Sc (#/bp) Tp (#/bp) Pt (#/bp) Vb (#/bp)

SINEs 6/344 29/1731 13/798 43/2943

LINEs 75/4545 265/18404 113/7830 305/23617
LTR 4/193 2/133 2/105 15/1478
elements
DNA 32/1955 64/4725 41/2587 115/9614
elements
Total 7221 bp 24993 bp 11320 bp 37905 bp
interspers
ed 0.02% 0.08% 0.04% 0.05%
repeats
Small 95/8514 87/10854 67/9859 101/16741
RNA 0.02% 0.03% 0.04% 0.02%
Simple 14985/561 6757/2833 2543/1047 124000/44
repeats 722 64 99 04840
1.20% 0.91% 0.40% 6.06%
Low 1095/5282 23307 106/4580 5017/2310
complexit 1 0.11% 0.07% 0.02% 96 0.32%
y
 All_categories_gen Cell growth Chloroplast Glutamine family Nitrogen Phosphorus Response to
e amino acid compound metabolic process stimulus
metabolic process transport

S: 2553 485 1412 58 522 1424 1932

T: 2708 528 1472 56 555 1463 2061

P: 2561 478 1407 62 517 1343 1954

A: 3605 850 1936 75 806 1998 2796

STPA: 1039 141 577 30 164 560 755

STP: 508 104 277 8 108 281 391
SPA: 64 14 37 3 18 23 51
STA: 155 34 94 4 28 86 108
TPA: 181 30 105 4 38 85 138
ST: 257 54 137 0 69 151 204
SP: 87 11 46 0 17 39 58
SA: 49 10 29 1 12 23 38
TP: 151 41 74 2 39 83 122
TA: 71 18 35 1 17 35 59
PA: 101 20 59 3 18 48 86
S: 394 117 215 12 106 261 327
T: 346 106 173 7 92 182 284
P: 430 117 232 12 115 224 353
A: 1945 583 1000 29 511 1138 1561

the number of 324 106 184 10 93 224 273

duplicated genes

2
Sequence ID Number of expansion kog id kog defline kog Class kog Group
jgi|Phatr2|40634| 111 KOG0192 Tyrosine kinase Signal transduction CELLULAR
fgenesh1_pg.C_chr specific for mechanisms PROCESSES
_25000002 activated (GTP- AND SIGNALING
bound)
p21cdc42Hs

jgi|Phatr2|40278| 73 KOG0192 Tyrosine kinase Signal transduction CELLULAR

fgenesh1_pg.C_chr specific for mechanisms PROCESSES
_22000240 activated (GTP- AND SIGNALING
bound)
p21cdc42Hs

jgi|Thaps3|264269| 64 NA
thaps1_ua_kg.chr_
15000007

jgi|Auran1|12439 57 KOG0229 Phosphatidylinosit Signal transduction CELLULAR

ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Auran1|52027 55 KOG0229 Phosphatidylinosit Signal transduction CELLULAR

ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Phatr2|50519| 51 KOG0192 Tyrosine kinase Signal transduction CELLULAR

estExt_fgenesh1_p specific for mechanisms PROCESSES
g.C_chr_300103 activated (GTP- AND SIGNALING
bound)
p21cdc42Hs

jgi|Phatr2|19094| 46 NA
estExt_gwp_gw1.C
_chr_40281

jgi|Thaps3|8145| 45 KOG0519 Sensory Signal transduction CELLULAR

fgenesh1_pg.C_chr transduction mechanisms PROCESSES
_9000313 histidine kinase AND SIGNALING

jgi|Thaps3|264653| 44 NA
thaps1_ua_kg.chr_
19c_29000020

jgi|Thaps3|264655| 42 NA
thaps1_ua_kg.chr_
19c_29000022

jgi|Thaps3|24942| 42 KOG2043 Signaling protein Transcription INFORMATION

estExt_fgenesh1_p SWIFT and related STORAGE AND
g.C_chr_140348 BRCT domain PROCESSING
proteins

jgi|Thaps3|24063| 42 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_90346 histidine kinase AND SIGNALING

jgi|Thaps3|9568| 41 NA
fgenesh1_pg.C_chr
_13000288

jgi|Thaps3|264621| 40 KOG0519 Sensory Signal transduction CELLULAR

thaps1_ua_kg.chr_ transduction mechanisms PROCESSES
19b_31000012 histidine kinase AND SIGNALING

jgi|Thaps3|264261| 40 NA
thaps1_ua_kg.chr_
14000168

jgi|Thaps3|263610| 40 KOG0519 Sensory Signal transduction CELLULAR

thaps1_ua_kg.chr_ transduction mechanisms PROCESSES
9000138 histidine kinase AND SIGNALING

jgi|Thaps3|9222| 39 NA
fgenesh1_pg.C_chr
_12000303

jgi|Thaps3|263599| 39 KOG0519 Sensory Signal transduction CELLULAR

thaps1_ua_kg.chr_ transduction mechanisms PROCESSES
9000127 histidine kinase AND SIGNALING

jgi|Thaps3|23598| 39 NA
estExt_fgenesh1_p
g.C_chr_70620

jgi|Thaps3|2131| 39 NA
fgenesh1_pg.C_chr
_2000086

jgi|Thaps3|268232| 38 NA
estExt_thaps1_ua_
kg.C_chr_20141

jgi|Thaps3|24712| 38 KOG0348 ATP-dependent RNA processing INFORMATION

estExt_fgenesh1_p RNA helicase and modification STORAGE AND
g.C_chr_130300 PROCESSING

jgi|Thaps3|23738| 38 NA
estExt_fgenesh1_p
g.C_chr_80193

jgi|Thaps3|21133| 38 NA
estExt_fgenesh1_p
g.C_chr_20101

jgi|Thaps3|24347| 37 NA
estExt_fgenesh1_p
g.C_chr_11a0156

jgi|Thaps3|261225| 36 NA
thaps1_ua_kg.chr_
2000049

jgi|Thaps3|7530| 35 NA
fgenesh1_pg.C_chr
_8000191

jgi|Thaps3|263129| 35 NA
thaps1_ua_kg.chr_
7000086

jgi|Phatr2|41562| 34 KOG1216 von Willebrand Defense CELLULAR

fgenesh1_pg.C_chr factor and related mechanisms PROCESSES
_31000066 coagulation AND SIGNALING
proteins

jgi|Phatr2|34199| 34 NA
fgenesh1_pg.C_chr
_4000554

jgi|Phatr2|11352| 34 KOG0229 Phosphatidylinosit Signal transduction CELLULAR

e_gw1.5.172.1 ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Thaps3|9175| 33 KOG0519 Sensory Signal transduction CELLULAR

fgenesh1_pg.C_chr transduction mechanisms PROCESSES
_12000256 histidine kinase AND SIGNALING

jgi|Thaps3|6560| 33 KOG1721 FOG: Zn-finger General function POORLY

fgenesh1_pg.C_chr prediction only CHARACTERIZE
_6000715 D

jgi|Thaps3|263899| 33 NA
thaps1_ua_kg.chr_
12000050

jgi|Thaps3|24704| 33 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_130285 histidine kinase AND SIGNALING

jgi|Phatr2|10974| 33 NA
e_gw1.4.78.1

jgi|Thaps3|268593| 32 NA
estExt_thaps1_ua_
kg.C_chr_40023

jgi|Thaps3|264851| 32 KOG0519 Sensory Signal transduction CELLULAR

thaps1_ua_kg.chr_ transduction mechanisms PROCESSES
22000104 histidine kinase AND SIGNALING

jgi|Thaps3|25870| 32 KOG4371 Membrane- Signal transduction CELLULAR

estExt_fgenesh1_p associated protein mechanisms PROCESSES
g.C_chr_230132 tyrosine AND SIGNALING
phosphatase PTP-
BAS and related
proteins, contain
FERM domain

jgi|Phatr2|48535| 32 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_180046 histidine kinase AND SIGNALING

jgi|Auran1|72863 32 KOG1216 von Willebrand Defense CELLULAR

factor and related mechanisms PROCESSES
coagulation AND SIGNALING
proteins

jgi|Auran1|69259 32 KOG4297 C-type lectin Defense CELLULAR

mechanisms PROCESSES
AND SIGNALING

jgi|Auran1|12409 32 KOG0229 Phosphatidylinosit Signal transduction CELLULAR

ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Thaps3|264262| 31 NA
thaps1_ua_kg.chr_
14000169

jgi|Thaps3|11287| 31 NA
fgenesh1_pg.C_chr
_19b_31000030

jgi|Thaps3|25872| 30 NA
estExt_fgenesh1_p
g.C_chr_230135

jgi|Thaps3|1870| 30 NA
fgenesh1_pg.C_chr
_1001004

jgi|Thaps3|25873| 29 KOG1187 Serine/threonine Signal transduction CELLULAR

estExt_fgenesh1_p protein kinase mechanisms PROCESSES
g.C_chr_230136 AND SIGNALING

jgi|Thaps3|24733| 28 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_130348 histidine kinase AND SIGNALING

jgi|Thaps3|6692| 27 KOG1987 Speckle-type POZ General function POORLY

fgenesh1_pg.C_chr protein SPOP and prediction only CHARACTERIZE
_7000075 related proteins D
with TRAF,
MATH and
BTB/POZ domains

jgi|Thaps3|24565| 26 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_120334 histidine kinase AND SIGNALING

jgi|Thaps3|21581| 26 KOG1216 von Willebrand Extracellular CELLULAR

estExt_fgenesh1_p factor and related structures PROCESSES
g.C_chr_21016 coagulation AND SIGNALING
proteins

jgi|Thaps3|10008| 26 NA
fgenesh1_pg.C_chr
_14000353

jgi|Auran1|68916 26 NA

jgi|Auran1|33279 26 KOG0229 Phosphatidylinosit Signal transduction CELLULAR

ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Thaps3|10042| 25 NA
fgenesh1_pg.C_chr
_15000032

jgi|Phatr2|50614| 25 NA
estExt_fgenesh1_p
g.C_chr_320032

jgi|Auran1|65363 25 KOG3765 Predicted Carbohydrate METABOLISM

glycosyltransferase transport and
metabolism

jgi|Thaps3|6585| 24 KOG1987 Speckle-type POZ General function POORLY

fgenesh1_pg.C_chr protein SPOP and prediction only CHARACTERIZE
_6000740 related proteins D
with TRAF,
MATH and
BTB/POZ domains

jgi|Thaps3|23988| 24 KOG1216 von Willebrand Defense CELLULAR

estExt_fgenesh1_p factor and related mechanisms PROCESSES
g.C_chr_90200 coagulation AND SIGNALING
proteins

jgi|Phatr2|49028| 24 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_200140 histidine kinase AND SIGNALING

jgi|Phatr2|45780| 24 KOG0519 Sensory Signal transduction CELLULAR

estExt_fgenesh1_p transduction mechanisms PROCESSES
g.C_chr_80094 histidine kinase AND SIGNALING

jgi|Phatr2|107| 24 NA
gw1.1.18.1

jgi|Phatr2|10781| 24 NA
e_gw1.4.389.1

jgi|Auran1|65882 24 KOG1995 Conserved Zn- General function POORLY

finger protein prediction only CHARACTERIZE
D
jgi|Auran1|54776 24 KOG0229 Phosphatidylinosit Signal transduction CELLULAR
ol-4-phosphate 5- mechanisms PROCESSES
kinase AND SIGNALING

jgi|Thaps3|9257| 23 KOG1878 Nuclear receptor Transcription INFORMATION

fgenesh1_pg.C_chr coregulator STORAGE AND
_12000338 SMRT/SMRTER, PROCESSING
contains Myb-like
domains

jgi|Phatr2|12927| 23 NA
e_gw1.9.7.1

jgi|Auran1|39500 23 KOG1472 Histone Transcription INFORMATION

acetyltransferase STORAGE AND
SAGA/ADA, PROCESSING
catalytic subunit
PCAF/GCN5 and
related proteins

jgi|Thaps3|23334| 22 KOG1216 von Willebrand Defense CELLULAR

estExt_fgenesh1_p factor and related mechanisms PROCESSES
g.C_chr_70017 coagulation AND SIGNALING
proteins

jgi|Thaps3|20565| 22 NA
estExt_fgenesh1_p
g.C_chr_10012

jgi|Auran1|68863 22 KOG0382 Carbonic anhydrase General function POORLY

prediction only CHARACTERIZE
D
jgi|Thaps3|7816| 21 KOG0519 Sensory Signal transduction CELLULAR
fgenesh1_pg.C_chr transduction mechanisms PROCESSES
_8000477 histidine kinase AND SIGNALING

jgi|Thaps3|269633| 21 NA
estExt_thaps1_ua_
kg.C_chr_120072

jgi|Thaps3|24694| 21 NA
estExt_fgenesh1_p
g.C_chr_130264

jgi|Auran1|19388 21 NA

jgi|Thaps3|7256| 20 NA
fgenesh1_pg.C_chr
_7000639

jgi|Thaps3|5043| 20 NA
fgenesh1_pg.C_chr
_5000085

jgi|Phatr2|50602| 20 NA
estExt_fgenesh1_p
g.C_chr_320016

3
 Sc Tp Pt Vb
Sil1 7 12 3 0
Sil2 6 9 0 0
Sil3 0 2 0 0
SIT1 2 3 4 0
SIT2 2 4 4 0
SIT3 2 3 4 0
TPSIL2 0 2 0 0
Gene Gene GO PMID
name ID
/Diatom
(Thalassi
osira)
Ammoniu 7446649, 15696 21729317
m 7443520,
transporte 7450192,
r 7452262,
7197550,
17362365,
7204486,
7198012,
7199619,
7201625,
7197168,
etc…

Glutamine 7203740, 1901704 21729317

synthetase 7448923
, type III
Mn- 17362203 21729317
dependent
inorganic
Plastid 21729317
inorganic
pyrophosp
hatase

V type H - 19947984,
+
21729317
translocati 19944515
ng
inorganic
pyrophosp
hatase
Acid 17362892, 3993 21729317
phosphata 9479008,
se 9477026,
9473232,
9473231,
9473229,
9461484,
9473233,
9473230,
17362334,
17360491,
etc…
Purple 9477026, 21729317
acid 17362334,
phosphata 17359840,
se 9469524,
9476790,
9469138,
19945140,
7444022

Alkaline 7445522, 4035 21729317

phosphata 9463011,
se 9463007,
7444164,
17360109,
7201029,
7198161,
7449328,
7443642,
7443114

Plastid 7197026, 21729317

phosphate 7196797,
translocat 7196130,
or 7444973

Glutamine 21729317
synthetase
, type II
phoR 7204469, 21729317
7200707,
9461455,
19945772

phoB 6335674, 21729317

6335570,
7204469,
7203123,
7202697,
7200707,
7200614,
7200611,
7199631,
7197731,
7195765,
etc…
dehydroge 7448291, 21729317
nase 7453058,
genes 7445754,
7451797,
7449745,
7450000,
7451068

glutamine 21729317
transcripti
onal
signal
phoA 7444247 16020 21729317
S- 30418 21729317
adenosyl-
methionin
Structural 7198482, 3735 21729317
consituent 7446135,
of 7441940,
ribosome 17362798,
17361770,
17360122,
7199620,
7194867,
9479349,
9472787,
9472135,e
tc..

Macromol 9059 21729317

ecule bio
synthetic
process 
Sulfur 96 21729317
amino
acid
metabolic
Gnenerati 6091 21729317
on of
precursor
metabolite
s and
UPD- 3979 21729317
glucose 6-
dehydroge
nase
activity
Cellular 44249 21729317
biosynthet
ic process
Nitrogen 21729317
compound
biosynthet
ic process

Coenzyme 6732 21729317

metabolic
process
Chloropla 9507 21729317
st
Photosyst 9521 21729317
em
Generatio 6091 21729317
n of
precursor
metabolite
s and
Structural 5198 21729317
molecule
activity
Magnesiu 287 21729317
m ion
binding
Cellular 44260 21729317
macromol
ecule
metabolic
process
sulfolipid 7452379 46506 25104951
cpn60 9470953, 42026 15459382
7197068,
7196793,
7446913,
7449248,
7449076,
7441817,
17360167,
17360044,
7204662,
7200509,
etc…
psb28 11542140, 19036835
7056000,
11541711,
10446793,
10043985,
19740605,
9740475,
19740298,
19740110,
19739892,
19739741,
etc…

Photosynt 19684 21729317

hesis,
light
reaction
Transcript 42793 21729317
ion from
plastid
promoter
Plastid 9536 21729317
Thylakoid 7450983, 42651 21729317
membrane 7447394,
7444259,
8594919,
8594842,
8594822,
8594814,
8594805,
8594802,
8594795,
8594792,
etc..

Cyanelle 9842 21729317

Light 17362614, 30076 25104951
harvesting 17362477,
complex 17360353,
17360156,
17359799

sil-1 7451772 51082 24065158

silaffins 7445519 24065158
Electron 9055 21729317
carrier
activity
Intracellul 43229 21729317
ar
organelle
Structural 3735 21729317
constituen
t of
ribosome
Structural 5198 21729317
molecule
activity
Structural 3735 21729317
constituen
t of
ribosome
Growth 17359916, 40007
7447702,
7447686,
7447360,
7447007,
7441790,
9461742,
7445131,
19954076,
19944831,
19943569,
etc…

MADS- 9464022 97162 15459382

box
metal 7450518 10038 25104951
detoxificat
ion
silicic acid 7450065, 15708 19829693
transporte 7447140,
r 7444619,
7194691,
7198177
Name Annotatio Proteins
(Gene ns
Ontology
Response 23,187 7,896
to
stimulus(0
050896)
Plastid(00 9,472 2,505
09536)
Photosynt 867 472
hesis(001
5979)
Photosynt 944 466
hetic
membrane
(0034357)
Transcript 72 66
ion from
plastid
promoter(
0042793)
Nitrogen 1,447 794
compound
transport(
0071705)

Glutamine 192 122

family
amino
acid
metabolic
process(0
cell 793 562
growth(00
16049)
phosphoru 17,892 5,023
s
metabolic
process(0
006793)
Name Annotatio Proteins
(Gene ns
Ontology
Response 2,099 939
to
stimulus
Plastid 3,065 1,017
Photosynt 870 406
hesis
Photosynt 796 345
hetic
membrane
Transcript 27 27
ion from
plastid
promoter
Nitrogen 216 92
compound
transport(
0071705)

Glutamine 72 39
family
amino
acid
metabolic
process(0
cell 55 38
growth
phosphoru 5,107 1,735
s
metabolic
process