Download - Parabasalia (Excavata, Metamonada)
PARABASALIA (Excavata, Metamonada)
Vera Tai1, Erick R. James2, Patrick J. Keeling2 1BC-‐CFE in HIV/AIDS, St. Paul’s Hospital, Vancouver, BC, Canada
Amitochondriate proOsts (but have hydrogenosome) that are best known as parasites of vertebrate hosts (eg. Trichomonas vaginalis, Tritrichomonas foetus) Greatest diversity is found as symbionts in the hindguts of wood-‐eaOng cockroaches and termites Phylum is named aUer the parabasal apparatus which consists of a parabasal body (modified Golgi) with parabasal fibres that are aWached to basal bodies Most have an axostyle which is a hollow tube of a rolled row of microtubules Ancestor is thought to be a trichomonad-‐like cell, simple in structure, bearing 4 flagella, one of which is recurrent and underlain by the costa forming an undulaOng membrane Assumed to have evolved from simple to complex and was divided into two classes, the simpler Trichomonadida and the mulOflagellated HypermasOgida This view was overly simplisOc and current classificaOon includes 6 classes of Parabasalia implying several transiOons of mulOplicaOon and reducOon in flagellar, cytoskeletal, and nuclear elements Many are misclassified, especially smaller ones, due to misunderstanding of morphological evoluOon Many other parabasalids remain unclassified because new taxonomic groups need to be defined
are needed. In the present study, Spirotrichonymphea andHypotrichomonadea are represented by only two taxa and afurther taxon sampling may improve the resolution; however,
Hypotrichomonadea comprises only two genera [26] both ofwhich are included in the analyses and Spirotrichonymphea cells,usually small in size, are very hard to distinguish by lightmicroscopy if multiple species occur simultaneously in the gut oftermites (and they very often do).
Table 3. Shimodaira-Hasegawa (SH) and approximatelyunbiased (AU) tests for parabasalian root positions.
Root position P value
SH AU
a 0.012* 0.001*
b 0.088 0.044*
c 0.005* ,0.001*
d 0.019* 0.001*
e 0.367 0.161
f 0.378 0.013*
g 0.491 0.148
h 0.009* 0.002*
i 0.018* 0.001*
j 0.065 ,0.001*
k Best Best
Root positions are depicted in Figure 3. Asterisks indicate that the root positionwas significantly different from the best ML topology at P,0.05.doi:10.1371/journal.pone.0029938.t003
Figure 4. Maximum likelihood tree based on concatenation of GAPDH, actin, EF-1a, and SSU rRNA gene sequences and rooted byTrimastix. Unambiguously aligned amino acid sites of GAPDH (257), actin (268), and EF-1a (274), and nucleotide sites of SSU rRNA (1338) genesequences were concatenated and analyzed in 28 parabasalian species with Trimastix as an outgroup. The tree was estimated in RAxML using theCAT model (CATMIX). The parameters and branch length were optimized for each gene partition individually. The supporting values (bootstrap inRAxML/Bayesian posterior probability) are indicated at the nodes. Values below 50% or 0.5 are indicated by hyphens. Vertical bars to the right of thetree represent the parabasalian classes. The scale bar corresponds to 0.10 substitutions per site.doi:10.1371/journal.pone.0029938.g004
Table 4. Exclusion of parabasalian taxa and the effect ontheir root.
No. of parabasalian taxaexcluded 23 outgroup taxa 13 outgroup taxa
3 10 NT
6 10 NT
12 10 10
16 4 8
18 5 6
Values represent the number of occurrences of root position k (shown inFigure 3) in 10 replicates of the random taxa exclusion analyses in each definednumber of excluded taxa. NT, not tested. The 23 outgroup taxa correspond tothe concatenate dataset of EF-1a, actin, and SSU rRNA gene sequences using 23outgroup taxa as shown in Figure 3, whereas the 13 outgroup taxa correspondto those remained after excluding 10 long-branch outgroup taxa (asinvestigated in Table S1). Note that in the cases of 16 and 18 taxa exclusions, allother replicates demonstrated the root position at the branch leading toTrichonymphea (position g).doi:10.1371/journal.pone.0029938.t004
Phylogeny and Evolution of Parabasalia
PLoS ONE | www.plosone.org 8 January 2012 | Volume 7 | Issue 1 | e29938
C. Trichomonadea O. Trichomonadida F. Trichomonadidae O. Honigbergiellida, F. Honigbergiellidae F. Hexamastigidae F. Tricercomitidae
C. Hypotrichomonadea O. Hypotrichomonadida F. Hypotrichomonadidae
C. Tritrichomonadea O. Tritrichomonadida F. Tritrichomonadidae F. Dientamoebidae F. Monocercomonadidae
C. Cristamonadea O. Cristamonadida F. Lophomonadidae
C. Trichonymphea O. Trichonymphida F. Hoplonymphidae F. Staurojoenidae F. Trichonymphidae F. Teranymphidae F. Spirotrichosomidae
C. Spirotrichonymphea O. Spirotrichonymphida F. Holomastigotoididae
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CURRENT CLASSIFICATION based on Cepicka et al. 2010
Cristamonadida
Trichonymphida
Spirotrichonymphida
Trichomonadida
Tritrichomonas murisImage caption: Scanning electron micrograph of cells from a rodent.
Page 1/1
image by G. Brugerolle
image by G. Brugerolle
Tritrichomonadida
Hypotrichomonadida image by J. Cole
2Department of Botany, University of BriOsh Columbia, Vancouver, BC, Canada
ARTICLE IN PRESS
I. Cepicka et al.418
PHYLOGENY OF MAJOR LINEAGES Noda et al. 2012
EVOLUTION of MORPHOLOGICAL TRAITS Cepicka et al. 2012
EXAMPLE IMAGES of MAJOR LINEAGES
MANY DESCRIBED ORGANISMS ARE UNCLASSIFIED or MISCLASSIFIED, MANY MORE ARE BEING DISCOVERED, WITH PARTICULARINTEREST ON FREE-‐LIVING ONES THAT MAY SHED LIGHT ON THE ROOT OF THE EXCAVATA
Cthylla microfasciculumque n. sp. James and Keeling,2012urn:lsid:zoobank.org:act:C5109A93-A1EC-4362-AEBF-
D2E538C55D66Type host: Reticulitermes virginicus (Isoptera, Rhinotermitidae:
barcode JX975354)Type locality: Ft. Lauderdale, Secrete Woods County Park,
Florida, USA: lat. 26.08567, long. 280.18017.Host collection: University of Florida termite collection,
accession number FL2261. Collector R. H. Scheffrahn. CollectedFeb 21, 2005.Description: Parabasalian flagellate with morphological
characteristics of the genus Cthylla. Cells are 10 to 15 mm inlength and 6 to 10 mm in width. Found in the hindgut ofReticulitermes virginicus. Distinct SSU rRNA sequence (GenBankaccession number JX975350)Hapantotype: Microscope slide deposited at the Beaty
Biodiversity Museum, University of British Columbia, Vancouver,Canada under accession number MI-PR201.Gene sequence: SSU rRNA accession number JX975350.Etymology: Species name refers to the small (micro) bunch
(fasciculumque) of flagella.
Materials and Methods
Host identification and barcodingParaneotermes simplex was collected Sept. 15, 2002 in Secret
Woods County Park, Ft. Lauderdale, Florida, (lat. 26.08567, long.280.18017) and deposited in the University of Florida termite
collection, accession number FL1563. Reticulitermes virginicus wascollected on Feb 21, 2005 at the same location and deposited inthe University of Florida termite collection, accession numberFL2261. Cryptotermes cylindroceps, Calcaritermes nearcticus, and Hetero-termes tenuis were collected as reported previously [21,22]. Nospecific permits were required for the described field studies, thelocations are not privately owned or protected, and no endangeredor protected species were collected.DNA barcodes at the mitochondrial 16S (LSU) rRNA marker
for P. simplex and R. virginicus were amplified using LR-N-13398CGCCTGTTTATCAAAAACAT and LR-J-13007TTACGCTGTTATCCCTAA under conditions previously de-scribed [21,22]. Since no comparable P. simplex barcode wasavailable, we also barcoded P. simplex from eight other indepen-dent isolations (University of Florida Termite collection accessionsFL2476, FL1793, PR348, BA2814, BZ87, GUA615, HN24, andHN700) from Florida, Puerto Rico, Bahamas, Belize, Guatemala,and Honduras (the latter three being new regional and countryrecords for this species). These new barcodes were submitted toGenBank under accessions KC140183-90. These were alignedwith all available Paraneotermes and Reticulitermes mt LSU termitebarcodes from Genbank using MAFFT [24], and refined by eyeusing SeaView [25]. Poorly aligned regions were automaticallyremoved with trimAl using a gap threshold of 0.9 [26]. AIC weightas calculated with the perl script MrAIC.pl [27] was used todetermine the evolutionary model that best fit the data, whichcorresponded to GTR+C+I in all cases. For the termite phylogeny,Maximum Likelihood (ML) estimation was carried out using
Figure 5. Phylogenetic relationships between Cthulhu, Cthylla, environmental sequences, and closely related parabasalians. Bayesiantree with posterior probabilities (upper) and maximum likelihood bootstraps (lower) indicated for each node, and major identified groups named tothe right. Cthulhu and Cthylla are both related to unidentified environmental sequences from Heterotermes tenuis and Reticulitermes chinensis,respectively. They are all closely related to a large clade of unidentified environmental sequences from Cryptotermes, Glyptotermes, and Calcaritermes,which has previously been hypothesized to represent Tricercomitus. If true, then Cthulhu and Cthylla would be best considered members of theTricercomitidae, thought this will depend on molecular characterization for this group.doi:10.1371/journal.pone.0058509.g005
Cthulhu and Cthylla
PLOS ONE | www.plosone.org 6 March 2013 | Volume 8 | Issue 3 | e58509
Ctuhlhu and Cthylla are possibly members of a yet to be described order of Trichomonadida (James et al. 2013)
Cthulhu
Kofoidia
Kofoidia is a Cristamonad, but taxa known as the lophomonads (*)are polyphyleOc and the type genus of the family Lophomonadidae groups outside of the Cristamonadea. A redefined taxonomy is needed for the cristamonads (Tai et al. 2015)
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REFERENCES Cepicka et al. 2010. CriOcal taxonomic revision of parabasalids with descripOon of one new genus and three new species. Pro8st. 161: 400-‐433
Tai et al. 2015. The phylogeneOc posiOon of Kofoidia loriculata (Parabasalia) and its implicaOons for the evoluOon of the Cristamonadea. J Euk Micro. 62: 255-‐259
James et al. 2013. Cthulhu macrofasciculumque n. g., n. sp. and Cthylla microfasciculumque n. g., n. sp., a newly idenOfied lineage of parabasalian termite symbionts. PLoSONE. 8: e58509
Noda et al. 2012. Molecular phylogeny and evoluOon of Parabasalia with improved taxon sampling and new protein markers of acOn and elongaOon factor-‐1α. PLoSONE. 7: e29938