These alignments of nuclear rRNA sequences from kinetoplastids were used for phylogenetic reconstructions involved in an ongoing analysis of the evolutionary origin of the U-insertion/deletion type of RNA editing. They are presented in the formats required for phylogenetic analysis.
Click on the specific Alignment to get the sequence file.
Content: small subunit ribosomal RNA dataset from 20 taxa, PAUP
format, cropped (unalignable or ambiguously aligned regions excluded).
Species names:
'Crifasci' - Crithdia fasciculata
'Leptomon' -
Leptomonas sp.
'Ldonovan' - Leishmania donovani
'Phytomon' - Phytmonas
serpens
'Blastcul' - Blastocrithidia culicis
'Crioncop' - Crithidia
oncopelti
'Tboisson' - Trypanosoma boissoni
'trotator' - Trypanosoma
rotatorium
'Ttriglae' - Trypanosoma triglae
'Tavium' - Trypanosoma
avium
'Try.cruz' - Trypanosoma cruzi
'Tjarrovi' - Trypanosoma
sceloporium
'Tcarassi' - Trypanosoma carassii
Tsimiae' - Trypanosoma
simiae
'Tvivax' - Trypanosoma vivax
Tcongo'-Trypanosoma congolense'
'TRYBRUCE' - Trypanosoma brucei
'Dimastig' - Dimastig '
trypaniformisella
'Rhynbodo' - Rhynchobodo sp.
'TBORRELI' -
Trypanoplasma borreli
Reference:
J. Lukes, M. Jirku, D. Dolezel, I. Kralova, L.
Hollar, D. Maslov. Analysis of ribosomal RNA genes suggests that trypanosomes
are monophyletic. J. Mol. Evol. (1997) 44:521-527.
[MED]
Same as Alignment #1, but contains full sequences (uncropped alignment). The line marked 'weights' indicates positions which were included in Alignment #1 (with weights equal 1) and excluded from it (with weights equal 0).
Content: combined small subunit and large subunit ribosomal RNA
dataset for 13 taxa, cropped, PAUP format.
Species names:
'Leptomon' - Leptomonas sp
'Ldonovan' - Leishmania donovani
'Phytserp'
- Phytomonas serpens
'Blastcul' - Blastocrithidia culicis
'Tboisson' -
Trypanosoma boissoni
'trotator' - Trypanosoma rotatorium
'Ttriglae' -
Trypanosoma triglae
'Tavium' - Trypanosoma avium
'Try.cruz' -
Trypanosoma cruzi
'Tcarassi' - Trypanosoma carassii
'TRYBRUCE' -
Trypanosoma brucei
'TBORRELI' - Trypanoplasma borreli
'TBORRELI' -
Trypanoplasma borreli
Reference:
D. Maslov, J. Lukes, M. Jirku, L. Simpson.
Phylogeny of trypanosomes as inferred from the small and large subunit rRNA:
implications for the evolution of parasitism in the trypanosomatid protozoa.
Mol. Biochem. Parasitol. (1996) 75:197-205.[MED]
Same as Alignment #3, but uncropped and weights indicated.
Content: small subunit rRNA dataset for 17 taxa, cropped, PAUP format
Species names:
'CRIFASCI' - Crithidia fasciculata
'LSPSSRRG' - Leptomonas sp.
'L_tarent' - Leishmania tarentolae
'E_monter' - Endotrypanum monterogei
'Phytserp' - Phytomonas serpens
'HERPMUSC' - Herpetomonas muscarum
'concop ' - Crithidia oncopelti
'Blastcul' - Blastocrithidia culicis
'Tavium ' - Trypanosoma avium
'Tboisson' - Trypanosoma boissoni
'Ttriglae' - Trypanosoma triglae
'trotator' - Trypanosoma rotatorium
'Try.cruz' - Trypanosoma cruzi
'T_sp_cp ' - Trypanosoma carassii
'TRYBRUCE' - Trypanosoma brucei
'TBORRELI' - Trypanoplasma borreli
'BODSSRRN' - Bodo caudatus
Reference:
D. Maslov, J. Lukes, M. Jirku, L. Simpson.
Phylogeny of trypanosomes as inferred from the small and large subunit rRNA:
implications for the evolution of parasitism in the trypanosomatid protozoa.
Mol. Biochem. Parasitol. (1996) 75:197-205.
[MED]
Same as Alignment #5, but uncropped, with weights indicated.
Content
Small subunit rRNA cropped alignment. Same as
Alignment #1 and #2, but in addition contains several Phytomonas SSU
sequences.
Reference
L. Hollar, D.A. Maslov (1997) A phylogenetic view
on the genus Phytomonas. Mol. Biochem. Parasitol. 89:295-299.
Content
Cytochrome oxidase subunit I gene from kinetoplastids
and Diplonema
Saccerev - Saccharomyces cerevisiae
Isonema -
Diplonema (Isonema) papillatum
Euglena - Euglena gracilis
Tborreli -
Trypanoplasma borreli
Tbrucei - Trypanosoma brucei
Wheat - Triticum
aestivum
Ltarent - Leishmania tarentolae
Reference:
D.A. Maslov and L. Simpson (1999) Phylogenetic
affinities of Diplonemawithin the Euglenozoa as inferred from the SSU
rRNA gene and partial COI protein sequences. Protist. 150:33-42 (1999)
Content:
SSU rRNA alignments of kinetoplastids and
Diplonema
'Ltarent' - Leishmania tarentolae
'Herpmusc'-
Herpetomonas muscarum
'Phytse1G' - Phytomonas serpens
'Blastcul' -
Blastocrithidia culicis
'TRYBRUCE' - Trypanosoma brucei
'Dimastig' -
Dimastigella trypaniformis
'Rhynbodo' - Rhynchobodo sp.
'TBORRELI' -
Trypanoplasma borreli
'Bocaudat' - Bodo caudatus
'Isonema' -
Diplonema (Isonema) papillatum
'DIPLONEM' - Diplonema sp.
'Euglena' -
Euglena gracilis
'Khawkine' - Khawkinea quartana
'Lepocinc' -
Lepocinclis ovata
'Petalomo' - Petalomonas cantuscygni
'PHYSARUM' -
Physarum polycephalum
'Saccerev' - Saccharomyces cerevisiae
Reference:
D.A. Maslov and L. Simpson (1999) Phylogenetic
affinities of Diplonema within the Euglenozoa as inferred from the SSU
rRNA gene and partial COI protein sequences. Protist. 150:33-42 (1999)
Content:
'Crifasci' - Crithidia fasciculata
'Herpmusc' - Herpetomonas
muscarum
'Phytse1G' - Phytomonas serpens 1G
'Herproit' - Herpetomonas
roitmani TCC080
'Try.cruz' - Trypanosoma cruzi
'Dimastig' -
Dimastigella trypaniformis Ulm
'DimaGlas' - Dimastigella trypaniformis
Glasgow
'Dimimosa' - Dimastigella mimosa
'Rhynbodo' - "Rhynchobodo" sp.
'TBORRELI' - Trypanoplasma borreli
'crypbull' - Cryptobia bullocki
'crypsalm' - Cryptobia salmositica
'crypcato' - Cryptobia catostomi
'Cruzemar' - Cruzella marina
'Crypthel' - Cryptobia helicis
'BosaltK' - Bodo saltans Konstanz
'BosaltP' - Bodo saltans St.
Petersburg
'Buncinat' - Bodo uncinatus
'bodesign' - Bodo designis
'Bodosoro' - Bodo sorokini
'Parabodo' - Parabodo nitrophilus
'Bocaudat' - Bodo caudatus
'Isonema' - Diplonema papillatum
'DIPLONEM' - Diplonema sp.
'Euglena' - Euglena gracilis
'Khawkine'
- Khawkinea quartana
'Lepocinc' - Lepocinclis ovata
Reference:
David Dolezel, Milan Jirku, Dmitri A. Maslov and Julius Lukes . Phylogeny of the bodonid flagellates (Kinetoplastida) based on small subunit rRNA gene sequences. International Journal of Systematic and Evolutionary Microbiology, 2000, In press.
Content: srRNA alignments of kinetoplastids
Abstract of the paper: With the aim of further investigating phylogenetic relationships in insect trypanosomatids, we have determined the sequences of small subunit rRNA genes from ten isolates, which were originally classified as Leptomonas, Blastocrithidia, and Wallaceina based on their morphology in the hosts. The inferred maximum likelihood, parsimony, and distance trees indicate that the Leptomonas and Blastocrithidia are polyphyletic, and confirm the polyphyly of Herpetomonas and Crithidia. Blastocrithidia triatoma and Leptomonas collosoma were among the earliest branching lineages among the insect trypanosomatids, while most other isolates were found within a closely related terminal clade, which also included Crithidia fasciculata. This analysis has clearly demonstrated that the morphological classification system of insect trypanosomatids does not always reflect their genetic affinities warranting its revision in the future. The presented alignments correspond to the alignments for taxon sets 1 (leptomon.paup), 2 (ingroup.paup) and 3 (crown.paup) described in the text.
Reference:
E. Merzlyak, V. Yurchenko, A.A. Kolesnikov, K. Alexandrov, S.A. Podlipaev, D.A. Maslov. Diversity and phylogeny of insect trypanosomatids based on small subunit rRNA genes: polyphyly of Leptomonas and Blastocrithidia. J. Euk. Micro., 48(2), 2001, 163-171.