Supplemental Material for Drouin and Tsang (JME, 2012)

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Supplemental Material for Drouin and Tsang (JME, 2012)

Supplemental table 1. Accession numbers and references for the arrangement of 5S rRNA genes in Stramenopile, Haptopte, Cryptophyte and Metamonada species.

Organism / Linked To / Orientation / Ref / Accession #
Vaucheria terrestris
(stramenopiles; Xanthophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Vaucheria dichotoma
(stramenopiles; Xanthophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Ophiocytium sp.
(stramenopiles; Xanthophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Scytosiphon lomentaria
(stramenopiles; Phaeophyceae) / rDNA / Sense / Kawai et al. (1995) / D16558
Heterosigma akashiwo
(stramenopiles; Raphidophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Olisthodiscus luteus
(stramenopiles; Raphidophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Phaeomonas parva
(stramenopiles; Pinguiophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Phaeosaccion collinsii
(stramenopiles; Chrysophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Synura petersenii
(stramenopiles; Synurophyceae) / Not linked to rDNA / Kawai et al. (1997) / Not deposited in GenBank
Eustigmatos vischeri
(stramenopiles; Eustigmatophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Pseudopedinella pyriformis
(stramenopiles; Dictyochophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Sulcochrysis biplastida / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Ditylum brightwellii
(stramenopiles; Bacillariophyceae) / Not linked to rDNA / Kawai et al. (1997) / Not deposited in GenBank
Nitzschia palea
(stramenopiles; Bacillariophyceae) / Not linked to rDNA / Kawai et al. (1997) / Not deposited in GenBank
Opalina sp.
(stramenopiles; Slopalinida; Opalinidae) / rDNA / Sense / Kawai et al. (1997) – Phylogenetic position not clear: not included in Fig.1 / Not deposited in GenBank
Proteromonas lacerate
(stramenopiles; Slopalinida; Proteromonadidae) / rDNA / Sense / Kawai et al. (1997) – Phylogenetic position not clear: not included in Fig.1 / Not deposited in GenBank
Achlya klebsiana / rDNA / Sense / Belkhiri et al. (1992) / Not applicable: PCR amplification
Pachymetra chaunorhiza / rDNA / Antisense / Belkhiri et al. (1992) / Not applicable: PCR amplification
Verrucalvus flavofaciens / rDNA / Antisense / Belkhiri et al. (1992) / Not applicable: PCR amplification
Phytophthora cryptogea / rDNA / Sense / Belkhiri et al. (1992) / Not applicable: PCR amplification
Phytophthora vignae / rDNA / Sense / Howlett et al. (1992) / Not applicable: PCR amplification
Phytophthora cinnamomi / rDNA / Sense / Howlett et al. (1992) / Not applicable: PCR amplification
Phytophthora megasperma / rDNA / Sense / Howlett et al. (1992) / Not applicable: PCR amplification
Saprolegnia ferax / rDNA– Phylogenetic position not clear: not included in Fig.1 / Sense / Howlett et al. (1992) / Not applicable: PCR amplification
Lagenidium giganteum / rDNA / Antisense / Belkhiri et al. (1992) / Not applicable: PCR amplification
Emiliania huxleyi / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Rhinomonas pauca / rDNA / Sense / Gilson et al. (1995) / Not deposited in GenBank
Storeatula major / rDNA / Sense / Gilson et al. (1995) / Not deposited in GenBank
Komma caudata / rDNA / Sense / Gilson et al. (1995) / Not deposited in GenBank
Trichomonas vaginalis / rDNA / No / Torres-Machorro et al. (2009) / FJ492751
Trichomonas tenax / rDNA / No / Torres-Machorro et al. (2009) / FJ492747,
FJ492748
Trichomonas foetus / Ubiquitin genes (type A) and pseudogenes (type B) / Sense / Torres-Machorro et al. (2009) / FJ492749, FJ492750
Giardia lamblia / rDNA / No / Morrison et al. (2007) / AACB02000003, AACB02000013, AACB02000031, AACB02000054,

Belkhiri A, Buchko J & Klassen GR (1992) The 5S ribosomal RNA gene in Pythium species: two different genomic locations. Mol Biol Evol 9: 1089-1102.

Gilson PR, Adcock GJ, Howlett BJ & McFadden GI. (1995) Organisation and sequence analysis of nuclear-encoded 5s ribosomal RNA genes in cryptomonad algae. Curr Genet 27:239-242.

Howlett BJ, Brownlee AG, Guest DI, Adcock GJ & McFadden GI (1992) The 5S ribosomal RNA gene is linked to large and small subunit ribosomal RNA genes in the oomycetes, Phytophthora vignae, P. cinnamomi, P. megasperma f.sp. glycinea and Saprolegnia ferax. Curr Genet 22: 455-461.

Kawai H, Muto H, Fujii T Kato A (1995) A linked 5S rRNA gene in Scytosiphon lomentaria. J Phycol 31: 306-311.

Kawai H, Nakayama T, Inouye I Kato A (1997), Linkage of 5S ribosomal DNA to other rDNAs in the chromophytic algae and related taxa. J Phycol 33: 505–511.

Morrison HG, McArthur AG, Gillin FD, Aley SB, Adam RD, Olsen GJ, Best AA, Cande WZ, Chen F, Cipriano MJ, Davids BJ, Dawson SC, Elmendorf HG, Hehl AB, Holder ME, Huse SM, Kim UU, Lasek-Nesselquist E, Manning G, Nigam A, Nixon JE, Palm D, Passamaneck NE, Prabhu A, Reich CI, Reiner DS, Samuelson J, Svard SG & Sogin ML (2007) Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317:1921-1926.

Torres-Machorro AL, Hernández R, Alderete JF & López-Villaseñor I (2009) Comparative analyses among the Trichomonas vaginalis, Trichomonas tenax, and Tritrichomonas foetus 5S ribosomal RNA genes. Curr Genet 55: 199-210.

Supplemental table 2. Accession numbers and references for the arrangement of 5S rRNA genes in Alveolates (Dinoflagellates, Apicomplexa and Ciliates).

Dinoflagellates
Species / Linked To / Orientation / Ref / Accession #
Karlodinium sp. KAMS0708
(Alveolata; Dinophyceae) / rDNA / Sense / FN357291
Karlodinium veneficum
(Alveolata; Dinophyceae) / SL and unlinked / Antisense / Zhang H. (2009) / GQ199970 toGQ200017,
FJ434789 to FJ434800
Karenia brevis
(Alveolata; Dinophyceae) / SL and U6 / Antisense / Zhang et al (2009) / FJ434722 to
FJ434729
Pfiesteria piscicida
(Alveolata; Dinophyceae) / SL / Antisense / Zhang H (2009) / FJ434781-FJ434788
Prorocentrum minimum
(Alveolata; Dinophyceae) / Not linked / Zhang H (2009) / FJ434801 to
FJ434805
Prorocentrum micans
(Alveolata; Dinophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Polarella glacialis
(Alveolata; Dinophyceae) / SL / Antisense / Zhang H (2009) / FJ434764 to FJ434776
Heterocapsa arctica
(Alveolata; Dinophyceae) / SL / Antisense / Zhang H (2009) / FJ434818-
FJ434763
Amphidinium sp.
(Alveolata; Dinophyceae) / rDNA / Sense / Kawai et al. (1997) / Not deposited in GenBank
Perkinsus andrewsi
(Alveolata; Perkinsea) / rDNA / Sense / Pecher et al. (2004) / AY305326, AY305327
Perkinsus olseni
(Alveolata; Perkinsea) / rDNA / Sense / AF466527,
AF466532
Perkinsus sp.
(Alveolata; Perkinsea) / rDNA / Sense / AF466533-
AF466540
Perkinsus atlanticus
(Alveolata; Perkinsea) / rDNA / Sense / Robledo JA (2002) / AF509333
Perkinsus marinus
(Alveolata; Perkinsea) / rDNA / Sense / Robledo JA (1999) / AF497479
Apicomplexa
Plasmodium vivax
(Alveolata; Apicomplexa) / Not linked to rDNA (3 copies) / Carlton (2008) / AAKM01000002
Plasmodium knowlesi
(Alveolata; Apicomplexa) / Not linked to rDNA (1 copy) / Pain A. (2008) / NC_011904
Plasmodium falciparum
(Alveolata; Apicomplexa) / Not linked to rDNA (3 clustered copies) / Shippen-Lentz and Vezza (1988)
Gardner et al. (2002)
Pain (2002) / M19136
NC_004317
Theileria annulata
(Alveolata; Apicomplexa) / Not linked to rDNA / Pain (2005) / NC_011099
Theileria parva
(Alveolata; Apicomplexa) / Not linked to rDNA (1 copy) / Gardner MJ (2005) / AAGK01000002
Neospora caninum
(Alveolata; Apicomplexa) / Not linked to rDNA / BLAST at NCBI / FR823385,
FR823390, FR823391,
Toxoplasma gondii
(Alveolata; Apicomplexa) / rRNA / Sense / Gagnon et al. (1996)
Fazaeli et al. (2000) / X75429,
AF158092-AF158095
Cryptosporidium parvum
(Alveolata; Apicomplexa) / Not linked to rDNA (3 copies) / Abrahamsen MS (2004) / AAEE01000004
Cryptosporidium hominis
(Alveolata; Apicomplexa) / Not linked to rDNA (2 and 3 copies on 2 diff. chr.) / Xu P (2004) / NW_667385 and
NW_667307
Ascogregarina taiwanensis
(Alveolata; Apicomplexa) / rRNA / Sense / Unpublished / EF666482
Ciliates
Tetrahymena pyriformis
(Alveolata; Ciliophora) / Two 5S genes in between polyubiquitin genes / Sense / Guerreiro et al. (1993) / Z22614
Paramecium tetraurelia
(Alveolata; Ciliophora) / Not linked to rDNA / Findly and Gall (1980) / Not sequenced (Southern blots)

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Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM & Barrell B (2002) Genome sequence of the human malaria parasite Plasmodium falciparum. Nature 419: 498-511.

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Gagnon S, Morency MJ, Bourbeau D & Levesque RC (1996) Toxoplasma gondii: structure and characterization of the 26S ribosomal RNA and peptidyl transferase domain. Exp Parasitol 83: 346-351.

Guerreiro P, Neves A & Rodrigues-Pousada C (1993) Clusters of 5S rRNAs in the intergenic region of ubiquitin genes in Tetrahymena pyriformis. Biochim Biophys Acta 1216: 137-139.

Kawai H, Nakayama T, Inouye I Kato A (1997) Linkage of 5S ribosomal DNA to other rDNAs in the chromophytic algae and related taxa. J Phycol 33: 505–511.

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