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Protistology 13 (4), 179-191 (2019) Protistology
Mitochondrial genomes of Amoebozoa
Natalya Bondarenko1, Alexey Smirnov1, Elena Nassonova12, Anna Glotova12 and Anna Maria Fiore-Donno3
1 Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, 199034 Saint Petersburg, Russia
2 Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 194064 Saint Petersburg, Russia
3 University of Cologne, Institute ofZoology, Terrestrial Ecology, 50674 Cologne, Germany
| Submitted November 28, 2019 | Accepted December 10, 2019 | Summary
In this mini-review, we summarize the current knowledge on mitochondrial genomes of Amoebozoa. Amoebozoa is a major, early-diverging lineage of eukaryotes, containing at least 2,400 species. At present, 32 mitochondrial genomes belonging to 18 amoebozoan species are publicly available. A dearth of information is particularly obvious for two major amoebozoan clades, Variosea and Tubulinea, with just one mitochondrial genome sequenced for each. The main focus of this review is to summarize features such as mitochondrial gene content, mitochondrial genome size variation, and presence or absence of RNA editing, showing if they are unique or shared among amoebozoan lineages. In addition, we underline the potential of mitochondrial genomes for multigene phylogenetic reconstruction in Amoebozoa, where the relationships among lineages are not fully resolved yet. With the increasing application of next-generation sequencing techniques and reliable protocols, we advocate mitochondrial genomes as a promising tool for understanding evolutionary patterns in Amoebozoa.
Key words: Amoebozoa, protists, amoeba, mitochondria, mitochondrial genome
Abbreviations: mt — mitochondrial; cox1-3 - cytochrome oxidase subunit I, II, and III genes; cob — cytochrome b gene; atp1,6,8,9 — ATP synthase subunit 1,6,8,9 genes; nad1-7,9,11 — NADH dehydrogenase subunit 1-7, 9,11 and 4L genes; tRNA — transfer RNA genes; rrnL, rrnS — ribosomal RNA genes; ORF — open reading frames; PCGs — protein-coding genes; rps - small ribosomal subunit protein genes; rpl - large ribosomal subunit protein genes; SSU rRNA — small-subunit ribosomal RNA; LSU rRNA — large-subunit ribosomal RNA
doi:10.21685/1680-0826-2019-13-4-1 © 2019 The Author(s)
Protistology © 2019 Protozoological Society Affiliated with RAS
Introduction
One of the most captivating and still unresolved questions in the evolutionary biology of eukaryotes is the origin and evolution of the mitochondrial genome and the evolutionary processes by which a basic alpha-proteobacterial gene core has been modified during eukaryogenesis (Gray et al., 2001; Burger et al., 2003a; Cavalier-Smith, 2009; Gray, 2015). Our knowledge considerably advanced with the advent of comparative genomics of protistan mitochondria, showing that there was no "typical mitochondrial genome" (Gray et al., 2004). Since it is assumed that >90% of the initial bacterial gene complement must have been lost during the transition from endosymbiont to organelle, not surprisingly the mitochondrial genomes display a wide range of size, structure, codon-usage, and coding capacity (Adams et al., 2003; Burger et al., 2003b). Analysis of evolutionary trends over time demonstrated that gene transfers to the nucleus were non-linear, that they occurred in waves of exponential decrease, and that much of them took place comparatively early, independently, and at lineage-specific rates (Janouskovec et al., 2017). This process led to differential gene retention so that each lineage should possess a specific core of shared mitochondrial genes (Kannan et al., 2014). Examining the mitochondrial genomes in early diverging eukaryotes could help to solve the gene composition of the "last mitochondrial common ancestor" (LMCA) and how it evolved.
To date, the most gene-rich mitochondrial genomes (ca 66 genes) were found in the jakobids (excavates). Based on this, it was postulated that all other eukaryotes would possess only a subset of the jakobid genes (Kannan et al., 2014). However, two gene-rich mitochondrial genomes (that of Ancoracysta twista and Diphylleia rotans), have been found in unrelated taxa, suggesting a perhaps less linear evolutionary pattern (Kamikawa et al., 2016; Janouskovec et al. 2017). The large mitochondrial genome of Diphylleia is especially intriguing in this respect since the species belongs to Opimoda - the other main domain of eukaryotes, rather than excavates (the latter belong to Diphoda domain) (Derelle et al., 2015). Opimoda includes three main lineages, Amoebozoa, animals and fungi, and among them, the basal Amoebozoa is the lineage where the shortage of data is especially sensitive. The molecular study of Amoebozoa is hampered by large discrepancies between evolutionary rates
(Pawlowski and Burki, 2009), difficulties in cultu-ring and identifying taxa, and therefore suffers from drastic undersampling (Kang et al., 2017).
The last general review about protistan mitochondrial genomes was that ofGray et al. (2004). The review by Miller (2014) is focused on Amoebozoa, but it is dedicated to the comparison of three genomes only (Acanthamoeba, Dictyostelium, and Physa-rum). We provide here an updated summary of the current knowledge about amoebozoan mitochon-drial genomes, discussing their organization and gene diversity.
Available mitochondrial genomes in Amoe-bozoa
To date, complete mt genomes have been reported for 18 amoebozoan species (Fig. 1, Table 1). The first complete amoebozoan mt genome obtained using Sanger sequencing was that of Acanthamoeba castellanii strain Neff (Discosea: Centramoebia) (Burger et al., 1995). Successively, the mt genomes of the model organisms Dictyostelium discoideum (Ogawa et al., 2000) and Physarum polycephalum (Takano et al., 2001) (Evosea: Macromycetozoa) were also obtained with Sanger sequencing. Focus on Dictyostelia as a model for intercellular communication provided, along with several nuclear genomes, the mt genomes of Dictyostelium fascicu-latum (now Cavenderia fasciculata), D. citrinum and Polysphondylium pallidum (now Heterostelium pallidum) (Heidel and Glöckner, 2008).
Later, genomes were obtained with next-generation sequencing of the total DNA. This expanded the number of mt genomes available in other major taxonomic divisions ofAmoebozoa, i.e. three members of Variosea, Phalansterium sp. (Pombert et al., 2013) and two Protostelium species (GenBank data). Among Tubulinea, the only species with sequenced mitochondrial genome remains Vermamoeba vermiformis (Echinamoebida) (Fucikova and Lahr, 2016). Among Discosea, several strains of the pathogenic amoeba Balamuthia mandrillaris were added to the closely related Acanthamoeba (Greninger et al., 2015), as well as another species of Acanthamoeba, A. polyphagia (Karlyshev, 2019). Among other Discosea, the mt genomes of two marine species belonging to Dactylopodida were recently obtained, that of Neoparamoeba pemaqui-densis (Tanifuji et al., 2017) and that of Paramoeba aparasomata (Bondarenko et al., 2019b). Still in
Fig. 1. Schematic phylogenetic tree ofAmoebozoa, drawn mainly from Kang et al. (2017), illustrating the number of genera per order (according to Adl et al. 2019 and http://eumycetozoa.com/data/index.php; last accessed Oct. 2019) and the coverage of mitochondrial genomes. Level of RNA editing: "high" = massive editing in many genes; "low" = few editing sites in several genes. Branch length not to scale.
Table 1. Mitochondrial genomes of amoebozoan species, GenBank accession number, and references. Genome size, number of protein-coding genes (PCGs) and number of tRNAs are provided. The level of RNA editing is indicated (when known) as "low" (few editing sites in several genes) or "extensive" (numerous editing sites in many genes). More detailed data on editing are provided only when available from the relevant publications. Translation tables are indicated following the usual definition (Table 1 - "standard code"; Table 4 - "mold, protozoan, and coelenterate mitochondrial code" and the "Mycoplasma/Spiroplasma code"). Sequences labeled as "unverified" by the NCBI staff are highlighted in gray and probable reasons are explained in the footnotes. Strain sources: ATCC
- American Type Culture Collection (USA); CCAP - Culture Collection of Algae and Protozoa (UK); CCM of SPbSU
- Culture collection of the Core facility center "Culturing of Microorganisms" of Saint Petersburg State University.
Other strain designations are the author's ones (according to GenBank data).
Species and strain Size of the genome (bp) Number of protein coding genes Number of tRNAs Level and notes on RNA editing GenBank accession number and translation table Reference (according to GenBank database)
Acanthamoeba castellanii strain Neff; ATCC 30010 41,591 32 16 Low (In several clusters of tRNA genes) U12386 Table = 4 Burger et al., 1995
Acanthamoeba castellanii strain TN 41,588 32 NA No editing KX580904 Table = 4 Greninger et al., 2016, unpublished
Acanthamoeba castellanii isolate BCP-EM3VF21-1 39,205 36 13 Low (5 sites in tRNA genes) KT185628 Table = 4 Fucikova and Lahr, 2016
Acanthamoeba polyphaga strain Line Ap-1 39,215 32 15 No editing KP054475.2 Table = 4 Karlyshev, 2019
Dictyostelium discoideum strain AX3, partially X22* 55,564 36 18 Low (in tRNA genes) AB000109 Table = 1 Ogawa et al., 2000
Dictyostelium fasciculatum strain SH3 54,563 40 17 No editing EU275727 Table = 1 Heidel and Glöckner, 2008
Dictyostelium citrinum 57,820 43 19 No editing DQ336395.4 Table = 1 Heidel and Glöckner, 2008
Physarum polycephalum 62,862 20 No data Extensive (in PCG, ORFs and tRNAs) AB027295 Table = 1 Takano et al., 2001
Polysphondylium pallidum strain CK8 47,653 35 19 No data AY700145 Table = 1 Burger et al., 2004, unpublished
Polysphondylium pallidum strain PN500 48,042 40 20 No editing EU275726 Table = 1 Heidel and Glöckner, 2008
Phalansterium sp. strain PJK-2012 53,614 19 24 Extensive (in tRNA genes) KC121006 Table = 1 Pombert et al., 2013
Balamuthia mandrillaris strain SAM 41,707 33 13 No editing KT030673 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain RP5 41,784 33 13 No editing KT030672 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain OK1 42,823 33 14 No editing KT030671 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain V451 42,217 33 13 No editing KT030670 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain V039 39,996 32 13 No editing KT175741 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain 2046-1 41,656 33 13 No editing KT175740 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain GAM-19 41,570 33 13 No editing KT175739 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain V188 41,571 33 13 No editing KT175738 Table = 4 Greninger et al., 2015
Balamuthia mandrillaris strain 2046 41,656 30 18 No editing KP888565 Table = 4 Greninger et al.,2015
Balamuthia mandrillaris strain CDC-V039 39,894 No data No data No data CM003363 no translation provided Detering and Kiderlen ,2015, unpublished
Balamuthia mandrillaris strain BeN 42,217 33 13 No data NC 027736** Table = 4 Greninger et al., 2015, unpublished
Vermamoeba vermiformis isolate BCP-EM3VF21-2 52,068 37 25 No editing KT185627 Table = 4 Fucikova and Lahr, 2016
Vermamoeba vermiformis (as Hartmannella) 51,645 37 25 No editing GU828005 Table = 4 Bullerwell et al., 2010
Neoparamoeba pemaquidensis CCAP 1560/4 (as Paramoeba) 48,522 34 20 No editing KX611830 Table = 4 Tanifuji et al. ,2017
Table 1. (Continuation).
Species and strain Size of the genome (bp) Number of protein coding genes Number of tRNAs Level and notes on RNA editing GenBank accession number and translation table Reference (according to GenBank database)
Paramoeba aparasomata 46,254 31 19 No editing MK518072 Table = 4 Bondarenko et al., 2019
Paravannella minima CCAP 1533/1 - type strain 53,464 30 23 No editing MH910097 Table = 1 Bondarenko et al., 2019
Vannella croatica strain CCMA KRKA 29.9.7.6.1 (type strain) 28,933 12 16 Extensive MF508648 *** Table = 4 Bondarenko et al., 2018a
Vannella simplex strain CCMA0008 34,145 27 17 Extensive MF496657 *** Table = 4 Bondarenko et al., 2018b
Clydonella sawyeri strain CCMA0009 (type strain) 31,131 17 21 Low (in 5 PCG) MH094141 *** Table = 4 Bondarenko et al., 2018c
Protostelium mycophagum 48,607 16 24 No data KY775056 **** Table = 4 Glöckner, 2017, unpublished
Protostelium sp. Jena Gg-2016a 44,490 16 22 No data KY775057**** Table = 4 Glöckner, 2017, unpublished
* The mt genome of Dictyostelium discoideum is a composite, originating from two strains
** This B. mandrillaris strain mt genome is identical to that of the strain V451 KT030670, and has not yet been subject to final NCBI review.
*** Labeled in GenBank as "unverified" because the type of editing is not known.
**** Labeled in GenBank as "unverified", presumably because of incomplete annotation.
Discosea, mt genomes of four species ofVannellida were recently sequenced: Vannella croatica (Bondarenko et al., 2018a), V. simplex (Bondarenko et al., 2018b), Clydonella sawyery (Bondarenko et al., 2018c) and Paravannella minima (Bondarenko et al., 2019a). Among them the mt genome of Vannella croatica was obtained into two steps: the purified mitochondrial DNA that was isolated by pulsed-field gel electrophoresis was sequenced using NGS. Further, the obtained contig was checked by Sanger sequencing of the genomic DNA using a set of custom-made primers. The results of the two sequencing methods were almost identical (Bondarenko et al., 2018a).
Differences in size and gene content
All mt genomes of Amoebozoa sequenced to date are circular and display little size variation, from 28.9 to 62.8 kb, within the range found in animals, i.e. 11 to 77 kb (Lavrov and Pett, 2016) and in fungi, 16—110 kb (database of curated fungal mt genomes: http://mitofun.biol.uoa.gr/, last accessed Oct. 2019). In contrast, mitochondrial genomes of plants are significantly larger and range from 180 to 600 kb (Lynch et al., 2006).
A typical amoebozoan mitochondrial genome contains on average 30 protein-coding genes (Fig. 2). They are involved in the electron transport chain (three cytochrome oxidase subunits, ten NADH dehydrogenase subunits and apocytochrome b), ATP synthesis (seven ATP synthase subunits)
and several mitochondrial ribosomal protein genes (rpL and rpS) (Burger et al., 1995; Ogawa et al., 2000; Takano et al., 2001; Pombert et al., 2013; Greninger et al., 2015; Fucikova and Lahr, 2016; Tanifuji et al., 2017 Bondarenko et al., 2018a, 2018b, 2018c, 2019a, 2019b). Similar to metazoans, most of the amoebozoan mt genomes have duplicated tRNA genes for serine and leucine and in some cases for methionine (Vannellasimplex, V. croatica, Clydonella sawyeri, Paravannella minima, Phalansterium sp., Vermamoeba vermiformis, Physarum polycephalum, Dictyostelium citrinum), isoleucine (Vermamoeba vermiformis, Dictyostelium discoideum, D. citrinum, Acanthamoeba castellanii strain TN, A. polyphagia), phenylalanine (Polysphondylium pallidum), lysin ( Vannella simplex, V. croatica) and arginine ( Clydonella sawyeri, Paravannella minima, Vermamoeba vermiformis) (Heidel and Glöckner, 2008; Bondarenko et al., 2018a, 2018b, 2018c, 2019a, 2019b).
Along with the genes of known function, there are open reading frames (ORF) without recognizable counterpart in other mt genomes (Fig. 2). These ORFs might code for additional proteins whose sequences have diverged too much to be identified as such, and/or because of the incompleteness of the reference database, especially lacking representatives of free-living protists (del Campo et al., 2014). They also may represent a captured DNA, such as mitochondrial plasmids (Nakagawa et al., 1998). Their number depends on the species: Acanthamoeba castellanii isolate BCP-EM3VF21-1 is devoid of them, while Protostelium mycophagum has the maximum number of 19. The length of
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Datp genes O cob gene S rpl genes ■ en genes m ai genes ^ tufA gene ■I rRNA IS ORFs ■ cox 9enes ^ rPs 9enes ■ tRNA ■ nad 9enes
Fig. 2. Linearized maps of 15 amoebozoan mitochondrial genomes. The same functional groups of genes share the same colour code. The map illustrates gene order and functional groups, but not the mt genome size and relative length of genes, so it is drawn not to scale.
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2
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ORF may vary from hundreds to several thousand nucleotides. The longest known ORF belongs to Paramoeba aparasomata and consists of 5,871 bp.
The protein-coding genes in amoebozoan mt genomes are predominantly initiated with the start codons AUG, AUU or AUA and terminated with UAA or UAG (with UGA coding for tryptophan) that are also used in the unrelated protistan lineages Excavata: Euglenozoa and Alveolata: Ciliata. Some amoebozoans use only AUG as starting codon (which is the standard genetic code for nuclear genes): Physarum polycephalum, Polysphondylium pallidum, Phalansterium sp., and Paravannella minima (Table 1).
There is a huge variability in non-coding regions in the amoebozoan mt genomes, usually ranging in length from 50 to 2,500 bp. The longest one reaches 11,701 bp and was found in Physarum polycephalum (Takano et al. 2001). In some mt genomes, e.g. in Paravannella minima and Vannella croatica, the non-coding regions are scarce and short: they do not exceed 250 bp in length (Bondarenko et al., 2018a, 2019a).
The diversity of gene composition and gene order
Despite the conserved size and similarity in the overall gene content ofthe amoebozoan mt genome, gene composition can significantly vary even between closely related species (Fig. 2). For example, genes encoding the ATP synthase subunits alpha and C are missing in all known mt genomes, except in that of Balamuthia mandrillaris (Fig. 2), which makes it stand out from its relative Acanthamoeba spp. Similarly, the genes enl, en2 were identified only in two dictyostelids (Polysphondylium pallidum strain PN500 and Dictyostelium fasciculatum strain SH3) (Heidel and Glöckner, 2008). The tufA gene was found in Vermamoeba vermiformis (Fig. 2). In addition to variations in protein-coding genes, the number of tRNA genes can range from 13 to 25 among different amoebozoan species (Fig. 2).
In contrast to animals, where mt genes are predominantly encoded on both strands (Burger et al., 2003a), in many species of Amoebozoa the number of genes encoded in the minus strand is always low and concerns mainly tRNA genes. Genes encoded on the minus strand were found in Discosea (Vannella croatica, Paravannella minima, Clydonella sawyeri, Acanthamoeba castellanii isolate BCP-EM3VF21-1, and Neoparamoeba pemaquidensis)
and in Evosea: Physarum polycephalum and Proto-stelium mycophagum (see Table 1 for relevant references).
While closely related amoebozoan species show almost complete synteny in their mt genomes (Bondarenko et al., 2019b; Karlyshev, 2019), the order of genes is altered and the same pattern is no more recognizable with increasing phylogenetic distance (Bondarenko et al., 2018a, 2018b, 2018c). The genome alignment made for available mt genomes ofVannellida, Dactylopodida and Acanthamoeba (Fig. 3) clearly indicated that within the same genus the level of synteny between genomes is relatively high (e.g. within the genus Vannella or the genus Acanthamoeba); the same occurs between phylogenetically closely related genera (Neoparamoeba, Paramoeba). However, it is much lower between more distant lineages. For example, the genera Clydonella and Paravannella are separated by significant evolutionary distance from Vannella (Kudryavtsev, 2014), and the level of synteny between these genera and Vannella is much lower. The homologies between orders are always low, and even gene blocks recognized as homologous may differ in their gene content and their position in the genome (Fig. 3). The evolution ofthe mt genome structure is potentially a powerful marker to test the phylogenetic hypotheses, however, at present, its power is limited by the low number of available genomes.
Besides changes in the gene order, amoebozoan mt genomes show size differences due to introns and duplications of protein-coding genes. Introns were found in the mt genomes of Acanthamoeba castellanii strain Neff and strain TN (Burger et al., 1995), Dictyostelium discoideum, D. fasciculatum, D. citrinum (Ogawa et al., 2000; Heidel and Glöckner, 2008) and all strains of Balamuthia mandrillaris (Greninger et al., 2015). In Dictyostelium discoideum, Physarum polycephalum, Balamuthia mandrillaris and Acanthamoeba castellanii strain Neff the introns have been characterized as Group I introns. In Dictyostelium discoideum mt genome Group I introns encode homing endonucleases, active in self-splicing (Ogawa et al., 2000; Lang et al., 2007; Greninger et al., 2015). An extra source of polymorphism may be a recombination of mt DNA in presence of plasmids, like mF plasmid, shown to enhance this process in Physarum polycephalum (Nomura et al., 2005).
Duplication of protein-coding genes is not a common event in the mt genomes of Amoebozoa. It is known in three amoebozoan species only. In
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Fig. 3. Alignment of several amoebozoan mitochondrial genomes made by Mauve genome aligner (http://darlinglab.org/mauve/mauve.html). Potentially homologous gene blocks share the same colour. The connecting lines show how their respective positions vary within Discosea. Note that recognition of homologous fragments by Mauve is done ex novo, so that it may not correspond to available annotations of mt genomes. Only protein-coding genes are listed. Please refer to Fig. 2 and Gen Bank annotations for exact gene order and length, including ORFs and tRNAs.
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Neoparamoeba pemaquidensis and Phalansterium sp. the cob gene (part of oxidative phosphorylation chain) is duplicated (Pombert et al., 2013; Tanifuji et al., 2017), and in Polysphondylium pallidum the duplicated gene is rps3 (participates in the ribosomal complex and DNA repair) (Burger et al., 2004 unpublished, source - GenBank data AY700145).
RNA editing in amoebozoan mitochondrial genomes
While RNA editing is observed across many taxa and all domains of life, it involves fundamentally different modes and underlying mechanisms, suggesting that it is a derived trait within the lineages in which it is found, rather than a primitive feature inherited from a common evolutionary ancestor (Horton and Landweber, 2000; Gray, 2012). RNA editing converts primary RNA transcripts into mature and functional transcripts and occurs in mitochondria, plastids or nuclei of a wide range of eukaryotes (Burger, 2016; Moreira et al., 2016; Valach et al., 2017). It can affect both protein-coding RNAs and ribosomal and transfer RNAs (Yang et al., 2017). Among protists, massive editing of RNAs is observed in the kinetoplast of trypanosomes (Göringer, 2012), in Heterolobosea (Yang et al., 2017) and in diplonemids (Valach et al., 2017). The latter one has attracted much attention in the last years since it involves the assembly of fragmented genes (Valach et al., 2017).
There are little data on the distribution and occurrence of editing among basal clades of Amoe-bozoa (Fig. 1). However, Amoebozoa contains a group of organisms that perhaps provides a greater challenge to RNA editing than any other living organisms. These are the plasmodial slime molds (Myxogastria), mostly studied through the model organism Physarumpolycephalum. Of them, Physarum carries out one of the most complex sets of RNA editing events yet described (Houtz et al., 2018 and citations therein) — with the site-specific insertion of over 1,300 nucleotides (sometimes di-nucleotides) and base conversions.
Our recent studies revealed the existence of mitochondrial RNA editing in amoebae ofthe order Vannellida, although with an interesting distribution along its phylogeny. We observed extensive RNA editing in two crown species — Vannella croatica and Vannella simplex, while members oftwo other, more basal, genera — Clydonella and Paravannella — had
little or no editing (Bondarenko et al., 2018a, 2018b, 2018c, 2019a).
In some Amoebozoa lineages, there are no sequenced mt genomes, but sequences of the CoxI gene are available. We looked for evidence of editing by translating the gene using Expasy (https://web. expasy.org/translate/, last accessed Nov. 2019). There was no evidence of editing in the genus Korotnevella (Zlatogurski et al., 2016), in Parvamoe-ba rugata (JN202434 sequence), Cochliopodium pentatrifurcatum (KC489470), C. megatetrastylus (KC747719), C. actinophorum (CQ354207) and Squamamoeba japonica (JN6380333). Certainly, results based on translation of a single gene are no proof of the absence of editing in the entire lineage. In contrast, numerous stop-codons in all possible variants of translation were found in the sequences of the Cox I gene of testate amoebae (Kosakyan et al., 2011), suggesting a scattered distribution of RNA editing in the order Arcellinida. These data further advocate for the independent origin of RNA editing in different amoebozoan lineages.
Mitochondrial genomes as a potential tool to reconstruct amoebozoan phylogeny
Orthologous mitochondrial protein-coding genes are valuable tools for multigene phylogenies (Kannan et al., 2014; Janouskovec et al., 2017). In Amoebozoa especially, mt genomes would represent a valuable complement to full genomes, since the latter are notoriously difficult to assemble due to their large size, high repeat content and numerous and large introns (Clarke et al., 2013; Detering et al., 2015; Schaap et al., 2015). Mitochondrial genomes provide up to 37 genes widely distributed in eukaryotes that can be used for inferring evolutionary trends (Janouskovec et al., 2017); at least 25 of them are present in Amoebozoa (Bondarenko et al., 2019c). Among them, there are 13 genes of the respiratory chain (e.g. nad1-6, nad4L, cox1-3, cytb, atp6, and atp8), two subunits of the ribosomal RNA and transfer RNAs. In particular, the cox1 gene — a recognized DNA barcode for many groups of animals (e.g. butterflies, birds) has been used in the phylogeny and systematics of some taxa of Amoebozoa (Nassonova et al., 2010; Kosakyan et al., 2012; Zlatogursky et al., 2016) and thus shows a potential as a phylogenetic marker for the whole group.
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■ Vannella simplex MF496657
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-Paravannella minima MH910097
- Clydonella sawyeri MH094141
_r Acanthamoeba polyphaga KP054475
L Acanthamoeba castellanii KT185628 -Balamuthia mandrillaris KT175741
-Vannella croatica MF508648 Vannellida
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Neoparamoeba pemaquidensis KX611830 - Paramoeba aparasomata MK518072 ■Vermamoeba vermiformis GU828005
rDictyostelium citrinum DQ336395 - Dictyostelium discoideum AB000109 -Dictyostelium fasciculatum EU275727
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-Polysphondylium pallidum EU275726 -Phalansterium sp. KC121006
—Protostelium mycophagum KY775056
-Protostelium sp. KY775057
-Aspergillus niger NC007445 -Fusarium oxysporum NC017930
-Candida orthopsilosis NC006972
-Synchytrium microbalum NC042878
Dictyostelia
Variosea
Fungi
(outgroup)
Fig. 4. Phylogenetic tree based on a multigene alignment of 19 mitochondrial genes shared between 17 amoebozoan species, obtained by Bayesian inference. One representative genome was selected for each species; Physarum polycephalum mt genome was not included because it is not properly annotated. The analysis included a total of5,214 amino-acids; Bayesian analysis was conducted using PhyloBayes (LG model, G4, CAT approximation; final maxdiff value was 0.08) and Maximum Likelihood analyses with RAxML (LG model, GTRG4, ProtCAT, 1,000 bootstrap pseudoreplicates). Bayesian posterior probabilities/bootstrap supports are shown for each branch; "—"indicates a conflicting configuration with the ML analysis. Black dots mark fully supported nodes (1.0/100).
As an example, we performed a phylogenetic analysis of an alignment consisting of19 mt genes of 17 amoebozoans. The number of analysed amino-acid positions varied from 3,685 in Clydonella sawyeri to 5,195 in Dictyostelium citrinum mt genomes. Differences in the number of retained positions depended on genome length, annotation quality and level ofhomology between genes. The resulting tree showed highly supported branches for all groups recovering well-established monophyletic taxa (Fig. 4), i.e. Vannellida, Centramoebida, Dactylopodida, Dictyostelia. The Variosea were recovered as a paraphyletic group, with both sequences of Protostelium robustly grouping together. However, the basal branching of our tree and the relative positions of the three classes are weakly supported or are contradictory between Maximum Likelihood and Bayesian analyses. Only the class Discosea is monophyletic, as in most trees
(Cavalier-Smith et al., 2015; Kang et al., 2017), while Evosea is paraphyletic to it (compare with Fig. 1). This configuration is probably an artifact due to the current unbalanced representation of taxa. Any robust conclusions will be possible only after obtaining more amoebozoan mitochondrial genomes.
Acknowledgements
Supported with RSF 17-14-01391 grant. The present study utilized equipment of the Core facility centres "Development of molecular and cell technologies", "Biobank", "Computing Centre SPSU" and "Culture Collection ofMicroorganisms" of the research park of Saint Petersburg State University.
References
Adams K.L. and Palmer J.D. 2003. Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol. Phyl. Evol. 29, 380-395.
Bondarenko N., Nassonova E., Mijanovich O., Glotova A., Kamyshatskaya O., Kudryavtsev A., Masharsky A., Polev D. and Smirnov A. 2018a. Mitochondrial genome of Vannella croatica (Amoebozoa, Discosea, Vannellida). J. Eukar. Microbiol. 65, 820-827.
Bondarenko N., Glotova A., Nassonova E., Masharsky A., Kudryavtsev A. and Smirnov A. 2018b. The complete mitochondrial genome of Vannella simplex (Amoebozoa, Discosea, Vannellida). Europ. J. Protistol. 63, 83-95.
Bondarenko N., Glotova A., Kamyshatskaya O., Mesentsev E., Lotonin K. A., Masharsky A., Polev D., Nassonova E. and Smirnov A. 2018c. The complete mitochondrial genome of Clydonella sawyeri (Amoebozoa, Discosea, Vannellida). Protistology 12, 47-54.
Bondarenko N., Glotova A., Nassonova E., Masharsky A., Polev D. and Smirnov A. 2019a. The complete mitochondrial genome of Paravannella minima (Amoebozoa, Discosea, Vannellida). Europ. J. Protistol. 68, 80-87.
Bondarenko N., Volkova E., Masharsky A., Kudryavtsev A. and Smirnov A. 2019b. A comparative characterization of the mitochondrial genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae). J. Eukar. Microbiol. https://doi.org/10.1111/jeu.12767.
Bondarenko N., Bondarenko A., Starunov V. and Slyusarev G. 2019c. Comparative analysis ofthe mitochondrial genomes of Orthonectida: insights into the evolution of an invertebrate parasite species. Mol. Genet. Genomics 294, 715-727.
Bundschuh R., Altmüller J., Becker C., Nürnberg P. and Gott J.M. 2011. Complete characterization ofthe edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA. Nucleic Acids Res. 39, 6044-6055.
Burger G., Plante I., Lonergan K. M. and Gray M. W. 1995. The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization. J. Mol. Biol. 245, 522-537.
Burger G., Gray M.W. and Lang B.F. 2003a. Mitochondrial genomes: anything goes. Trends Genet. 19, 709-716.
Burger G., Forget L., Zhu Y., Gray M. W. and Lang F. B. 2003b. Unique mitochondrial genome
architecture in unicellular relatives of animals. Proc. Natl. Acad. Sci. USA, 100, 892-897.
Burger G. 2016. Non-functional genes repaired at the RNA level. C. R. Biol. 339, 289-295.
Cavalier-Smith T. 2009. Predation and euka-ryote cell origins: A coevolutionary perspective. Int. J. Biochem. Cell. Biol. 41, 307-322.
Cavalier-Smith T., Fiore-Donno A.M., Chao E., Kudryavtsev A., Berney C., Snell E.A. and Lewis R. 2015. Multigene phylogeny resolves deep branching of Amoebozoa. Mol. Phylogenet. Evol. 83, 293-304.
Clarke M., Lohan A. J., Liu B., Lagkouvardos I., Roy S., Zafar N., Bertelli C., Schilde C., Kianianmomeni A., Bü rglin T.R., Frech C., Turcotte B., Kopec K.O., Synnott J.M., Choo C., Paponov I., Finkler A., Heng Tan C.S., Hutchins
A.P., Weinmeier T., Rattei T., Chu J.S., Gimenez
G., Irimia M., Rigden D.J., Fitzpatrick D.A., Lorenzo-Morales J., Bateman A., Chiu C.H., Tang P., Hegemann P., Fromm H., Raoult D., Greub G., Miranda-Saavedra D., Chen N., Nash P., Ginger M.L., Horn M., Schaap P., Caler L. and Loftus
B.J. 2013. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution oftyrosine kinase signaling. Genome Biol. 14:R11. doi:10.1186/gb-2013-14-2-r11.
del Campo J., Sieracki M.E., Molestina R.E., Keeling P.J., Massana R. and Ruiz-Trillo I. 2014. The others: our biased perspective of eukaryotic genomes. Trends Ecol. Evol. 29, 251-259.
Derelle R., Torruella G., Klimes V., Brinkmann
H., Kim E., Vlcek C., Lang F.B. and Elias M. 2015. Bacterial proteins pinpoint a single eukaryotic root. Proc. Natl. Acad. Sci. USA. 112, e693-e699.
Detering H., Aebischer T., Dabrowski P.W., Radonic A., Nitsche A. and Renard B. 2015. First draft genome sequence of Balamuthia mandrillaris, the causative agent of amoebic encephalitis. Genome Announc. 3. doi: 10.1128/genomeA.01013-15.
Fucikovâ K. and Lahr D. J. 2016. Uncovering cryptic diversity in two amoebozoan species using complete mitochondrial genome sequences. J. Eukar. Microbiol. 63, 112-122.
Gray M.W. 2012. Evolutionary origin of RNA editing. Biochemistry. 51, 5235-5242.
Gray M. W. 2015. Mosaic nature of the mitochondrial proteome: implications for the origin and evolution of mitochondria. Proc. Natl. Acad. Sci. USA 112, 10133-10138.
Gray M.W., Burger G. and Lang B.F. 2001. The origin and early evolution ofmitochondria. Genome Biol. 2. doi: 10.1186/gb-2001-2-6-reviews1018.
Gray M.W., Lang F.B. and Burger G. 2004. Mitochondria of protists. Annu. Rev. Genet. 38, 477-524.
Göringer U.H. 2012. 'Gestalt,' composition and function ofthe Trypanosoma brucei editosome. Ann. Rev. Microbiol. 66, 65-82.
Greninger A.L., Messacar K., Dunnebacke T., Naccache S.N., Federman S., Bouquet J., Mirsky D., Nomura Y., Yagi S., Glaser C., Vollmer M., Press C.A., Kleinschmidt-DeMasters B.K., Dominguez S.R. and Chiu C.Y. 2015. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med. 1; doi: 10.1186/s13073-015-0235-2.
Heidel A., J. and Glöckner G. 2008. Mitochondrial genome evolution in the social amoebae. Mol. Biol. Evol. 25, 1440-1450.
Horton T.L. and Landweber L.F. 2000. Evolution of four types of RNA editing in myxomycetes. RNA 6, 1339-1346.
Houtz J., Cremona N. and Gott J.M. 2018. Editing of mitochondrial RNAs in Physarum polyce-phalum. In: RNA metabolism in mitochondria (Eds: Cruz-Reyes J. and Gray M.W.). Springer, Cham. pp. 199-222.
Janouskovec J., Tikhonenkov D.V., Burki F., Howe A.T., Rohwer F. L., Mylnikov A.P. and Keeling P.J. 2017. A new lineage of eukaryotes illuminates early mitochondrial genome reduction. Curr. Biol. 27, 3717-3724.
Kamikawa R., Shiratori T., Ishida K., Miyashita H. and Roger A.J. 2016. Group II intron-mediated trans-splicing in the gene-rich mitochondrial genome of an enigmatic eukaryote, Diphylleia rotans. Genome Biol. Evol. 8, 458-466.
Kang S., Tice A. K., Spiegel F.W., Silberman J.D., Panek T., Cepicka I., Kostka M., Kosakyan A., Alcantara D.M.C., Roger A. J., Shadwick L. L., Smirnov A., Kudryavtsev A., Lahr D. J. G. and Brown M. W. 2017. Between a pod and a hard test: the deep evolution of amoebae. Mol. Biol. Evol. 34, 2258-2270.
Kannan S., Rogozin I.B. and Koonin E.V. 2014. MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evol. Biol. 25, 214-237.
Karlyshev A.V. 2019. Remarkable features of mitochondrial DNA of Acanthamoeba polyphagia Linc Ap-1, revealed by whole-genome sequencing. Microbiol. Resour. Announc. doi: 10.1128/MRA. 00430-19.
Kosakyan A., Heger T.J., Leander B.S., Todo-rov M., Mitchell E.A.D. and Lara E. 2012. COI barcoding of nebelid testate amoebae (Amoebozoa: Arcellinida): extensive cryptic diversity and redefinition of family Hyalospheniidae Schultze. Protist. 163, 415-434.
Kudryavtsev A. 2014. Paravannella minima n.g. n.sp. (Discosea, Vannellidae) and distinction of the genera in the vannellid amoebae. Europ. J. Protistol. 50, 258-269.
Lang B.F., Laforest M.J. and Burger G. 2007. Mitochondrial introns: a critical view. Trends Genet. 23, 119-125.
Le P., Fisher P.R. and Barth C. 2009. Transcription of the Dictyostelium discoideum mitochon-drial genome occurs from a single initiation site. RNA 15, 2321-2330.
Lavrov D.V. and Pett W. 2016. Animal mitochondrial DNA as we do not know it: mt-genome organization and evolution in nonbilaterian lineages. Genome. Biol. Evol. 8, 2896-2913.
Lynch M., Koskella B. and Schaack S. 2006. Mutation pressure and the evolution of organelle genomic architecture. Science. 311, 1727-1730.
Miller D. 2014. Mitochondrial genomes in Amoebozoa. In: Molecular life sciences. Springer, New York. doi.org/10.1007/978-1-4614-6436-5_114-2.
Moreira S., Valach M., Aoulad-Aissa M., Otto C. and Burger G. 2016. Novel modes of RNA editing in mitochondria. Nucleic Acids Res. 44, 49074919.
Nakagawa C.C., Jones E.P. and Miller D.L. 1998. Mitochondrial DNA rearrangements associated with mF plasmid integration and plasmodial longevity in Physarum polycephalum. Curr. Genet. 33, 178-187.
Nassonova E., Smirnov A., Fahrni J. and Paw-lowski J. 2010. Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae. Protist. 161, 102-115.
Nomura H., Moriyama Y. and Kawano S. 2005. Rearrangements in the Physarum polycephalum mitochondrial genome associated with a transition from linear mF-mtDNA recombinants to circular molecules. Curr. Genet. 47, 100-110.
Ogawa S., Yoshino R., Angata K., Iwamoto M., Pi M., Kuroe K., Matsuo K., Morio T., Urushihara H., Yanagisawa K. and Tanaka Y. 2000. The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization. Mol. Gen. Genet. 263, 514-519.
Pombert J.-F., Smirnov A., James E. R., Janouskovec J., Gray M. W. and Keeling P. J. 2013. The complete mitochondrial genome from an unidentified Phalansterium species. Protist Genomics. 1, 25—32.
Schaap P., Barrantes I., Minx P., Sasaki N., Anderson R. W., Benard M., Biggar K. K., Buchler N. E., Bundschuh R., Chen X., Fronick C., Fulton L., Golderer G., Jahn N., Knoop V., Landweber L. F., Maric C., Miller D., Noegel A. A., Peace R., Pierron G., Sasaki T., Schallenberg-Rüdinger M., Schleicher M., Singh R., Spaller T., Storey K.B., Suzuki T., Tomlinson C., Tyson J.J., Warren W. C., Werner E. R., Werner-Felmayer G., Wilson R.K., Takano H., Abe T., Sakurai R., Moriyama Y., Miyazawa Y., Nozaki H., Kawano S., Sasaki N. and Kuroiwa T. 2001. The complete DNA sequence ofthe mitochondrial genome of Physarum polycephalum. Mol. Gen. Genet. 264, 539-545.
Tanifuji G., Cenci U., Moog D., Dean S., Nakayama T., David V., Fiala I., Curtis B.A.,
Sib-bald S. J., Onodera N. T., Colp M., Flegontov P., Johnson-MacKinnon J., McPhee M., Inagaki Y., Hashimoto T., Kelly S., Gull K., Lukes J. and Archibald J. M. 2017. Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis. Sci. Rep. 7, 11688.
Valach M., Moreira S., Hoffmann F., Stadler P. F. and Burger G. 2017. Keeping it complicated: Mitochondrial genome plasticity across diplone-mids. Sci. Rep. 7, 14166.
Yang J., Harding T., Kamikawa R., Simpson A.G.B. and Roger A.J. 2017. Mitochondrial genome evolution and a novel RNA editing system in deep-branching heteroloboseids. Genome Biol. Evol. 9:1161-1174.
Zlatogursky V.V., Kudryavtsev A., Udalov I. A., Bondarenko N., Pawlowski J. and Smirnov A. 2016. Genetic structure of a morphological species within the amoeba genus Korotnevella (Amoebozoa: Discosea), revealed by the analysis oftwo genes. Europ. J. Protistol. 56, 102-111.
Address for correspondence: Natalya Bondarenko. Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Universitetskaya nab. 7/9, 199034 Saint Petersburg, Russia; e-mail: n.bondarenko@spbu.ru.
