Hartmannella vermiformis
598 - Hv Contig 598 is removed due to the hit to a Jakobid
sequence in PEPdb.
863 - Despite the presence of multiple eukaryotic sequences in
the tree, this sequence passes as an LGT due to strong
clustering with actinobacterial sequence and high levels of
bootstrap support for separation from the other eukaryotic
sequences.
918 - This clone is a strong pass – there is only one
actinobacterial sequence similar to it, and no other eukaryotic
hits in any database anywere.
465 - This is a strong positive hit, with no eukaryotic
orthologs or paralogs and strong bootstrap clustering with
bacterial taxa.
59 - There are some eukaryotic hits, but the Hartmannella
sequence clusters strongly apart on a bacterial branch.
664 - There is a single eukaryotic hit to an EST from Sorghum.
The identity is sufficiently strong that we regard it as a
likely case of amoebal contamination in the EST library. Apart
from that there are no eukaryotic hits.
1187 - Eliminated as a lateral candidate due to the presence of
clear Fungal orthologs. Nonetheless this could be a basal (to
Amoebozoa+Fungi) LGT for an anaerobic-linked nitrite reductase.
However there may be poorly supported clustering with plant
paralogs as well.
277 - Cluster 277 hits only three bacterial sequences and no
eukaryotic sequences. It is thus a solid candidate for an LGT
event.
1030 - Pinus has a perfect match hit to a single EST – once
again we are inclined to classify this as a contaminant due to
the excessively high level of sequence similarity. There appear
to be plant paralogs to this gene, but they are not strongly
similar to the Amoebozoan sequences. This is nonetheless a very
questionable candidate even based upon bootstraps in the absence
of the additional EST.
474 - There are a large number of eukaryotic hits to this
sequence in both Genbank and PEPdb. We therefore reject it at
the secondary screening.
480 - This sequence is a strong pass.
It clearly clusters with
cyanobacterial sequence and has no obvious eukaryotic orthologs
or paralogs.
102 - This sequence is another strong pass as it clusters
strictly with bacterial genes.
891 - This sequence is eliminated – multiple databases contain
multiple eukaryotic genes which have substantial sequence
similarity.
946 - Fructokinase. This sequence is eliminated on secondary
screening due to the presence of multiple eukaryotic sequences
with strong similarity.
143 - This sequence is eliminated on tertiary screening due to
poor bootstrap support for basal nodes, with possible linkage to
other eukaryotic sequences.
1198 - Rejected on tertiary screening – not strongly separated
from the Arabidopsis sequence.
65 - Reject due to incomplete seperation from
Giardia/Spironucleus sequences on tertiary screening (poor
bootstraps).
445 - Rejected on tertiary screening – clearly clusters with
other eukaryotic sequences.
486 - Rejected on secondary screen due to hits against multiple
eukaryotes in multiple databases.
496 - No eukaryotic hits, tertiary screening clusters it clearly
with proteobacteria. Passes as LGT candidate.
504 - Rejected on secondary screen due to presence of multiple
eukarotic hits.
524 - Rejected on secondary screen due to presence of multiple
eukarotic hits.
584 - Clusters at 63% bootstraps with with spirochaete sequence.
Appears to be cleanly separate from other eukaryotic sequences.
615 - Rejected on secondary screen due to presence of many
eukarotic hits.
627 - Clusters strongly with Lactobacillus, Streptococcus,
Burkholderia.
733 - Rejected on tertiary screen due to insufficient separation
from other eukaryotic sequences (poor bootstraps).
751 - Rejected on secondary screen due to multiple eukaryotic
hits in other databases.
782 - Rejected on secondary screen due to multiple eukaryotic
hits in other databases.
1048 - Rejected on secondary screen due to multiple eukaryotic
his in other databases.
1091 - Strong clustering with cyanobacterial sequences, no
apparent eukaryotic sequences in any database.
Toxoplasma
837 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Apicomplexa.
425 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Apicomplexa.
1194 - Eliminated on secondary screen due to many eukaryotic
hits outside of the Apicomplexa.
Chlamydomonas
391 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Chlorophyta.
648 - Eliminated on secondary screen due to multiple eukaryotic
hits outside of the Chlorophyta.
727 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Chlorophyta.
611 - Eliminated on secondary screen due to multiple eukaryotic
hits outside of the Chlorophyta.
854 - Eliminated on tertiary screen due to strong clustering
with the cyanobacteria.
Drosophila
74 - Eliminated on tertiary screening – does not strongly
separate from other eukaryotic sequences.
MUST DO PROPER BOOTS
195 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Metazoa.
645 - Passes tertiary screen as a candidate LGT since there are
no hits to eukaryotic phyla apart from Metazoa.
948 - Eliminated on secondary screen due to many eukaryotic hits
outside of the Metazoa.
1462 - Passes tertiary screen as a candidate LGT since there are
no hits to eukaryotic phyla apart from Metazoa.
1497 - This is essentially an identical sequence to 1462 – may
have an unprocessed intron.
1499 - Eliminated on secondary screen due to many eukaryotic
hits outside of the Metazoa.
620 - Eliminated on secondary screen due to eukaryotic hits
outside of the Metazoa.
876 - Eliminated on secondary screen due to eukaryotic hits
outside of the Metazoa.
1174 - Eliminated on secondary screen due to many eukaryotic
hits outside of the Metazoa.
1397 - Eliminated on secondary screen due to many eukaryotic
hits outside of the Metazoa.
153 - Eliminated on tertiary screen due to clustering with
additional eukaryotic taxa beyond the Metazoa.
Dictyostelium AF
275 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
303 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
382 - Eliminated on tertiary screen due to clustering with
Jakoba libera.
1031 - Reject on secondary and tertiary screen due to clustering
with eukaryotes outside of Amoebozoa. This is on the other hand
one of the LGT candidates which could tie Amoebozoa with a
subset of the Excavates and must be looked at carefully (HV598).
Reject at current stringent screening level, but keep in the
larger queue.
235 - Rejected due to hits to Metazoa.
548 - Hits only Microbulbifer degradans.
Hits to some other
Amoebozoans as well. Very distant (e-05) eukaryotic hits are so
divergent as to be unalignable. Microbulbifer also an extremely
poor alignment. Inclined to dismiss, but accept on a technical
level.
685 - No hits to any eukaryotic sequences.
candidate.
Passed as an LGT
737 - No hits to any eukaryotes outside of the Amoebozoa.
Passed as an LGT candidate.
816 - Rejected due to clustering with additional eukaryotic taxa
outside the Amoebozoa.
Dictyostelium VF
151 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
196 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
227 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
228 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
502 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
613 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
781 - Thymidylate synthase. This candidate has been rejected
due to clustering with Reclinomonas americana.
792 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
890 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
997 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
998 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
18 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
138 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
208 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
429 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
456 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
707 - Ornithine/Arginine decarboxylase.
Dictyostelium with Malawimonas.
Appears to cluster
842 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
984 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
999 - Glycosyl hydrolase but not HV598. Appears to cluster
Dictyostelium with Acanthamoeba and Trimastix.
Acanthamoeba
216 - cmfA-like.
Appears to cluster Dictyostelium with
Acanthamoeba, Hartmannella, and Malawimonas.
233 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
367 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
452 - Appears to cluster strongly away from other Eukaryotic
paralogs. This sequence therefore passes as an LGT candidate.
565 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
705 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
832 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
896 - Eliminated on tertiary screen due to possible clustering
with broad eukaryotic radiation. Bootstraps are unconvincing.
1020 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
1161 - Hits a Micromonas cluster in PEPdb.
secondary screen.
Eliminated on
114 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
115 - Eliminated on tertiary screen due to possible clustering
with eukaryotic taxa apart from the Amoebozoa.
434 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
559 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
630 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
850 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
971 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
977 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
1002 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
1138 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
1140 - Only hits prokaryotic sequences.
LGT.
Passes as a candidate
1155 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.
1199 - Eliminated on tertiary screen due to clustering with
eukaryotic taxa apart from the Amoebozoa.
1203 - Only hits prokaryotic sequences.
LGT.
Passes as a candidate
1287 - Eliminated on secondary screen due to eukaryotic hits
outside the Amoebozoa.