Supporting Fig. 6. Amino acid sequence alignment of TERTs and PLEs. Included are the TERT sequences (cyan),
telomere-associated EN-deficient PLEs (red), and the EN-containing PLEs from three major PLE groups shown in Fig. 4:
Neptune (green), Nematis (magenta), and Penelope/Poseidon (blue). Numbering on the top corresponds to the position in
the entire alignment, and numbering on the left – to amino acids within each sequence. The amino acid residues are
shaded in Vector NTI (InforMax, Inc.) as follows: identical, red letters / yellow background; block of similar, blue letters /
light blue background; conservative, black letters / green background; weakly similar, green letters / light green
background. Previously described sequence motifs in TERTs are marked on the top (Xia et al., Mol. Cell. Biol. 20:51965207; Huard et al., Nucleic Acids Res. 31:4059-4070). GIY-YIG EN motifs A-E are designated as in Kowalski et al.,
Nucleic Acids Res. 27:2115-2125. The GenBank identifier (GI) numbers for TERT amino acid sequences are as follows:
Homo sapiens (4507439), Mus musculus (6678291), Gallus gallus (45686257), Xenopus laevis (12003360), Tetraodon
nigroviridis (47229475), Aspergillus nidulans (40740771), Kluyveromyces lactis (50306115), Saccharomyces cerevisiae
(6323350), Magnaporthe grisea (38110208), Candida albicans (6716754), Schizosaccharomyces pombe (2340169),
Tetrahymena thermophila (3335167), Euplotes aediculatus (2072336), Paramecium caudatum (11463858), Arabidopsis
thaliana (9755737), Oryza sativa (13625302), Encephalitozoon cuniculi (19173151), Giardia lamblia (9049518). Accession
numbers for PLE sequences are as follows: Danio rerio Nep1 (NW_634120.1), D. rerio Nep2 (NW_634335.1),
Caenorhabditis
briggsae
(CAAC01000421.1),
Branchiostoma
floridae
(BW883725.1),
Ciona
intestinalis
(AABS01001109.1), Perere-10 from Schistosoma mansoni (BN000801), Cercyon from S. mansoni (BK000685.1),
Poseidon from Fugu rubripes (CAAB01007635.1), and Penelope from Drosophila virilis (U49102). Sequences of Athena
elements from Adineta vaga and Philodina roseola were obtained in this study (GenBank accession Nos. EF485018EF485020). All other PLEs were assembled from trace archives, and consensus sequences were deposited in Repbase
Update (see ref. 17 for a complete list).
Athena
a. AvM
AAAAATTTAAAAAAAAACTACATAAAACAAAACAACTCTTTTTTTTTCTTTTCTATCTCAAACATTTTAT
CCTTTAAAGGGTTTCA
TTAAATTTAAATTTAAAAAAGTTCTGATGAAGTCAAGTCTTAACTTGACAGAAAC
TTTTTTGT
TCTTTGATAAATCGGTTATTTCTTTCGAACAGGAAATAACCAACTGCTTTCTTTTTCGTATAGTTGAGTATTTAGTTTGTCGTTAGTTAGCTATTTTATATAGAGTCGTAAGA
[.................................................................CGCGAAAAATGAATCCAGTATTACGAAAGGATTTCACGCTCCAAAT]
[.................................................................aataatctccttttcttttgaattctaatcttttctatatattaca]
[.................................................................aaaaacctccaaaattcagacactttcctgacttttcagacaatct]
AvM <-------------------------------------------------------------|-------------------> flanking DNA
b. AvO
CACCCACACCCACCACACCCACACCCACCCACACCCACACCCACACCCACACCCACACCCACCCACCCACACCCTCAAGATGTACTTGTGCCAGAAGAAAAGCCTGGCTATGT
GGATCCCAAGTGGGGACTGGTTCTATAGTAACCAAGATCCGCAAGAGAACCAGTCAATAGCAGCATTTGCGCAAGCAAATAGCAGGTCTACCAATAAATGGGTAGAACGGACG
AAACGTCCGACACCTTATGAGAGGCCGAA GGGCCTGATCTGAATCAGATCAGAGAAGAGGAGAGACGTCGTGAGCGTCTCGAAAAGGAAAGGAGTTCGAAGTCAGCA
AATTCCTTTTCCTTAAAAAAAAAATTTTAATTGGAAAAAATTCCCCAATTAATTTTTTTTAACCTTTTAAGG))4 CTTTTCTTTTCTCTTATTATTAGTTTTTC N1]
ACCCATCTTCTAAAAATTATGAAATCCATATTTTACTTAG)
AAAAGGA
GAAAAAGA
GGAAAAG
TAAAGAAG
[............................((T
(T
AAAAGGAACCAATTCCTTTTCCTTAAAAAAAAAATTTTAATTGGAAAAAATTCCCCAATTAATTTTTTTTAACCTTTTAAGG))2 TGTTGAATATATTCACGATATTTTTGTCG O2]
GAAAAAGACATCTTCTAAAAATTATGAAATCCATATTTTACTTAG)
GGAAAAG
TAAAGAAG
[............................((T
(T
[............................(((TTTAAAGGGAAAAAAGGGAAAAAAAAAGGGAAACCCAAATTTCCCTTTTTTCCCTTTAAAAAAAAAAAAAAATTTTTTAAATTTGGGAAAAAAAAATTTCCCCCCAAATTTAAATTTTTTTTTTTTAAACCCTTTTTTAAAGGG)))3 AAACGATCAACCAACTATTTCTGATCATC O1]
ACTTCGAAAGTGCCAACACCACCTCCGAACAATGACCGGCCGTCAACGTCAGCCGACGCTGGCCTGCCGCAGTTGGAGAAAAGTGAACGAGTTCGAAAGAAGCTCGCATTTTG
GAAGGCACAAAGGGAGATGAGAAAAACAGCGAATAAAGTCGCTGCAAATCCACCCCGACAAGCTCCACCACCTCGTCCTAAAGCACCAGTACCACCTGCTCCGCTTGTTTCAC
CCCCAGAGATGAGTCGACGACAGCCTGTCGAACAGACTGTACAACCTGGTAATCAGATTGTTTCACCGGTGCCCGGTCACCAACCGGCGCCTGTAGCAGCATCAACACCAGAA
TCGGTCCTTTCAGATCGAGCTAATTCGGTGTTAGGTCCACCAAATGATTCGGTAGTGTCTTTCGGTGATTTCTTACCTGTTGACATCAACGACATCAACATTCATGATCTTCT
CCTCAACGAAGATTAAAGGTGGTCGCCTTGGTGCTCGTTCTTCCCGTCGTCGTGCTTCCTCAGCTCCTCCTTCTTTCTTCTTTTTTGAAGTTTTTTGTAGTAGTTGTTCCATC
1|_____>
2|_____>
TT TATTCTGAACTAAA
AA TGTTGTTTTTTCCTGAAGATCTTTATTTTTTACAATAAAGTGAAACCGGTCGAAAACAAACAATTTCTTCTTT
TTGTTAAAGTTTTTTGTTCTTCTAGA
3|____>
TT CAGGGTTGTTTCTTCCAACTTCTTCTTCTTCTTCAACCACACCCACA
AAAAAAAATTTAAAAAAAAAAGCAACTACAAGTCTTAGCTAGTTTTGTTTCACTAGCTTCCTTCGACACTAAGACATT
CA
ATCTTCACAACTCGTCGTTAGTGCACAACTGCCGCCGCGTTCAAGAACAACCGTCTTAAACAAGTGTCGATATCCTACAATAAATTTGGG..................(((OOORRRFFFsss)))...................................................
.........TTTGGGAAATCGTATAATATATAGACAACCTCA((TTAAGGAAAAGGAAAAAAGGAACCAATTCCTTTTCCTTAAAAAAAAAATTTTAATTGGAAAAAATTCCCCAATTAATTTTTTTTAACCTTTTAAGG))4 AAGAGTCCTTCAAATATTATGTGGTAAA. M1
(TAGAAGAAAGACATCTTCTAAAAATTATGAAATCCATATTTTACTTAG)
........ ........................((TTAAGGAAAAGGAAAAAAGGAACCAATTCCTTTTCCTTAAAAAAAAAATTTTAATTGGAAAAAATTCCCCAATTAATTTTTTTTAACCTTTTAAGG))10TGTTGAATATATTCACGATATTTTTGTC O3]
[.......
(TAGAAGAAAGACATCTTCTAAAAATTATGAAATCCATATTTTACTTAG)
.
.
.
.
.
.................................(((TTTAAAGGGAAAAAAGGGAAAAAAAAAGGGAAACCCAAATTTCCCTTTTTTCCCTTTAAAAAAAAAAAAAAATTTTTTAAATTTGGGAAAAAAAAATTTCCCCCCAAATTTAAATTTTTTTTTTTTAAACCCTTTTTTAAAGGG)))8 AAACGATCAACCAACTATTTCTGATCAT O4]
[.
AvO <--------------------------------------------------------------------------|----------------------------> AvN
c. AvN
|_____>
CCCTTATTACAACTTACCAAGAGACATGCGAATGATAAACGATCAACCAACTATTTCTGATCATCCAAAACAGTCGAAGAAACGTAAACGAGATCTATCGCAACAGAATCTTAAATTTGGG
..................................................................................................................................................................(((OOORRRFFFsss)))...............................................................................................................................................................
CAATATATAAGCAAACCATGAATGAACTATAAAGAGTTGCAATGTCAGCAACTATATAATAACCGAACCCAGCCGTCTGAAGAGTCCTTTAGCAGGGACGAAATCATGATAAC
GGTAGCTATACTCACCCCAACTATACGGGTACCTATATATCCTTGAAAAATTCCTTGTGAATTTACTTGGATAAAATTTAGGTTATACACTTTGTTTATGATCTTAGGATCAT
CCGAACAAGTGTTGCTATTAAAGCCGTCTGAAGAGTCCTTTAGCAGGGACGAAATCATGATAACGGTAGCTATACTCACCCCAACTATACGGGTACCTATATATCCTTGAAAA
ATTCCTTGTGAATTTACTTGGATAAAATTTAGGTTATACACTTTGTTTATGATCTTAGGATCATCCGAACAAGTGTTGCTATTAAAGCCGTCTGAAGAGTCCTTTAGCAGGGA
CGAAATCATGATAACGGTAGCTATACTCACCCACACCCACACCCATCTGATGAGAACCGTAGCGGGTTCGAAACGCGTCATGGCTGCTGGAACACCCACACCCACCCGCACCC
d. PrR and PrR*
\
CAGTAATTTGAAAAAAT--CGTTGCTTGTATTCTAATTTAAGTT---CAAAACTTGGAAGTCAT----ACTTCTTTTGTTTGAAA--TTAAATTTA--TTATGCAACAAAAAA
[AGTAACTCGAAAAAATATCGTTGCTTGTATAGTAATTTGTTTTTTTCAAAAAATTGGAGTGAT-ATAACTTCGATTGCTTGAAAAATCAAATTT---TGATGCAACAAAAAA
[GATGATCTCCCATGAAA-CATTTCCTCTTTTTCTATTCACCTGGCTTGTAAAATTGCAGTTGTCACAACTTTCATTAATTGAAAT-TCAAATACAGATGCTGCAACCAAAAA
* * *
* *
* ** * * * *
***
*
** * * *** * *
***
** ****** * ****
* ****** *****
TTGAGCTACCTGATGAGGTCCTGGTAAATCAGGCCGAAACGCGTCGTAGCCGATTCTTTCTAATTTACTCACCCCAGTAATTTGAAAAAATCGTTGCTTGTATTCTAAT C.2
TAAAGCTACCTGATGAGGTCCTCATAA-CGAGGCCGAAACGCGTCGTAGCGTATT-TCTTTGATTTACTCACCCtcaagaacaaaacatccgacatcgacaacaagtg] C.1
TTATGCTACCTGATGAGGCCTTGG-AATTTAGACCGAAACGCGTCGTGGTAATTAATCTTGGAT--ACTCACCCTCCTCACCCTCtcgtctcgatacacaggcaatag] PrR
*
************** * *
**
** ************** *
* * *
** ********
PrR <--------------------------------------------------------------------|-------------------> flanking DNA
Coprina
e. Cc1
CCCCCAAAGGGCCCTTTCGCCTTCGAAAAAAGTCTCGC
TTAAATTTAAAAAAGAAGTCGAAAGCGGACCAGGTTGTTTCGACAACCCGCTTGAC
CCCTTTTAGAAAAGAAAGCACAGGTCCTGAAGAGACTT
TTCGCTCGACTTTTTTCTCCACCCACCCTAACCCTAACCCTAACCCTAACCCTAAgggacggagcaagtggattcgagagtgagggaacgaatatgagatcgggatttgaaa
[.......................ACCCTAACCCTAACCCTAACCCTAACCCTcacgagacaccctaactgcattaggcctatagagaaactgccctagagcagtatcgct]
[.......................ACCCTAACCCTAACCCTAACCCttgatcaaggtttcgaggaagaggatgaactccgcccgtagtgactggccgtcgatgtccacgat]
[.......................ACCCTAACCCTAAgtccgagaagccgtttcaagggcgatggtcgcatgcatcgctgtgggatacaatctccggaagaagggcgaata]
[.......................ACCCTAACCCTAAgcgtttcacctgtatcccacaagcatttactcaccgtcgtcgtccacagtcacctgtcacgatgtctgccgcca]
Cc1 <-------------------------------|------------------------------------------------------> flanking DNA
f. Pc1
TTCCCAAAGGGCCCGCGACACAACAGTGTCGGCTGCCTTCGGTTTTCCTG
TTAAATTTAAATTTAAATTTCCCAGTAGGAAACCGCTGATGAGTCTTCACGACGAAAGCT
CTTCGGGCCTGGCGGTTGCAAGGGGT
AATTTGGGCCCGCCCAAGACACTACTCGCCGTGC
TGAAGCATTCCGCGCTCGCCGCTCACTACGCTCGCGTCTCGCGCCCCCCAAACCCTAATCAAATCGAGTAAGCACTCTTCACCA
[................................................AAACCCTAAACCCTAAACCCTAAACCCTAAtacccgcccttgtacgcgtaacttacacttgg]
[................................................AAACCCTAAACCCTAAACCCaggctgtaccaaggctgtgtcacgaggctgcatcatcaggct]
[................................................AAACCCTAAACCCTAAACCCgctgtggagtatgcgcatgaacctgggccttcttgacgtcct]
[................................................AAACCCTAAACCCTAAAaaccgaccgggctagacgtcgtcggagtcgagcgtcccgctctct]
[................................................AAACCCTAAACCCTAAgcgcagggttggatcttttcatcacggaagaccttacgctcaaacc]
[................................................AAACCCTAAACCCTcagacattgcccggatcaccggtctgccttgcaaccggtcccccggat]
[..........AT....................................AAACCCTAAACCCTcagtacatgtgagtgctatacaagcatctcggcatcactactggtctc]
[......................................T.........AAACCCTAAACCCcgatgcgttcacctcaatctgccgtcagaattccaccttgatagcggga]
[................................................AAACCCTAAAgcggatattcaaactcgagccggcagatctgctcaagaaggtaggtcgtgta]
[A..................A................T...........AAACCCTAAggtaccagtaaaaaaccagtataatggctaagctcacggaagattcgggagat]
Pc1 <----------------------------------------------------|---------------------------------> flanking DNA
g. Pc2
TTCCCAAAGGGCCCGCGGCCCCCCAAAGGCCCCACCTTCACTTTCGTCCCTTGCCTC
TTAAATTTAAATTTAAAAAACTAGGGACTCTGAGTGCTGATGAGGCATCGCCGAAAGGTT
GAGTTTGAGCCCTAGGCGT
AATTTGGGTCCTCTCGCGCCACTTCGCTGCCCCCCGCCTTCGCAGGACTCGGCCTCGGCGAATCTCGTC
CCTCCACCTCTTTCACCCTTACTAAACCCTAACAAAGGAGTAAGCACCA
[.....................TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAGCCCTAAAGCCTAAAtattcattagcgtctccctcacaggcctaaaccccc]
[.....................TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCtgcatcaatgtcgttcacgaactcaccccggtg]
[.....................TAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCGTAAA]
Pc2 <--------------------------|-----------------------------------------------------------> flanking DNA
Supporting Figure 7. Nucleotide sequences of the Athena and Coprina 5' and 3’ extremities.
PLE sequences are in color uppercase letters, and the adjacent flanking host DNA is in black
lowercase. In each case, a continuous sequence is shown on several lines; if its segment is included
into a multiple sequence alignment, other members of the alignment are shown underneath in square
brackets.
(a) The 3' ends of three fosmid-borne copies of Athena-AvM. The italicized sequence is the 5' UTR of
the full-length downstream AvM copy; the junction below is to a 5' truncated AvM copy; two other
junctions are to unidentified host DNA.
(b) Complex structure of Athena-AvO noncoding regions, based on eight AvO copies from telomeres
M1, N1, and O1-O4 (Supporting Table 1). One of the genomic copies (M1) shows a pseudo-LTR
structure (6), i.e. the segment shown immediately adjacent to telomeric repeats, upstream of the ORFs,
is found again downstream of the ORFs, representing an extended 3' UTR region. Thus, it constitutes
both the 3' UTR and a functional promoter for the downstream copy, as described for HeT-A in
Drosophila (14). RNA start sites 1-3, determined by 5' RACE, are italicized and shown by arrows. AvO
can be terminated by addition of 2-10 copies of a 48-bp repeat at two locations within the 3' UTR, where
it is joined to a variably 5' truncated end of AvN (blue). In the M1 copy, the 3' UTR extends further, and
the element ends in a long stretch of telomeric repeats, two units of which are present at the tandem
junction (underlined), as is also the case for Coprina elements (e-f).
(c) Noncoding regions of Athena-AvN. In the 5' UTR of AvN, the arrow indicates the position of the RNA
start site determined by 5' RACE, and the ATG codon of ORF1 is shown in bold italics. The 3' end of
AvN features two complete and one partial copy of a 177-bp tandem repeat, with each unit ending in a
telomeric repeat (underlined).
(d) The 3' UTR of a cosmid-borne full-length PrR copy (also found in the telomere-enriched plasmid
mini-library) is aligned with telomeric groups C1 and C2 (Supporting Table 1). In the telomeric clones,
the depicted segment (180 bp in C1, and 174 bp in C2 and K) exists as a tandem repeat, each unit
ending in a telomeric repeat (underlined). The telomeric tail attachment site (\) in group K, which ends in
a tandem repeat identical to C2, is shown on the top. For C2, the uppercase sequence following the
underlined telomeric repeat represents the beginning of the next tandem repeat unit. The tandem
repeats could originate from an as yet unidentified Athena variant, tentatively designated PrR*
(Supporting Table 1), or could be mobilized in trans by PrR-encoded RT interacting with homologous
regions (asterisks).
(e-g) For each Coprina family, the 3’ flanking sequences of several copies adjacent to telomeric repeats
(underlined) are presented; for Pc1 and Pc2, the italicized uppercase 3’ flanking sequence (with the
ATG codon in bold italics) at the same time represents the 5’ terminal sequence of the adjacent
downstream copy of the same element in a tandem arrangement (pseudo-LTR). Putative TATA boxes,
initiator motifs, and poly(A) signals are underlined.
DAPI
Red
Merged
Interphase
Supporting Fig. 8. Fluorescent in situ hybridization (FISH) of the Athenacontaining cosmids, labeled with the red fluorophore Alexa 568-dUTP, to P.
roseola embryo nuclei. Two mitotic nuclei are shown, with arrows pointing to
chromosome ends, fluorescent signals, or both. Smaller arrows point at the dot
chromosome. Left to right: DAPI-stained DNA; Red fluorescent signals; Merged
images. Also shown are two interphase nuclei with fluorescent signals
concentrated on the nuclear periphery, as often observed for telomeres in other
organisms. Scale bar, 1 µm.
Ts
n
TE
R
eido
pe
lo
ne
Pe
al
Vertebrate TERTs
s
RT
Pos
ng
te
lia
TE
N
Fu
un
t
ep
e
Ci
Osir
is
A
Coprina
T
nt
Pla
Athen
a
Ts
ER
B mori
97
B
98
99
A a e g y p t iA
Penelope
87
61
Pe n e lo p e D v
28
Cerc y onS m
56
20
H y d r a Po s
79
55
C io n a in t
99
92
Poseidon
B f lo r id a e
97
58
99
Po s e id o n F r
A a e g y p t iB
100
84
100
A a e g y p t iE
99
13
A a e g y p t iC
100
85
A a e g y p t iD
N e m a to s te l
99
94
67
D r e r io N e p 2
97
42
99
69
D r e r io N e p 1
A th e n a A v M
98
100
A th e n a A v O
100
100
99
Neptune
X tr o p N e p t
87
A t h e n a Pr R
Athena
71
95
A th e n a A v N
99
82
100
A t h e n a Pr B
S e la g in e l1
81
100
S e la g in e l2
35
Ph a e o d a c t i
61
31
Ph y s a r u m
30
C o p r in a Pc 2
100
98
Coprina
C o p r in a Pc 1
72
73
C o p r in a C c 1
E c u n ic u li
T e tr a h y m e n
52
69
100
83
95
68
Pa r a m e c iu m
Eu p lo t e s a
88
80
Ciliate TERTs
A r a b id o p s i
97
91
Plant TERTs
O r y z a s a ti
P t r ic o r n u
59
G a llu s g a l
98
48
95
80
26
X e n o p u s la
45
H o m o s a p ie
96
Mus mus c ul
Vertebrate TERTs
97
T e tr a o d o n
99
58
45
91
A s p e r g illu
M a g n a p o r th
57
Sc h pombe
48
99
75
C c in e r e a
P c hry s os p
Fungal TERTs
G ia r d ia T E
1
Supporting Fig. 9. Analysis of the TERT-PLE dataset by different methods.
(A) NeighborNet estimate of the data structure of the TERT-PLE dataset.
Uncorrected p-distances were used to construct a NeighborNet agglomerate
network graph in SPLITSTREE 4.6 (36). Complete names of individual elements
and taxa are listed in Supporting Fig. 6. Larger groupings are indicated on the
perimeter; color-coding is the same as in Fig. 4.
(B) Clade support values in the PLE-TERT phylogenetic tree. Numbers above
the branches were obtained by maximum likelihood analysis (rtREV+I+G8+F
model, with rate heterogeneity parameters obtained from PROTTEST) and
represent approximate bootstrap support (1000 replicates) for reconstructed
edges computed from maximum likelihood scores in TREEFINDER (39;
www.treefinder.de) by applying to all local rearrangements of tree topology
around an edge the Shimodaira-Hasegawa (SH) test with RELL approximation
(Shimodaira and Hasegawa, MBE 16:1114-1116), where the edges are assigned
100 percent minus the worst SH p-value obtained. Numbers below the branches
were obtained by neighbor-joining analysis in MEGA 3.1 (38), with 100 bootstrap
replications, pairwise deletion, and JTT substitution model with gamma
distributed rates and gamma parameter estimated as above.
Supporting Table 1. Telomeres of A. vaga and P. roseola.
Each telomere has a letter designation and is represented by a group of plasmid clones sharing a unique
sequence at the junction between telomeric repeats and the subtelomeric region and ending with a HincII halfsite, with 1-34 clones in each group. The exact length of the telomeric repeat tail, where known, is shown in
parentheses; in other cases, BigDyeTerminator mix failed to read through the entire GT-rich strand and there is
a gap between subtelomeric and telomeric sequences. PrR* is derived from an as yet unknown Athena variant
and has 75% similarity to the 3' UTR of Athena-PrR (Supporting Fig. 7). The last three P. roseola clones were
not capped by telomeric repeats and do not have a letter designation.
A. vaga
Telomere
A
B
C
D1
D2
E
F
G
H
I
J
K
L
M1
M2
N1
N2
O1
O2
O3
P1
P2
Q
R
S
T1
T2
U
V
W
X
Y
Z
AA
AB
AC
AD
AE
AF
AG
AH
AJ
AK
AL
AM
Accession No.
(number of clones)
EF484951 (14)
EF484952 (34)
EF484953 (2)
EF484954 (3)
EF484955 (3)
EF484956 (1)
EF484957 (1)
EF484958 (5)
EF484959 (8)
EF484960 (7)
EF484961 (2)
EF484962 (1)
EF484963 (3)
EF484964 (3)
EF484965 (1)
EF484966 (2)
EF484967 (1)
EF484968 (1)
EF484969 (1)
EF484970 (1)
EF484971 (1)
EF484972 (1)
EF484973 (1)
EF484974 (4)
EF484975 (1)
EF484976 (1)
EF484977 (1)
EF484978 (2)
EF484979 (2)
EF484980 (1)
EF484981 (1)
EF484982 (2)
EF484983 (2)
EF484984 (1)
EF484985 (1)
EF484986 (1)
EF484987 (1)
EF484988 (1)
EF484989 (1)
EF484990 (1)
EF484991 (1)
EF484992 (1)
EF484993 (1)
EF484994 (2)
EF484995 (1)
Insert length
1125+tail(320/95)
1142+tail(309)
870+tail
2011+tail(147)
1925+tail
179+tail
>5756+tail
2217+tail
802+tail
1547+tail
871+tail
4309+tail
6944+tail
2356+tail
41+tail(>650)
1495+tail
1666+tail
1756+tail
571+tail
641+tail
>1028+tail
387+tail
3234+tail
213+tail(105)
400+tail
745+tail
>750+tail
323+tail(108)
3128+tail
929+tail
79+tail(307)
1293+tail(111)
273+tail(186)
>746+tail
41+tail(75)
774+tail(38)
351+tail(41)
296+tail(39)
172+tail(51)
408+tail(26)
8+tail(450)
230+tail(107)+35
17+tail(170)
>920+tail(52)
697+tail(54)
P. roseola
Notes
Telomere
orf frag.
orf frag.
orf frag.
Ath-AvM
Ath-AvM
AvO+AvN
Ath-AvN
AvO+AvN
Ath-AvO
AvO+AvN
fosmid
Hobo
AvN
orf
A
B
C1
Accession No.
(number of clones)
EF484996 (1)
EF484997 (1)
EF484998 (4)
Insert length
Notes
>655+tail
1003+tail(197)
>1244+tail
orf frag.
C2
EF484999 (1)
>617+tail
D
E1
E2
E3
E4
F
G
EF485000 (1)
EF485001 (2)
EF485002 (3)
EF485003 (1)
EF485004 (5)
EF485005 (1)
EF485006 (4)
H
I
J
K
EF485007 (3)
EF485008 (2)
EF485009 (1)
EF485010 (6)
116+tail(194)
342+tail
275+tail
270+tail
37+tail
187+tail
1895+tail
609 (no tail)
319+tail(57)
>688+tail
>562+tail
>1037+tail
L
M
N
P
PR_A_IV_4
PR_A_V_1
PR_A_III_3
EF485011 (1)
EF485012 (1)
EF485013 (1)
EF485014 (1)
EF485015 (1)
EF485016 (1)
EF485017 (1)
202+tail(135)
>582+tail
27+tail
>1200+tail
2442
532
981
Ath-PrR*,
3x repeat
Ath-PrR*,
4x repeat
Ath-PrT
Ath-PrR*,
4x repeat
rDNA
Gag
Ath-PrR
Ath-PrR
Ath-PrT
Coprinus cinereus
Telomere
C. cinereus telomeric reads (ti)
Mate-pairs (ti)
Matching contig
Cc1.1
211617341, 211634836, 215117731
215319947, 215176391, 211620966
211633064
214363379, 214342904
214358209, 214358160
216030683, 216586163, 216037555
216029176, 215833309, 215836918
216687798, 216676781, 223023857
222955659, 222765563, 216710384
216700288, 223037572
228082942, 228093429
211340407, 211344234, 210714591
215176297, 215318579, 211623374
211603286, 211627562, 211634893
214351121, 214350504, 214353697
227995062, 227969413, 228005097
223362976
216620368, 216626044, 215838354
215829090, 216622736, 216586938
215824626, 215840535, 222846619
222764599, 222767513, 216694123
223132751, 223053585, 223049192
223123446, 231270591, 231277900
215823695,
227975865
210689220, 210721332
210724451, 211618846
214354183, 227979755, 228073284
228082597, 228081102, 228066964
216621583, 215820272, 215828043
216609631, 216006074, 215820544
222839591, 222846221, 216690287
223128800, 216686309, 222929011
216714124, 222840840, 231335439
231362233, 231715106, 231353020
210687528, 210702594, 210725581
210742826, 210711705, 210715524
214799179, 214362998, 228087187
227989181, 228078631, 231882819
231887998
222935495
215175505
214345276, 214347995, 214366412
214798212, 228000347, 228058717
227979895, 227980240, 228086150
228059942, 228089872, 228064129
228081423, 228062916, 228058812
228063230, 223356523
216612408, 215833906, 216582075
216607484, 223026800, 216040085
216685990, 216032989, 222854168
222853434, 222768978, 223028727
222939908, 216680981, 222766209
222919662, 223198426
209018915, 209020288, 210685867
211633907, 215118976, 210712384
210714621, 210718438, 215314473
211628780, 215177798, 211634203
214347974, 228091040, 227990723
228002046, 223363166
216002258, 216001090, 215819308
216031234, 223028244, 216692637
216709171, 222837729, 231375549
211623428, 211628650, 215173869
215176088, 215172560, 211624860
211636879
214359562, 214339078
214362032, 214361980
216036855, 216582332, 216031475
216025259, 215837226, 215830732
216683983, 216672952, 223020041
222959482, 222769387, 216714204
216704093, 223043765
228086752, 228089611
211344234, 211340407, 210710691
215110118, 215172351, 211617189
211607136, 211633748, 211631085
214357294, 214354320, 214347515
227988992, 227973232, 228001277
223359163
216626460, 216622237, 215832163
215825169, 216626545, 216583036
215828445, 215844370, 222852816
222770787, 222773578, 216698045
223126572, 223047386, 223045283
223119624, 231276768, 231271706
215829872,
222756463
210683036, 210725264
210720624, 211622665
214347999, 227983579, 228077116
228086402, 228084918, 228060776
216627679, 215824095, 215824135
216613452, 216009906, 215824349
222843427, 222850037, 216694111
223132598, 216680126, 222932834
216717964, 222836904, 231329249
231366054, 231718935, 231356835
210683613, 210708791, 210719402
210749001, 210715524, 210711705
214792988, 214359174, 228081104
227995360, 228084829, 231886637
231884074
222941677
215319332
214341465, 214351822, 214362512
214794255, 228004182, 228062542
227985995, 227984067, 228082330
228066127, 228093671, 228057952
228077596, 228059098, 228064934
228067048, 223362699
216616220, 215830104, 216588269
216603566, 223030696, 216033906
216679825, 216039089, 222857989
222847253, 222302754, 223032546
222935995, 216684803, 222770019
222923481, 223202239
209012841, 209014193, 210679674
211627724, 215172752, 210716297
210718438, 210714621, 215170618
211634977, 215171719, 211628018
214351880, 228097115, 227996899
227998207, 223356984
216008369, 216004914, 215813224
216035066, 223024370, 216698819
216712992, 222841561, 231369376
cont1.407_scaffold82
Insert
length
40 kb
cont1.350_scaffold31
10 kb
cont1.350_scaffold31
5 kb
cont1.167_scaffold7
40 kb
cont1.367_scaffold48
10 kb
cont1.427_scaffold102
5 kb
cont1.427_scaffold102
5 kb
cont1.309_scaffold21
40 kb
cont1.309_scaffold21
10 kb
cont1.309_scaffold21
5 kb
cont1.318_scaffold22
40 kb
cont1.319_scaffold22
10 kb
cont1.249_scaffold14
cont1.298_scaffold19
cont1.297_scaffold19
5 kb
40 kb
10 kb
cont1.397_scaffold73
(Cc1)
5 kb
cont1.327_scaffold25
40 kb
cont1.327_scaffold25
cont1.319_scaffold22
cont1.397_scaffold73
(Cc1)
10 kb
Cc1.2
Cc1.3
Cc1.4a
Cc1.4b
Cc1.5a
Cc1.5b
5 kb
Phanerochaete chrysosporium
Telomere
Pc1.1
Pc1.2
Pc1.3
Pc1.4
Pc2.1
Pc2.2
Pc2.3
Pc2.4
P. chrysosporium telomeric
reads (ti)
589120750
258451408,258473550
258418123
589253044,589270902
589432948,589076795
589127246
258420173,589280832
589122938,589209977
589074076,589277774
589326027,589325450
258420836,589325960
258462222,258666734
258652269,258459744
258646300,258646301
258451617
589220586,589243138
589240126,589278046
589133565,258470632
258652333
258518952,258542250
589205271,589452989
589453766,589218483
258547099,589386555
589337549,589211372
258637939,258459048
258614064,258648532
258648108,258635864
258600185,258495265
258518952,589205271
Mate-pairs (ti)
589122286
258451407,258473551
258418122
589253140,589264758
589432852,589076699
589129358
258420172,589279680
589121402,589206233
589071388,589269134
589330593,589330012
258420835,589330524
258462221,258666735
258652268,258459745
258646298,258646299
258451616
589219050,589253602
589242526,589269406
589137693,258470633
258652332
258518951,258542249
589207863,589454909
589451078,589217235
258547098,589381221
589337931,589211276
258637938,258459049
258614063,258648531
258648107,258635863
258600186,258495264
258518951,589207863
Matching contigs
Assembly I
White_Rot564*
Matching contigs
Assembly II
Scaffold_23*,24*
White_Rot564*
White_Rot539
Scaffold_24*
Scaffold_8*
White_Rot368
White_Rot564*
Scaffold_24*,23*
White_Rot820*
Scaffold_27*,2*
White_Rot820*
Scaffold_2*,27*
White_Rot820*
Scaffold_27*
Scaffold_26
No match
Scaffold_2*,27*
Matching contigs
Assembly I
Scaffold_4
Notes
Phaeodactylum tricornutum
Telomere
Pt1.1
P. tricornutum telomeric reads
(ti)
497470457,497467564
497466195,497438805
497433017,497432006
497473526,497462443
497439000,497475793
497436130,497435745
497433138,497431433
497428964,497426458
497426012,497327814
497201633,497196540
496688873,496687672
496687368,496540102
496501694,496442151
496368157,496287854
496237494,495955811
495862426,497475953
497468402,497470592
495491415,497436948
496049654,496556801
Mate-pairs (ti)
497469401,497467468
497463123,497431029
497433113,497430278
497472278,497462539
497438328,497475697
497436034,497440257
497433042,497431529
497429924,497426362
497427548,497327718
497200577,497191260
496688777,496685560
496684680,496540198
496503998,496438215
496368061,496287758
496239510,495955907
495862522,497475857
497473010,497469536
495495845,497437044
496051094,496556033
Pt1
taaccc
Selaginella moellendorffii
Telomere
S. meoellendorfii telomeric reads (ti)
Mate-pairs (ti)
Sm1.1
719652872,724381173,719721086,
724376452,759747506,890615144,
890629764,914888276,972912407,
723719484,1322567959
724377577,890728390,915002155,
963685248,725423635,915157800,
725423635,880044498
720076640,720341965,721061234,
721062270,914746476,914815049,
914978092,915048289,914926716,
914781105,890833335,880041317,
721035379
721056470,719761008,890799146,
914822624,914773281,759868321,
915046892,759822430,914989658
724405630,862141340,914830891,
719789463,719869212,719873610,
869270232,914827798,963751564,
914830891
719848926,719851227,862184720,
890674679,914747049,914928966,
915024149,963722392,964581542,
914919053,1373881150
759774573,725437065,915149230,
719926801,719907813,862173217,
759929666,759825654,724413280,
915009301,914810029,1372156212
721020322,719682553,720329563,
759724681,964560193
719767379,862156389,724392273,
915058592,1322560550
964583099,724365622,931566014,
914977027,719689425
883644317,722079112,915157322,
914885305,914809547,719814220,
724368260,1415630143
719653256,724381557,719720318,
724376068,759749522,890615048,
890631300,914891252,972912023,
723719580,1322564503
724378338,890726470,915002059,
963682562,759740858,915151476,
759740858,880046994
720070112,720344749,721061330,
721060542,914746092,914814953,
914977036,915050593,914926333,
914781009,890833239,880041221,
719890082
721056566,719754128,890799050,
914823004,914771752,759869473,
915049580,759821086,914989754
724406014,862141436,914827798,
719791383,719869308,719868714,
862196443,914830891,963751468,
914827798
719844710,719844710,862184336,
890674775,914746666,914930981,
915023765,963715523,964578950,
914919149,1373880094
759773325,725438601,915149609,
719926417,719907717,862172449,
759931490,759826710,725414886,
915010645,914809261,1372153140
721952031,719682937,720328027,
759724300,964560289
719767475,862156293,723758493,
915056193,1322561126
963781720,724366390,931564107,
914978083,721022224
883644221,721070063,915150998,
914887513,914810315,719814603,
723719891,1415633407
Sm1.2
Sm1.3
Sm1.4
Sm1.5
Sm1.6
Sm1.7
Sm2.1
Sm2.2
Sm2.3
Sm2.4
Notes
Interstitial
Supporting Table 2. Retroelement-containing telomeres from Coprinus cinereus,
Phanerochaete
chrysosporium,
Phaeodactylum
tricornutum
and
Selaginella
moellendorffii. Scaffolding of telomeric reads from trace archives of each species with the
corresponding subtelomeric contigs from C. cinereus and P. chrysosporium assembly 1
(GenBank), P. chrysosporium assembly 2 (JGI) and P. tricornutum assembly 1 (JGI) was done
by BLASTN using mate-pairs for each telomeric read as queries. For S. moellendorffii, the
assembly is not yet available. Sequences are identified by GenBank trace ID (ti) numbers and
contig numbers from the corresponding assembly. Analysis of trace reads is required in addition
to analysis of assembled contigs, since automated sequence assemblers tend to misassemble
telomeres because of their repetitive nature and frequent detachment of telomeric reads from
assembled contigs. Only PLE-containing telomeres are shown; a complete list of all C. cinereus
and P. chrysosporium telomeric reads is available from the corresponding author upon request.
Telomeres are numbered and listed in the same order as they appear in Fig. 2 (where they are
marked by red letters T), from left to right for each element.
Supporting Table 3. Genomic copy number of Athena and Coprina elements.
(A) Results of A. vaga genomic library screening with Athena-specific probes (AvO and
AvM). Shown is the number of fosmids containing each of the Athena variants listed on
top (variants O.2 and M.2 contain minor defects in the reading frame). The presence of
Athena was verified by Southern blot hybridization and sequencing. Numbers in
parentheses represent fosmids which also yielded hybridization signals with the
telomeric repeat probe. Also shown is the number of A. vaga hsp82 copies present on
the same membranes (cumulative for all four copies).
Membrane
A
B
C
Hsp82 total
(4 copies)
9
10
21
AvO.1
AvO.2
AvM.1
AvM.2
7(5)
7(7)
-
4(4)
5(5)
-
7(2)
5(1)
5(5)
1(1)
(B) Results of BLASTN searches of the C. cinereus and P. chrysosporium genome
assemblies with Coprina elements as queries. Graphical output of BLASTN searches is
used to visualize all hits on different contigs from the same scaffolds. Several telomeric
copies were not assembled into scaffolds and are present only in trace archives.
Element
Coprina-Cc1
Coprina-Pc1
Coprina-Pc2
RT ORF
cont1.397_scaffold73
cont1.171_scaffold8
Supporting Table 4. Likelihood-based statistical tests of alternative topologies within
the PLE clade. Tests were performed in TREE-PUZZLE 5.2 under WAG+I+G8+F model of
rate heterogeneity, with parameter estimates from PROTTEST. The columns show the pvalues of the following tests, with 1000 resamplings using the RELL method: SH Shimodaira-Hasegawa test; 1sKH - one sided Kishino-Hasegawa test based on pairwise
SH tests; ELW - Expected Likelihood Weight (Shimodaira & Hasegawa, Mol Biol Evol
16:1114-1116; Goldman et al., Syst Biol 49:652-670; Kishino & Hasegawa, J Mol Evol
29:170-179; Strimmer & Rambaut, Proc R Soc Lond B 269:137-142).
Tree
log L
difference
S.E.
p-1sKH
p-SH
c-ELW
------------------------------------------------------------------1
-52170.34
11.32
9.3290
0.1220
0.1220
0.0963
2
-52171.35
12.32
8.8585
0.0880
0.0930
0.0203
3
-52171.23
12.20
8.5707
0.0800
0.0920
0.0155
4
-52159.03
0.00
<---- best
1.0000
1.0000
0.8637
5
-52173.67
14.64
7.6827
0.0380
0.0400
0.0042