-
Notifications
You must be signed in to change notification settings - Fork 0
/
cvx-cactaceae-si.tex
251 lines (215 loc) · 22.9 KB
/
cvx-cactaceae-si.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
% -*- program: pdflatex -*-
\documentclass[11pt]{article}
\usepackage{evolution}
\usepackage[section]{placeins}
\usepackage{geometry}
\usepackage{pdflscape}
\usepackage{soul}
\begin{document}
\section*{Supplemental information}
\bigskip
\clearpage
%
% FIGURES
%
%Fig S1: Gene 2 tree
\begin{suppfigure}
\centering
\caption{
RdRp gene tree with bootstrap values.
}
\includegraphics[width=1.5\textwidth]{supplementaryinfo/rdrp_tr.pdf}
\label{fig:genetree2}
\end{suppfigure}
\clearpage
%Fig S2: Gene 2 tree
\begin{suppfigure}
\centering
\caption{
TGB1 gene tree with bootstrap values constructed with the same method as Figure S1.
}
\includegraphics[width=1.5\textwidth]{supplementaryinfo/tgb1_tr.pdf}
\label{fig:genetree2}
\end{suppfigure}
\clearpage
%Fig S3: Gene 3 tree
\begin{suppfigure}
\centering
\caption{
TGB2 gene tree with bootstrap values constructed with the same method as Figure S1.
}
\includegraphics[width=1.5\textwidth]{supplementaryinfo/tgb2_tr.pdf}
\label{fig:genetree3}
\end{suppfigure}
\clearpage
%Fig S4: Gene 4 tree
\begin{suppfigure}
\centering
\caption{
TGB3 gene tree with bootstrap values constructed with the same method as Figure S1.
}
\includegraphics[width=1.2\textwidth]{supplementaryinfo/tgb3_tr.pdf}
\label{fig:genetree4}
\end{suppfigure}
\clearpage
%Fig S5: Gene 5 tree
\begin{suppfigure}
\centering
\caption{
CP gene tree with bootstrap values constructed with the same method as Figure S1.
}
\includegraphics[width=1.3\textwidth]{supplementaryinfo/cp_tr.pdf}
\label{fig:genetree5}
\end{suppfigure}
\clearpage
%Fig S6: Summary of cophylo plots
\begin{suppfigure}
\centering
\caption{
A summary of cophylogenetic comparisons of gene trees (Figures S2-S5) generated using the phytools package in R. Tree topologies largely do not vary between ORF and full sequence.
}
\includegraphics[width=1\textwidth]{supplementaryinfo/cophylo_sum.pdf}
\label{fig:cophylosum}
\end{suppfigure}
\clearpage
%The support values are posterior probabilities of the respective
%delimitations, that is that the split defined by the respective branch
%splits the tree into two distinct species.
%
%The Bayesian version samples alternative delimitations.
%
%So the blue and red colors show you the most plausible delimitation into
%species and individuals from the same species.
%Fig S7: mPTP tree
\begin{suppfigure}
\centering
\caption{
%TODO
%I am not sure that this is sufficiently clear to an average reviewer or reader. (Both this and the previous figure.) Maybe including this nearer to a color-coded delimitation figure or pointing the reader there would clarify better. Moreover, the description from S6 is slightly better. Also, the posteriors are very hard to see.Someone will complain about that. mPTP whole genome tree with delimitation represented by green and red coloration. Green branches represent delimitation outside of clades and red branches represent delimitation inside of clades.
%Possibly combine these two?; Clarify coloration
}
\includegraphics[width=0.8\textwidth]{supplementaryinfo/mptp.pdf}
\label{fig:mptptree}
\end{suppfigure}
\clearpage
%Fig S7: bPTP tree
\begin{suppfigure}
\centering
\caption{
bPTP whole genome tree with delimitation represented by blue and red coloration. Numbers on nodes represent the posterior probability of the delimitation.
}
\includegraphics[width=0.4\textwidth]{supplementaryinfo/bptp.pdf}
\label{fig:bptptree}
\end{suppfigure}
\clearpage
%Fig S13: RDRP heatmap
\begin{suppfigure}
\centering
\caption{
Heatmap displaying sequence similarity for aligned ORF1 gene RdRp (RNA-dependent RNA polymerase), which is the largest gene in the potexvirus genome. The genes (n=95) were extracted from each assembled sequence and aligned with MAFFT v7.490. Sequence similarity percentage was calculated across the 5268 nt aligned sequences in \textit{R} using the \textit{dist.dna} function from ape v. 5.7-1. Darker squares represent areas of higher percentage similarity, and values below the ICTV-suggested 72 percent nt identity are represented in a lighter yellow green.
}
\includegraphics[width=1\textwidth]{figures/heatmap.rdrp_jun25.pdf}
\label{fig:heat}
\end{suppfigure}
\clearpage
%Fig S13: CP heatmap
\begin{suppfigure}
\centering
\caption{
Heatmap displaying sequence similarity for Coat Protein (CP) sequences, using the same coloration as above. CP in potexviruses is typically located in ORF5 and this alignment represents 93 sequences each 714 nt in length.
}
\includegraphics[width=1\textwidth]{figures/heatmap.cp_jun25.pdf}
\label{fig:heatmapcp}
\end{suppfigure}
\clearpage
%
% TABLES
% Please add the following required packages to your document preamble:
% \usepackage{booktabs}
% \usepackage{graphicx}
% \usepackage[normalem]{ulem}
% \useunder{\uline}{\ul}{}
\begin{supptable}[ht]
\caption{
Genomes and gene sequences downloaded from the NCBI GenBank genome browser, descriptions of the genome, and associated hosts.
}
\resizebox{2in}{!}{%
\rotatebox{90}{\begin{tabular}{@{}llllllll@{}}
\toprule
Name & Accession & Created Date & Description & Organism & Sequence Length & Size & host \\ \midrule
AF308158 & AF308158.2 & Mon Jul 02 00:00:00 CDT 2001 & Cactus virus X, complete genome & Cactus virus X & 6614 & 21 KB & Selenicereus undatus \\
AY366207 & AY366207.2 & Fri Apr 23 00:00:00 CDT 2004 & Schlumbergera virus X strain K11, complete genome & Schlumbergera virus X & 6633 & 19 KB & \\
AY366208 & AY366208.1 & Fri Apr 23 00:00:00 CDT 2004 & Zygocactus virus X strain B1 replication-associated protein, triple gene block protein 1, triple gene block protein 2, triple gene block protein 3, and coat protein genes, complete cds & Zygocactus virus X & 6624 & 18 KB & \\
AY366209 & AY366209.1 & Fri Apr 23 00:00:00 CDT 2004 & Opuntia virus X strain CC10 replication-associated protein, triple gene block protein 1, triple gene block protein 2, triple gene block protein 3, and coat protein genes, complete cds & Opuntia virus X & 6653 & 18 KB & \\
AY800279 & AY800279.1 & Fri Jul 01 00:00:00 CDT 2005 & Nandina mosaic virus isolate PLH 1, complete genome & Nandina mosaic virus & 6066 & 16 KB & \\
AY863024 & AY863024.1 & Fri Dec 23 00:00:00 CST 2005 & Alternanthera mosaic virus, complete genome & Alternanthera mosaic virus & 6607 & 26 KB & Phlox stolonifera cv. Sherwood Purple \\
CYMRNA & D29630.1 & Fri Mar 25 00:00:00 CST 1994 & Clover yellow mosaic virus genomic RNA, complete sequence & Clover yellow mosaic virus & 7015 & 11 KB & \\
FJ822136 & FJ822136.1 & Sun Apr 05 00:00:00 CDT 2009 & Alternanthera mosaic virus from Portulaca grandiflora, complete genome & Alternanthera mosaic virus & 6606 & 21 KB & Portulaca grandiflora \\
GQ179646 & GQ179646.1 & Wed Sep 16 00:00:00 CDT 2009 & Alternanthera mosaic virus isolate SP 3-1, complete genome & Alternanthera mosaic virus & 6607 & 19 KB & Phlox stolonifera cv. Sherwood Purple \\
GQ179647 & GQ179647.1 & Wed Sep 16 00:00:00 CDT 2009 & Alternanthera mosaic virus isolate SP 4-7, complete genome & Alternanthera mosaic virus & 6607 & 19 KB & Phlox stolonifera cv. Sherwood Purple \\
JF930326 & JF930326.1 & Tue Jul 01 00:00:00 CDT 2014 & Zygocactus virus X isolate P39, complete genome & Zygocactus virus X & 6624 & 18 KB & Selenicereus sp. \\
JF930327 & JF930327.1 & Tue Jul 01 00:00:00 CDT 2014 & Pitaya virus X isolate P37, complete genome & Pitaya virus X & 6677 & 18 KB & Selenicereus sp. \\
JF937699 & JF937699.1 & Tue Jul 01 00:00:00 CDT 2014 & Cactus virus X isolate NTU, complete genome & Cactus virus X & 6627 & 18 KB & Selenicereus sp. \\
JX524226 & JX524226.1 & Sun Oct 28 00:00:00 CDT 2012 & Papaya mosaic virus isolate PMV-HN, complete genome & Papaya mosaic virus & 6656 & 19 KB & Carica papaya \\
KM288842 & KM288842.1 & Fri Sep 30 00:00:00 CDT 2016 & Zygocactus virus X isolate TW-4XB-2 replication-associated protein (RdRP) gene, partial cds; and triple gene block protein 1 (TGB1), triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Zygocactus virus X & 2403 & 15 KB & Selenicereus sp. (pitaya) \\
KM288843 & KM288843.1 & Fri Sep 30 00:00:00 CDT 2016 & Zygocactus virus X isolate TW-456Y-4 triple gene block protein 1 (TGB1) gene, partial cds; and triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Zygocactus virus X & 1671 & 13 KB & Selenicereus sp. (pitaya) \\
KM288844 & KM288844.1 & Fri Sep 30 00:00:00 CDT 2016 & Zygocactus virus X isolate TW-5149-5 replication-associated protein (RdRP) gene, partial cds; and triple gene block protein 1 (TGB1), triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Zygocactus virus X & 2399 & 16 KB & Selenicereus sp. (pitaya) \\
KM288845 & KM288845.1 & Fri Sep 30 00:00:00 CDT 2016 & Zygocactus virus X isolate TW-5149-17 replication-associated protein (RdRP) gene, partial cds; and triple gene block protein 1 (TGB1), triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Zygocactus virus X & 2397 & 16 KB & Selenicereus sp. (pitaya) \\
KM288846 & KM288846.1 & Fri Sep 30 00:00:00 CDT 2016 & Cactus virus X isolate TW-5XB-1 replication-associated protein (RdRP) gene, partial cds; and triple gene block protein 1 (TGB1), triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Cactus virus X & 2418 & 16 KB & Selenicereus sp. (pitaya) \\
KM288847 & KM288847.1 & Fri Sep 30 00:00:00 CDT 2016 & Cactus virus X isolate TW-456Y-1 triple gene block protein 1 (TGB1) gene, partial cds; and triple gene block protein 2 (TGB2), triple gene block protein 3 (TGB3), and coat protein (CP) genes, complete cds & Cactus virus X & 1675 & 13 KB & Selenicereus sp. (pitaya) \\
KM365479 & KM365479.1 & Mon Nov 17 00:00:00 CST 2014 & Cactus virus X isolate TW-5149-20 replication-associated protein (CVXgp1) gene, partial cds; and triple gene block protein 1 (CVXgp2), triple gene block protein 2 (CVXgp3), triple gene block protein 3 (CVXgp4), and coat protein (CVXgp5) genes, complete cds & Cactus virus X & 2396 & 15 KB & Selenicereus sp. (pitaya) \\
KP090203 & KP090203.1 & Tue Jan 27 00:00:00 CST 2015 & Schlumbergera virus X isolate Palma-PE, complete genome & Schlumbergera virus X & 6615 & 20 KB & Opuntia cochenillifera \\
KT717325 & KT717325.1 & Sat Feb 13 00:00:00 CST 2016 & Plantago asiatica mosaic virus isolate kr, complete genome & Plantago asiatica mosaic virus & 6101 & 19 KB & Lilium sp. \\
KU159093 & KU159093.1 & Wed Apr 20 00:00:00 CDT 2016 & Plantago asiatica mosaic virus isolate Ko-YS, complete genome & Plantago asiatica mosaic virus & 6102 & 17 KB & lily \\
KU697313 & KU697313.1 & Mon Mar 07 00:00:00 CST 2016 & Plantago asiatica mosaic virus isolate Gunwi, complete genome & Plantago asiatica mosaic virus & 6130 & 19 KB & Plantago asiatica \\
KU854929 & KU854929.1 & Tue May 31 00:00:00 CDT 2016 & Schlumbergera virus X isolate nopal verdura 1, complete genome & Schlumbergera virus X & 6646 & 21 KB & Opuntia ficus-indica \\
KU854931 & KU854931.1 & Tue May 31 00:00:00 CDT 2016 & Opuntia virus X isolate nopal verdura-1, complete genome & Opuntia virus X & 6667 & 21 KB & Opuntia ficus-indica \\
KX196173 & KX196173.2 & Sun Jul 31 00:00:00 CDT 2016 & Senna mosaic virus isolate Brazilian, complete genome & Senna mosaic virus & 6775 & 20 KB & Senna occidentalis \\
KX883791 & KX883791.1 & Sat Dec 10 00:00:00 CST 2016 & Cactus virus X strain SCM51431 ORF1, ORF2, ORF3, and ORF4 genes, complete cds & Cactus virus X & 6610 & 20 KB & Diptera \\
KY348771 & KY348771.1 & Mon Nov 13 00:00:00 CST 2017 & Opuntia virus X isolate Noptuna-Mex, complete genome & Opuntia virus X & 6656 & 20 KB & Opuntia albicarpa cv. nopal tunero \\
LC107515 & LC107515.1 & Tue Feb 02 00:00:00 CST 2016 & Alternanthera mosaic virus genomic RNA, complete genome, isolate: Ac & Alternanthera mosaic virus & 6604 & 21 KB & Achyranthes bidentata \\
LC107517 & LC107517.1 & Tue Feb 02 00:00:00 CST 2016 & Hydrangea ringspot virus genomic RNA, complete genome, isolate: Gu2 & Hydrangea ringspot virus & 6196 & 22 KB & Hydrangea macrophylla \\
LC128411 & LC128411.1 & Wed Mar 30 00:00:00 CDT 2016 & Cactus virus X genomic RNA, complete genome & Cactus virus X & 6618 & 19 KB & Selenicereus undatus \\
LC155795 & LC155795.1 & Fri Mar 24 00:00:00 CDT 2017 & Plantago asiatica mosaic virus genomic RNA, complete genome, isolate: NJ & Plantago asiatica mosaic virus & 6122 & 20 KB & Nandina domestica \\
MF978248 & MF978248.1 & Tue Dec 26 00:00:00 CST 2017 & Babaco mosaic virus isolate Tandapi, complete genome & Babaco mosaic virus & 6692 & 20 KB & Vasconcellea x heilbornii \\
MG210801 & MG210801.1 & Tue Oct 30 00:00:00 CDT 2018 & Mytcor virus 1 replicative protein gene, partial cds; and protein 2 and protein 3 genes, complete cds & Mytcor virus 1 & 5689 & 14 KB & Mytilus coruscus \\
MH423501 & MH423501.1 & Sun Feb 17 00:00:00 CST 2019 & Alternanthera mosaic virus isolate DH, complete genome & Alternanthera mosaic virus & 6598 & 18 KB & Epiphyllum sp. cv. Dragon Heart \\ \bottomrule
\end{tabular}}%
}
\end{supptable}
\restoregeometry
\begin{supptable}[ht]
\caption{
Assembled viral sequences from \textit{Schlumbergera truncata} samples.
}
\resizebox{\textwidth}{!}{%
\begin{tabular}{@{}llllll@{}}
\toprule
Name & Description & Sequence Length & sample\_name & tissue\_type \\ \midrule
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H02 & sty \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H03 & pol \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H03 & pol \\
Schlumbergera\_truncata & NC\_011659 & 6633 & 15H03 & pol \\
Schlumbergera\_truncata & NC\_002815\_a & 6614 & 15H03 & sty \\
Schlumbergera\_truncata & NC\_002815\_b & 6614 & 15H03 & sty \\
Schlumbergera\_truncata & NC\_006059\_a & 6624 & 15H03 & sty \\
Schlumbergera\_truncata & NC\_006059\_b & 6624 & 15H03 & sty \\
Schlumbergera\_truncata & NC\_011659 & 6633 & 15H03 & sty \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H04 & pet \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H04 & pet \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H04 & pol \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H04 & pol \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H04 & sty \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H04 & sty \\
Schlumbergera\_truncata & NC\_002815 & 6553 & 15H05 & pol \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H06 & pol \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H06 & pol \\
Schlumbergera\_truncata & NC\_011659 & 6633 & 15H06 & pol \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 15H06 & sty \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 15H06 & sty \\
Schlumbergera\_truncata & NC\_011659 & 6633 & 15H06 & sty \\
Schlumbergera\_truncata & NC\_002815 & 6614 & 19JSF & sty \\
Schlumbergera\_truncata & NC\_006059 & 6624 & 19JSF & sty
\end{tabular}}
\end{supptable}
\end{document}