building the first ssu database of phagotrophic euglenids using single-cell approaches
TRANSCRIPT
Building the first SSU database of phagotrophic euglenidsusing single-cell approaches
SSU PhylogenyRAxML GTR gamma1000 bootstraps957 sites
Simpson Lab website:
protists.biology.dal.ca
Taxon sampling of phagotrophic euglenids is extremely limited for all molecular markers including the SSU gene, mainly because there are very few cultures available (see Table 1).
The culture-independent approach demonstrated here enables collection of micrographic data (for identification) and SSU genes from a single cell, using either multiple-displacement amplification (MDA) and PCR, partial shotgun-genomics, or single-cell transcriptomics.
The wide range of taxa successfully sampled with these methods shows that they can rapidly produce much-improved (and much-needed) coverage of phagotrophic euglenid diversity.
Fig. 1: Examples of SSU-typed phagotrophic euglenid cells. Top row, left to right: Anisonema acinus (SDB4), Chasmostoma nieuportense (UB23), Urceolus sp. (UB25), Petalomonas planus (UB22). Bottom row, left to right: Ploeotia cf. vitrea (U4), Neometanema sp. (SDB8), Dinema sp. (UB26), Heteronema globuliferum (BP3). Colors and symbols correspond to Table 1. Scale bars are 20µm.
MethodsPHOTOTROPHS
OSMOTROPHS
SYMBIONTIDS
OUTGROUP
Table 1: Genera of phagotrophic euglenids ordered by availability of SSU data (outside this study). 2 = sequences from 2 species only, 1 = 1 species only, 0 = no sequences available. New data obtained in this study shown in colored symbols (correspond to Fig. 1).
sedimentsample
extraction /analysisof SSU
pick single cells
photo-documentation
transcriptome
shotgungenome
seq.
SSU-PCR(via MDA)
Gordon Lax & Alastair Simpson Dalhousie University
PetalomonasNotosolenusAnisonemaPeranemaPloeotiaHeteronemaNeometanemaDinemaKeelungiaEntosiphonUrceolusJenningsiaSphenomonasLentomonasChasmostomaCalycimonasScytomonasDoliumDylakosoma
2
1
0
# SSU via PCR
# shotgun genome data
# transcriptomes
28 new SSU sequences+1 Entosiphon sulcatum(not shown)
0.1
Anisonema sp. W1
Lepocinclis ovum
Ploeotia costata (brackish)
Neobodo saliens
Anisonema sp. SDB1
Bihospites bacati isolate 2
Parmidium circulare
Trypanoplasma borreli
Ploeotia corrugata UB21
Dinema platysomum U5
Notosolenus ostium U1
Neometanema sp. BP5Neometanema exaratum U2
Anisonema sp. SMS2
Dinema litorale UBJ2
Peranema trichophorum CCAP1260/1B
Petalomonas sphagnophila GU477296
Peranema trichophorum PtR
Cryptobia helicis
Ploeotia cf. vitrea U4
Cryptoglena pigraMonomorphina pyrum
Keelungia pulex
Heteronema scaphurum
Peranema trichophorum
Ploeotia costata AF525486
Trachelomonas abrupta
Diplonema papillatum
Petalomonas cantuscygni
Colacium vesiculosum
Anisonema acinus B1
Heteronema globuliferum BP3
Environmental sequence AY821956
Petalomonas cantuscygni CCAP 1259/1
Eutreptia viridis
Urceolus sp. UB25
Bodo saltans
Rapaza viridis
Anisonema sp. SDB4
Distigma gracilis
Euglena viridis
Gyropaigne lefevrei
Dimastigella trypaniformis
Notosolenus urceolatus M49
Petalomonas planus UB22
Rhynchobodo sp.
Phacus parvulus
Anisonema sp. G1
Rhynchomonas nasuta
Dinema sulcatum
Calkinsia aureus
Notosolenus ostium
Peranema sp. AY048919
Environmental sequence GQ330643
Environmental sequence EF100248
Environmental sequence HM749952
Urceolus sp. UB24
Anisonema sp. PP1
Environmental sequence AY821958
Anisonema/Dinema sp. U3
Dinema/Heteronema sp. CD5
Neometanema sp. BP6
Neometanema sp. SDB8
Distigma curvatum
Petalomonas sphagnophila GU477297
Ichthyobodo necator
Neometanema larsenii SDB3
Neometanema parovale M51
Dinema sp. UB26
Environmental sequence AY821957
Petalomonas sphagnophila GU477295
Environmental sequence AB505539
Anisonema acinus
Anisonema sp. SAL5
Dinema litorale UB10
Menoidium pellucidum
Environmental sequence DQ310255
Heteronema sp. PP2
Rhabdomonas incurva
Ploeotia costata (marine)
Bihospites bacati isolate 1
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