycles and associated morphologies. Although we now have a much better understanding of their diversity, it is believed that there are still numerous genera of AF that remain to be described in gut ecosystems. Recent markergene based studies have shown that fungal diversity in the herbivore gut is much like the bacterial population, driven by host phylogeny, host genetics and diet. Since AF are major contributors to the degradation of plant material ingested by the host animal, it is understandable that there has been great interest in exploring the enzymatic repertoire of these microorganisms in order to establish a better understanding of how AF, and their enzymes, can be used to improve host health and performance, while simultaneously reducing the ecological footprint of the livestock industry. A detailed understanding of AF and their interaction with other gut microbes as well as the host animal is essential, especially when production of affordable high-quality protein and other animal-based products needs to meet the demands of an increasing human population. Such a mechanistic understanding, leading to more sustainable livestock practices, will be possible with recently developed-omics technologies that have already provided first insights into the different contributions of the fungal and bacterial population in the rumen during plant cell wall hydrolysis.

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Genomics of New Ciliate Lineages Provides Insight into the Evolution of Obligate Anaerobiosis

Cited by 61 publications

References 94 publications

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Ciliate SSU-rDNA reference alignments and trees for phylogenetic placements of metabarcoding data

Parallel functional reduction in the mitochondria of apicomplexan parasites

Anaerobic Fungi: Past, Present, and Future

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