Development 143: doi:10.1242/dev.129973: Supplementary information
Figure S1: Micro-CT 3D reconstruction of meristems from 15-day-old seedlings of Col-0, jba1D er-20 and clv3-2 jba1D/+ er-20. In blue, manual segmentation of the shoot apical meristem.
Development • Supplementary information
Scale bars: 100 µm.
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Figures S2 and S3: Mutants with disturbed meristem homeostasis display a gradual
increase in meristem size. Typical median longitudinal sections through 9-day (S2) and 15-day
(S3) old Arabidopsis seedlings show major differences in meristem size. For jba 1D/+ and jba
1D/+ er-20 which exhibits significant differences in meristem size, depending on the orientation
of sectioning, a different set of sections were done for each orientation: parallel to cotyledons
(Pl) and perpendicular to cotyledons (Pr). Genotypes are indicated. Scale bars = 100 The
analysis of measurements of 10 meristems width and height using the ImageJ software is
presented in Fig. 4.
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Figure S4. Reduction in CLV3, HD-ZIPIII and ER function affects meristem morphology in a
different manner. Top view of Scanning electron microscopy (SEM) images of inflorescence
meristems (IM) of different genotypes reveal different sizes and shapes. All meristems were
analyzed 35 days after germination at about 14 days after bolting. Typical meristems are shown
(A) All the Col-0 IM look similar, displaying a spiral phyllotactic pattern and a circular
meristems. (B and C) clv3-2 IM (in Col-0 background) displaying a round (top view) and tall
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
structure (side view) with altered phyllotaxis. All meristems analyzed exhibited similar shape
(D) jba-1D/+ fasciated IM (E) Addition of er to jba-1D/+ causes the meristem to become wider
and at later stages (24 days after bolting - right low corner) to split. This genotype shows the
highest variability in size and shapes (F) clv3-2 er IM exhibiting elongated meristems but later,
in mature plants all meristems are long and narrow as shown in Fig 5 (G) clv3-2 jba-1D/+ er-20
IM displaying enlargement in all directions. Top views show round meristems (I). Scale bars: (A
Development • Supplementary information
- F) 50 μm, (G) 500 μm.
Development 143: doi:10.1242/dev.129973: Supplementary information
Figure S5. Mutants with disturbed meristem homeostasis display altered inflorescent
meristem size and shape.
demonstrates the major differences among different genotypes. (A) Meristem maximal lengths.
(B) Meristems maximal widths. (C) The ratio between maximal length and maximal width for
each meristem. The mean of all ratios is indicated above the box in brown. All measurements
were done on meristems from 35-day-old plants at about 14 day after bolting. Black center lines
show the medians; box limits indicate the 25th and 75th percentiles; whiskers extend to 5th and
95th percentiles, outliers are marked by dots; for all measurements n=8. An example for typical
meristems presented in Fig S4. (D) Illustration of how the measurements were done.
Measurements were done in imageJ by stretching a line between maximal length or width points
for each meristem. In meristems with a curve, broken lines were measured. In meristems that
show a narrow region and a wider region like the one in D the wider region was measured.
Development • Supplementary information
Box-plot representation of length and width measurement of SEM images in imageJ
Development 143: doi:10.1242/dev.129973: Supplementary information
Figure S6. Illustration of sample preparation for mRNA-Seq analysis. Eight-day-old
seedlings were dissected under a stereomicroscope. The cotyledons and young leaves were first
trimmed at a position adjacent to the hypocotyl-meristem junction. Next, the hypocotyl was
excised and the samples were immediately frozen in liquid nitrogen. On the right, highlighted in
blue, is the meristem. The bottom image shows the exposed meristem (arrow). Scale bars: 1 mm
Development • Supplementary information
for seedling and 200 μm for trimmed meristem.
Figure S7. Relative transcript levels of STM, CLV3, MIR166, CNA, PHB and PHV in wildtype and mutants. Relative transcript levels were calculated from triplicate RT-qPCR reactions
of RNA samples prepared from SAM-enriched tissues from 8- and 15-day-old seedlings that
were collected as described in supplementary material Fig. S1. The transcript levels in Col are
set to 1. Relative expression is normalized to ACTIN2. Genotype and gene tested are indicated.
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Movies 1 and 2. X-ray micro-CT of 15-day-old seedling meristem of Col-0 and clv3-2 jba1D/+ er-20. Seedlings were fixed dehydrated and brought to 100% ethanol, were then soaked in
2% potassium iodide (IKI) and were scanned using the XRadia Micro XCT 400 system. (Movie
1, see: http://dx.doi.org/10.6084/m9.figshare.3084610). Rotation view of Col-0 seedling, the
meristem is almost undetectable. (Movie 2, see: http://dx.doi.org/10.6084/m9.figshare.3084613)
Rotation view of clv3-2 jba-1D/+ er-20 triple mutant seedling. The huge meristem exhibits a
cylindrical shape.
Movies 3-8. X-ray micro-CT of 15-day-old seedling meristem from Col-0, jba1D/+ er-20
and clv3-2 jba-1D/+ er-20. Seedlings were fixed dehydrated and brought to 100% ethanol, were
then soaked in 2% potassium iodide (IKI) and were scanned using the XRadia Micro XCT 400
system. (Movies 3-5) Manually reconstructed serial longitudinal section (RCS) movies of Col-0
(Movie 3, see: http://dx.doi.org/10.6084/m9.figshare.3084583), jba-1D/+ er-20 (Movie 4, see:
http://dx.doi.org/10.6084/m9.figshare.3084586) and clv3-2 jba-1D/+ er-20 (Movie 5, see:
http://dx.doi.org/10.6084/m9.figshare.3084592). The typical dome shaped meristem observed in
Col-0 and jba-1D/+ er-20, is shifted into a more rectangular shape. (Movies 6-8) Manually
reconstructed serial transverse section (RCS) movies of Col-0 (Movie 6, see:
http://dx.doi.org/10.6084/m9.figshare.3084595), jba-1D/+ er-20 (Movie 7, see:
http://dx.doi.org/10.6084/m9.figshare.3084604) and clv3-2 jba-1D/+ er-20 (Movie 8, see:
http://dx.doi.org/10.6084/m9.figshare.3084607). Demonstrating the effect of meristem
enlargement on phyllotaxis and showing the isodiametric shape of the triple mutant huge
Development • Supplementary information
meristem.
Development 143: doi:10.1242/dev.129973: Supplementary information
Materials and Methods
Differential expression analysis by mRNA-seq
Shoot apical meristems (SAM) from 8- and 15-day-old seedlings (including Col-0, clv3-2,
jba-1D/+, jba-1D/+ er-20, and jba-1D/+ er-20 clv3-2) were collected as described in Figure S1
(each sample comprised 40 to 45 meristems), and were immediately frozen in liquid nitrogen.
Total RNA was isolated using Qiagen RNeasy Mini-kit and was used to prepare ten libraries
using the TruSeqTM-RNA kit. Single-end sequencing was performed by multiplexing the libraries
in an Illumina HiSeq2500 system at the Technion Genome Center (Israel).
The reads (51 nt long) were quality filtered and trimmed using Trimmomatic version 0.32 (1)
with the following options: -threads 8 -phred33 ILLUMINACLIP:adapters/TruSeq3SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The resulting
reads were then aligned to the TAIR10 version of the Arabidopsis thaliana genome sequence
(https://www.arabidopsis.org/) using TopHat version 2.0.12 (2) and Bowtie 2 version 2.1.0 (3)
with the following options: -p 8 (number of threads) -G TAIR10_nucleus.gff, where
TAIR10_nucleus.gff is a file containing the annotation for the nuclear genes in the Arabidopsis
genome in general feature format (GFF), and default values for all other parameters. The
resulting read alignments (in bam format) were used for transcript quantification with Cuffdiff
version 2.2.1 (4) with the following options: -p 8 (number of threads) -M filter_nucleus.gff,
where filter_nucleus.gff is a file containing the annotation for rRNA, tRNA, snRNA and
snoRNA genes in the Arabidopsis nuclear genome, which were masked for quantification
purposes.
The gene expression level (reads per kilobase of transcript per million of sequenced reads
(RPKM) calculation) values were tabulated and subjected to k-means clustering using Gene
(centered)" as the similarity metric, and converging for 1000 runs. Genes that were not expressed
(i.e. with RPKM values equal to 0) across all samples were removed from the dataset before the
k-means analysis. We performed separate analyses for all samples, for samples corresponding to
the first collection date, and for samples corresponding to the second collection date. This
approach allowed us to identify co-expressed genes with highly correlated expression levels.
Heat maps were visualized using Java Tree view version 3.0 (6) after centering and normalizing
the expression values of selected genes. The RPKM values for each gene were centered by
subtracting their mean, and then normalize to make the sum of their squared deviations equal to
one. This step was performed to highlight the similar expression patterns regardless of their
absolute expression values (expressed as RPKM).
Development • Supplementary information
Cluster 3.0 software (5), selecting a k value (number of clusters) of 1000, using "correlation
Development 143: doi:10.1242/dev.129973: Supplementary information
Quantitative RT-PCR analysis
Total RNA was isolated from 8-day-old seedlings growing on MS plates using the Qiagen
RNeasy Mini-kit. cDNA synthesis was performed with the Invitrogen SuperScript II Reverse
Transcriptase, using 1 μg of RNA. RTqPCR analysis was carried out using a Rotor-Gene-Qinstrument (Qiagen), with Absolute-Blue-qPCR-SYBR-Green Mix (Thermo). Three independent
technical replicates were performed for each cDNA sample. ACTIN2 (AT3G18780) was used as
control and relative expression analysis was calculated using the 2-ddCT method (7). Primers
used for RT-qPCR analysis are as follows: ACT2-AT3G18780, GGATCTGT ACGGTAACATTGTGC (forward) and CCACCGATCCAGACACTGTAC (reverse); STMAT1G62360, GATAGGAACAATAATG - GGTCATCCG (forward) and
AACCACTGTACTTGCGCAAGAG (reverse); CLV3-AT2G27250, GTTCAAGGACTTTCCA
- ACCGCAAGATGAT (forward) and CCTTCTCTGCTTCTCCATTTG - CTCCAACC
(reverse);
1.
2.
3.
4.
5.
6.
7.
Bolger AM, Lohse M, & Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina
sequence data. Bioinformatics (Oxford, England) 30(15):2114-2120.
Kim D, et al. (2013) TopHat2: accurate alignment of transcriptomes in the presence of
insertions, deletions and gene fusions. Genome biology 14(4):R36.
Langmead B & Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature
methods 9(4):357-359.
Trapnell C, et al. (2013) Differential analysis of gene regulation at transcript resolution
with RNA-seq. Nature biotechnology 31(1):46-53.
de Hoon MJ, Imoto S, Nolan J, & Miyano S (2004) Open source clustering software.
Bioinformatics (Oxford, England) 20(9):1453-1454.
Saldanha AJ (2004) Java Treeview--extensible visualization of microarray data.
Bioinformatics (Oxford, England) 20(17):3246-3248.
Livak, K. J. and Schmittgen, T. D. (2001). Analysis of relative gene expression data using
real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402-408
Development • Supplementary information
References
Development 143: doi:10.1242/dev.129973: Supplementary information
Table S1: Meristem width and height measurements of 9 and 15 day old seedlings
8 Day
Col
W
Col
H
CLV3
W
CLV3
H
jba
W
(Pr)
Jba
H
(Pr)
jba
W
(Pl)
Jba
H
(Pl)
jba er
W (Pr)
jba er
H (Pr)
jba er
W (Pl)
jba er
H (Pl)
jba er
CLV3 W
jba er
CLV3 H
1
44.0
13.3
77.2
72.5
58.0
46.9
81.8
33.8
94.1
45.0
122.1
40.0
129.1
42.5
2
44.4
16.7
67.2
59.0
58.4
43.7
86.2
35.7
93.1
36.3
111.0
34.2
109.7
59.0
3
55.7
14.7
62.9
53.5
61.2
44.9
85.7
35.0
96.9
28.9
98.4
34.0
122.2
44.6
4
43.4
20.2
69.2
62.9
60.8
46.6
89.4
42.2
96.0
32.7
109.2
32.2
124.7
37.9
5
44.7
17.0
55.0
48.0
65.5
38.9
99.4
40.4
102.1
31.9
127.9
37.1
127.5
63.0
6
41.7
17.5
66.0
55.3
64.3
45.1
71.1
34.7
75.2
21.1
118.3
35.1
127.1
33.5
7
58.0
18.1
68.3
56.0
62.0
44.0
88.4
39.2
96.0
32.0
99.3
32.9
125.3
52.0
8
43.6
16.2
76.1
69.3
59.7
45.2
84.1
36.0
92.3
29.5
105.4
35.7
124.0
43.3
9
49.4
15.0
60.4
54.9
63.4
46.3
91.7
42.4
110.0
37.0
116.9
36.3
130.1
61.4
10
52.1
17.6
71.9
59.3
64.2
45.8
100.8
46.8
98.3
31.2
104.1
39.4
132.8
57.4
Avrage
47.7
16.6
67.4
59.0
61.8
44.7
87.9
38.6
95.4
32.5
111.3
35.7
125.2
49.5
Col
W
Col
H
CLV3
W
CLV3
H
jba
W
(Pr)
Jba
H
(Pr)
jba
W
(Pl)
Jba
H
(Pl)
jba er
W (Pr)
jba er
H (Pr)
jba er
W (Pl)
jba er
H (Pl)
jba er
CLV3 W
jba er
CLV3 H
1
56.7
22.5
92.0
76.4
61.9
38.2
90.5
121.4
40.6
111.3
134.6
76.7
2
61.2
19.5
74.6
70.8
76.4
42.0
114.5
93.3
39.4
122.2
151.6
72.3
3
62.3
22.0
84.4
72.0
67.3
36.9
101.0
99.5
32.0
112.9
147.8
64.9
4
59.4
20.0
83.8
74.7
75.6
37.3
107.8
109.2
36.9
128.1
144.4
65.0
5
69.2
21.9
73.0
78.0
73.2
40.9
94.9
110.2
27.4
151.2
162.3
54.0
6
66.1
24.9
92.7
82.6
69.0
42.5
101.7
102.1
34.1
114.5
140.3
63.7
7
61.6
22.0
76.2
69.5
66.1
39.9
98.0
108.9
32.5
123.9
162.9
53.0
8
63.9
23.0
89.7
77.3
71.4
38.0
105.7
118.4
34.4
120.8
148.3
65.8
9
46.4
23.6
86.6
70.1
76.7
44.0
111.5
107.2
44.8
129.2
129.7
68.9
10
65.7
20.6
65.9
68.9
62.8
27.9
105.7
119.0
31.8
113.0
156.3
74.8
Avrage
61.3
22.0
81.9
74.0
70.0
38.8
103.1
108.9
35.4
122.7
147.8
65.9
Width: W and Height: H in micrometer
Development • Supplementary information
15 Day
Development 143: doi:10.1242/dev.129973: Supplementary information
Supplementary material Table S2: mRNA-seq analysis quality control data
Col 8
clv3 8
jba1D/+ 8
jba1D/+ er 8
clv3 jba1D/+ er 8
Col 15
clv3 15
jba1D/+ 15
jba1D/+ er 15
clv3 jba1D/+ er 15
Raw reads
Mapped
reads
% of
input
Mapped
reads with
multiple
alignments
45,262,389
43,522,363
35,514,884
49,708,059
32,001,362
44,844,794
36,741,580
44,120,248
34,020,742
41,982,022
44643190
42711864
34654164
48667794
31544741
44295976
36271417
43142522
33564663
41428905
43,309,836
41,817,843
33,919,658
47,789,061
30,537,932
42,960,525
35,586,425
42,097,501
32,953,496
40,615,618
97
97.9
97.9
98.2
96.8
97.0
98.1
97.6
98.2
98.0
1152086
1222901
1033409
1261795
1249850
1310162
1262658
2071048
929566
1306244
Development • Supplementary information
Sample
Reads
after QC
% of
mapped
reads with
multiple
alignments
(relative to
total
mapped
reads)
2.7
2.9
3.0
2.6
4.1
3.0
3.5
4.9
2.8
3.2
Development 143: doi:10.1242/dev.129973: Supplementary information
Supplementary Table S3: Histones RPKM values
Description
RPKM (8-day-old apices)
AT1G01370
histone H3
13.7
10.2
11.7
11.4
AT1G06760
histone
H1.1
histone H4
352.1
321.8
279.9
298.6
304.3
366.1
436.8
411.0
431.0
395.0
522
129.3
41.1
43.0
44.9
40.1
56.6
32.3
31.6
54.0
47.0
961
341.7
111.0
130.4
131.2
158.2
146.1
53.4
54.6
204.3
118.0
734
AT1G07820
histone
H2B
histone H4
196.4
155.2
144.1
167.0
178.3
145.9
167.8
165.3
337.4
274.7
804
AT1G09200
histone H3
299.6
191.1
243.0
307.4
326.5
100.0
94.8
108.7
513.1
303.2
628
AT1G51060
histone
H2A 10
histone
H2A
protein 9
histone
H1-3
histone
H2B
histone H4
208.9
182.1
213.1
218.3
275.5
80.8
73.4
69.0
301.5
181.0
321
295.8
323.7
380.2
306.3
327.4
443.0
463.2
445.6
290.8
336.6
145
6.3
27.1
8.8
18.7
6.5
62.6
180.2
81.6
35.5
33.4
173
102.9
82.3
48.4
55.2
47.1
86.1
96.0
75.0
89.3
87.4
364
284.1
185.5
183.2
222.9
215.8
145.9
128.6
134.5
369.5
280.5
849
218.4
162.7
184.9
153.0
170.7
216.1
221.7
258.1
157.9
201.8
455
105.0
61.1
97.9
98.0
111.3
48.9
39.6
57.8
173.8
146.1
999
39.3
33.6
37.7
39.0
43.1
17.1
22.3
27.9
57.6
41.4
628
5.9
6.1
7.9
6.9
9.7
3.6
4.0
4.0
8.7
7.2
503
136.9
97.1
129.5
135.9
177.8
42.6
40.3
54.8
212.7
139.6
628
AT3G27360
histone
H1.2
histone
H2B
histone
H2A 8
histone
H2B
histone
H2A 13
histone H3
71.7
55.8
77.6
89.2
87.3
36.3
34.7
34.8
178.5
101.1
1
AT3G45930
histone H4
57.8
57.9
64.7
70.1
74.9
21.9
28.2
25.3
141.5
75.6
628
AT3G45980
histone
H2B
histone
H2B
histone H4
378.5
305.5
323.0
377.4
386.6
276.3
308.3
254.7
465.6
401.6
849
168.5
200.3
215.4
218.9
248.0
110.3
155.2
140.1
300.2
220.3
503
63.5
50.7
71.1
70.6
63.8
20.2
23.2
28.9
136.6
78.8
628
histone
H2B
histone H4
0.4
18.7
36.4
19.7
26.6
0.7
9.0
10.8
32.5
24.0
792
210.6
222.9
226.9
208.1
193.0
106.5
165.6
170.2
313.3
218.0
660
145.0
101.6
139.8
133.2
136.1
70.8
76.7
101.9
228.7
176.9
999
1.8
0.8
0.1
2.3
1.0
8.6
1.6
0.2
1.5
1.3
286
123.9
96.0
105.7
103.4
129.0
69.7
73.0
62.8
163.6
135.3
849
AT4G40030
histone
H2A
histone
H2A
histone
H2A 2
histone H3
530.6
483.2
493.3
464.2
456.8
564.6
592.8
556.5
613.1
527.9
20
AT4G40040
histone H3
748.0
888.5
725.7
743.2
741.8
850.5
1078.7
933.8
782.6
907.5
950
AT5G02560
histone
H2A 12
histone
H2B
6.0
8.3
8.5
8.8
7.0
8.6
7.1
7.3
14.2
7.5
138
0.8
1.7
1.0
1.0
2.6
0.2
0.6
0.6
3.3
2.0
503
AT1G07790
AT1G52740
AT2G18050
AT2G28720
AT2G28740
AT2G30620
AT2G37470
AT2G38810
AT3G09480
AT3G20670
AT3G46030
AT3G46320
AT3G53650
AT3G53730
AT3G54560
AT4G13570
AT4G27230
AT5G02570
clv3
jba
jba er
Col-0
clv3
jba
7.5
5.9
Cluster
clv3
jba er
14.6
AT1G07660
Col-0
RPKM (15-day-old apices)
7.3
jba
er
19.7
clv3
jba er
14.6
628
Development • Supplementary information
Locus ID
AT5G10390
histone H3
137.4
55.4
69.8
63.5
98.0
45.0
20.8
19.0
136.6
61.6
196
AT5G10400
histone H3
20.0
147.6
193.7
209.1
237.7
16.8
81.8
88.8
391.9
226.3
660
AT5G10980
histone H3
279.2
247.2
276.0
328.6
314.2
230.0
262.6
251.5
381.5
302.1
628
AT5G22880
histone
H2B
histone
H2A 7
histone
H2A
histone H4
230.4
368.7
254.9
467.2
468.8
121.7
204.8
116.1
757.0
449.0
318
122.6
137.5
107.1
138.3
150.1
73.6
94.1
75.1
163.2
129.0
959
65.6
63.0
62.0
67.2
68.5
51.1
59.9
50.7
94.2
73.8
1
362.7
283.0
370.6
330.3
420.6
166.3
236.2
311.5
522.5
546.9
206
268.9
161.3
227.8
254.2
304.4
92.2
73.7
90.3
472.4
268.6
628
386.8
337.2
373.9
388.2
448.3
243.7
251.9
242.2
570.7
410.7
628
AT5G59970
histone
H2A 6
histone
H2B
histone H4
182.5
133.6
142.7
176.9
175.3
70.4
64.1
74.9
294.7
156.8
628
AT5G65350
histone H3
3.6
16.0
11.1
11.7
10.5
1.8
5.6
3.3
9.8
3.8
462
AT5G65360
histone H3
305.0
201.2
261.4
284.5
323.2
88.6
81.6
81.8
501.0
245.2
628
AT5G27670
AT5G54640
AT5G59690
AT5G59870
AT5G59910
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information
Supplementary material Table S4: cell-cycle genes RPKM values
Description
RPKM (8-day-old apices)
RPKM (15-day-old apices)
AT4G27180
kinesin 2
28.6
23.7
25.0
26.1
24.4
21.6
22.4
20.5
36.2
clv3
jba
er
29.9
AT2G24490
replicon protein A2
17.5
17.3
20.0
18.6
26.9
5.8
5.2
5.9
26.8
11.7
11
AT5G08020
RPA70-kDa subunit B
11.3
9.4
10.3
10.6
15.5
3.7
2.8
2.8
14.2
6.3
11
AT1G07370
proliferating cellular
nuclear antigen 1
DNA polymerase epsilon
subunit B2
E2F target protein 1
35.5
30.8
36.3
33.4
50.4
12.5
8.9
10.3
47.4
22.6
11
4.9
4.7
4.4
4.2
6.0
2.3
1.9
1.7
5.7
3.2
11
14.9
15.3
17.5
15.8
21.6
8.5
8.2
8.1
20.4
12.5
11
49.8
45.6
39.6
51.2
49.7
31.4
46.9
52.7
53.3
72.8
17
AT3G11520
cyclin-dependent kinase
B2-1
cyclin-B1-3
16.7
13.2
11.0
15.7
14.5
5.5
5.0
8.0
10.6
10.8
51
AT1G44110
cyclin-A1-1
34.7
30.4
26.9
27.7
31.7
16.0
19.0
21.6
30.6
32.6
51
AT5G54670
kinesin 3
15.6
13.2
13.2
15.1
15.2
7.4
7.4
7.6
16.4
14.3
89
AT2G23430
3.7
5.5
7.9
6.7
6.0
2.1
2.6
2.5
3.7
3.4
158
14.1
13.9
10.1
9.5
11.2
6.5
6.5
6.1
13.2
8.0
160
AT5G60930
cyclin-dependent kinase
inhibitor 1
cyclin-dependent kinase
inhibitor 3
kinesin family member
29.0
23.2
17.1
21.3
21.9
15.9
19.5
21.3
25.4
29.8
170
AT4G05190
kinesin 5
27.2
21.2
16.0
21.5
21.5
13.8
16.9
17.8
19.9
27.9
170
AT1G44900
minichromosome
maintenance protein 2
DNA polymerase delta
subunit 4
kinesin 1
14.6
19.7
20.0
17.0
25.0
6.7
7.0
7.2
23.5
13.4
182
55.5
54.6
43.2
50.3
55.5
35.8
45.1
45.0
71.1
66.8
206
17.6
13.8
12.9
15.8
16.1
10.7
12.3
13.9
19.8
21.2
206
Replication factor-A
protein 1-like protein
DNA primase small
subunit
minichromosome
maintenance protein 6
cell division control
protein 45
cyclin A3-1
15.8
14.5
16.7
16.8
24.1
5.8
4.5
4.3
25.4
9.8
321
12.1
10.3
12.2
11.3
13.7
4.6
4.2
4.8
16.1
10.1
321
14.3
12.7
14.2
12.3
16.5
5.9
4.5
5.4
18.3
11.1
321
6.4
5.1
7.8
6.6
7.6
3.2
2.5
5.3
9.4
4.9
321
10.2
7.0
10.5
8.1
11.8
4.8
2.5
4.7
12.3
7.8
321
kinetochore protein
Nuf2
DNA polymerase alpha 2
9.8
8.6
9.3
10.1
11.1
5.6
5.1
5.6
12.8
8.5
321
12.8
10.5
12.4
10.3
13.0
7.3
6.8
7.9
15.2
11.6
321
16.0
12.2
16.3
13.7
16.8
9.3
8.5
7.4
19.7
12.4
321
AT3G44730
DNA primase large
subunit
kinesin-like protein 1
4.8
5.3
4.2
6.8
6.2
2.9
3.8
3.1
6.3
5.0
333
AT3G50070
cyclin-D3-3
33.3
31.4
27.4
25.6
32.5
20.4
22.0
25.0
46.1
32.6
469
AT5G63960
DNA polymerase delta
subunit 1
DNA polymerase epsilon
subunit 1
cyclin-B1-2
13.2
11.3
10.3
11.1
12.0
10.0
9.4
9.2
16.7
12.3
469
11.1
9.0
7.7
8.3
8.3
8.9
7.5
7.1
12.2
10.6
541
54.7
49.3
38.4
51.2
48.7
20.9
25.0
36.4
39.0
50.0
564
Kinesin motor family
protein
23.0
17.6
13.9
19.0
18.4
9.9
10.6
12.7
17.5
20.9
564
AT5G22110
AT2G40550
AT1G76540
AT5G48820
AT1G09815
AT4G21270
AT5G61000
AT5G41880
AT5G44635
AT3G25100
AT5G43080
AT1G61000
AT1G67630
AT1G67320
AT1G08260
AT5G06150
AT3G20150
Col-0
clv3
jba
jba
er
clv3
jba er
Col-0
clv3
jba
jba
er
Cluster
1
Development • Supplementary information
Locus ID
AT1G16330
cyclin B3-1
9.4
7.3
6.0
9.1
8.2
4.2
4.4
5.2
7.2
9.2
564
AT1G49620
8.6
10.9
7.1
8.8
10.7
4.6
6.4
4.2
7.6
7.4
579
67.4
54.8
59.0
72.1
81.1
24.9
21.6
27.3
42.9
42.4
583
AT2G45080
cyclin-dependent kinase
inhibitor 7
cell division protease
ftsH-12
cyclin-U2-1
8.8
5.1
3.7
3.1
2.6
4.5
5.5
3.9
7.8
4.3
589
AT5G27000
kinesin 4
3.1
2.9
2.8
2.9
3.1
2.4
2.1
5.0
3.4
3.9
611
AT3G54180
cyclin-dependent kinase
B1-1
Rad54-like protein
18.9
15.6
16.3
16.5
17.3
8.4
10.4
11.3
24.0
16.1
628
5.6
4.2
4.1
4.9
5.5
2.8
3.2
3.0
7.1
4.7
628
DNA polymerase alpha
catalytic subunit
DNA (cytosine-5)methyltransferase 1
DNA polymerase delta
subunit 2
cyclin-D5-1
12.6
10.9
12.4
11.2
13.7
6.8
6.0
7.9
16.2
13.0
628
27.5
21.4
24.8
24.2
27.6
16.3
13.7
16.8
33.7
27.1
628
10.9
10.4
11.1
11.3
12.5
8.1
6.2
7.7
15.6
11.6
628
5.5
5.2
6.3
5.7
6.7
3.7
4.0
3.7
6.6
4.1
661
cyclin-dependent kinase
D-1
cyclin-B1-4
4.0
5.2
3.9
5.0
5.2
1.1
2.8
3.9
4.6
4.2
667
19.2
21.8
18.1
23.0
24.0
8.1
12.2
15.8
19.0
23.4
667
cell cycle arrest protein
BUB3
microtubule-associated
protein 65-5
protein DP-E2F-like 1
32.8
25.7
23.8
27.9
28.3
15.1
17.0
18.4
36.1
32.2
688
3.2
3.8
3.2
9.8
12.3
1.2
1.2
1.1
12.7
7.3
708
6.2
5.5
5.0
5.8
8.4
3.6
3.6
4.0
8.7
6.1
708
25.7
17.6
16.2
19.2
20.5
13.7
17.2
18.6
29.8
31.0
804
10.0
9.6
7.6
8.1
9.3
6.5
8.7
8.8
12.0
10.6
804
17.0
16.0
19.1
29.4
26.4
6.9
8.8
7.4
28.7
27.4
823
15.4
16.4
13.4
16.1
16.8
12.8
16.9
18.0
20.9
21.0
824
9.5
9.4
7.4
8.3
10.6
5.4
5.6
4.7
12.2
8.2
834
89.2
74.2
64.7
94.4
90.4
47.7
52.6
42.8
119.7
94.6
849
AT3G05330
kinesin family member
11
kinetochore protein
NDC80
meiotic recombination
protein DMC1-like
protein
kinetochore protein
Spc25
histone-binding protein
RBBP4
cyclin-dependent
kinases regulatory
subunit 2
cyclin family protein
19.9
20.8
16.6
21.3
22.9
6.8
8.3
10.6
12.6
16.3
962
AT1G15660
centromere protein C
20.8
17.2
19.7
17.6
20.1
14.0
16.0
18.0
33.8
27.6
999
AT1G79560
AT3G19210
AT5G67100
AT5G49160
AT2G42120
AT4G37630
AT1G73690
AT2G26760
AT3G19590
AT2G38720
AT3G48160
AT2G36200
AT3G54630
AT3G22880
AT3G48210
AT4G29730
AT2G27970
Development • Supplementary information
Development 143: doi:10.1242/dev.129973: Supplementary information