Magnoliaceae. U. 5 shade. ITEOBL. 40,985,986 Itea oblonga. Saxifragaceae. U. 6 shade. LASJAP. 43,362,482 Lasianthus japonicus. Rubiaceae. S. 6 shade.
The role of transcriptomes linked with responses to light environment on seedling mortality in a subtropical forest, China. Baocai Han, Marí a Natalia Umaña, Xiangcheng Mi, Xiaojuan Liu, Lei Chen, Yunquan Wang, Yu Liang, Wei Wei and Keping Ma
Table S1. The 47 light related gene ontology (GO) terms. Bold GO terms were used in this study. NO.
GO ID
GO Terms
1
GO:0007602
phototransduction
2
GO:0007603
phototransduction, visible light
3
GO:0009416
response to light stimulus
4
GO:0009584
detection of visible light
5
GO:0009585
red, far-red light phototransduction
6
GO:0009637
response to blue light
7
GO:0009638
phototropism
8
GO:0009639
response to red or far red light
9
GO:0009640
photomorphogenesis
10
GO:0009642
response to light intensity
11
GO:0009643
photosynthetic acclimation
12
GO:0009644
response to high light intensity
13
GO:0009646
response to absence of light
14
GO:0009648
photoperiodism
15
GO:0009765
photosynthesis, light harvesting
16
GO:0009767
photosynthetic electron transport chain
17
GO:0009768
photosynthesis, light harvesting in photosystem I
18
GO:0009773
photosynthetic electron transport in photosystem I
19
GO:0009785
blue light signaling pathway
20
GO:0009853
photorespiration
21
GO:0009854
oxidative photosynthetic carbon pathway
22
GO:0010017
red or far-red light signaling pathway
23
GO:0010109
regulation of photosynthesis
24
GO:0010114
response to red light
25
GO:0010117
photoprotection
26
GO:0010196
nonphotochemical quenching
27
GO:0010201
response to continuous far red light stimulus by the high-irradiance response system
28
GO:0010205
photoinhibition
29
GO:0010206
photosystem II repair
30
GO:0010207
photosystem II assembly
31
GO:0010218
response to far red light
32
GO:0010304
PSII associated light-harvesting complex II catabolic process
33
GO:0010362
negative regulation of anion channel activity by blue light
34
GO:0015979
photosynthesis
35
GO:0019684
photosynthesis, light reaction
36
GO:0019685
photosynthesis, dark reaction
37
GO:0042331
phototaxis
38
GO:0043153
entrainment of circadian clock by photoperiod
39
GO:0043481
anthocyanin accumulation in tissues in response to UV light
40
GO:0048571
long-day photoperiodism
41
GO:0048573
photoperiodism, flowering
42
GO:0048574
long-day photoperiodism, flowering
43
GO:0048586
regulation of long-day photoperiodism, flowering
44
GO:0071482
cellular response to light stimulus
45
GO:0071485
cellular response to absence of light
46
GO:0080005
photosystem stoichiometry adjustment
47
GO:2000030
regulation of response to red or far red light
Table S2. Species used in the analyses. Species code is a unique code with 6 letters assigned to each species in GTS FDP. Light rank was assigned based on Song (2013). “T “refers to Tree species, “U” refers to understory tree species and “S” refers to shrub species. The raw data is the number of reads by the sequencing.
species
Light raw data
species name
Family
lifeform
code
guild rank
ADIMIL
41,819,960 Adinandra milletii
Theaceae
T
6
Shade
AIDCOC
44,396,716 Aidia cochinchinensis
Rubiaceae
U
4
shade
ALAKUR
44,583,250 Alangium kurzii
Alangiaceae
U
7
light
ARACHI
43,657,362 Aralia chinensis
Araliaceae
U
6
shade
ARDCRE
45,662,030 Ardisia crenata
Myrsinaceae
S
3
shade
CALBOD
47,925,184 Callicarpa bodinieri
Verbenaceae
S
6
shade
CALRUB
33,530,908 Callicarpa rubella
Verbenaceae
S
6
shade
CAMCHE
57,046,460 Camellia chekiang-oleosa
Theaceae
U
6
shade
CAMCUS
37,782,598 Camellia cuspidata
Theaceae
U
6
shade
CASCAR
41,294,450 Castanopsis carlesii
Fagaceae
T
6
shade
CASEYR
42,834,538 Castanopsis eyrei
Fagaceae
T
5
shade
CASFAR
40,980,302 Castanopsis fargesii
Fagaceae
T
7
light
CELBIO
42,048,902 Celtis biondii
Ulmaceae
T
7
light
CHISAL
45,656,960 Chimonanthus salicifolius
Calycanthaceae
S
6
shade
CHOAXI
44,192,216 Choerospondias axilloaris
Anacardiaceae
T
7
light
CLECYR
56,392,436 Clerodendron cyrtophyllum
Verbenaceae
S
7
light
CLEJAP
33,486,222 Cleyera japonica
Theaceae
U
6
shade
CLETRI
46,092,664 Clerodendron trichotomum
Verbenaceae
U
7
light
CORGLA
46,231,796 Corylopsis glandulifera
Hamamelidaceae
U
7
light
CUNLAN
48,005,756 Cunninghamia lanceolata
Taxodiaceae
T
7
light
CYCGLA
40,115,184 Cyclobalanopsis glauca
Fagaceae
T
6
shade
CYCMYR
44,806,724 Cyclobalanopsis myrsinaefolia
Fagaceae
T
7
light
DALHUP
42,178,804 Dalbergia hupeana
Leguminosae
T
7
light
DAPOLD
38,269,884 Daphniphyllum oldhamii
Daphniphyllaceae
T
6
shade
DIOGLA
54,147,292 Diospyros glaucifolia
Ebenaceae
T
7
light
DIOMOR
47,465,754 Diospyros morrisina
Ebenaceae
T
6
shade
DISMYR
53,783,536 Distylium myricoides
Hamamelidaceae
U
7
light
EHRACU
38,080,636 Ehretia acuminata
Boraginaceae
T
6
shade
ELADEC
37,610,852 Elaeocarpus decipiens
Elaeocarpaceae
T
5
shade
ELAJAP
43,669,578 Elaeocarpus japonicus
Elaeocarpaceae
T
5
shade
EURMUR
46,215,522 Eurya muricata
Theaceae
U
6
shade
EURRUB
49,906,396 Eurya rubiginosa
Theaceae
S
6
shade
EUSJAP
49,136,578 Euscaphis japonica
Staphyleaceae
U
7
light
EVOFAR
36,455,292 Evodia faugeaii
Rutaceae
T
7
light
FICERE
57,044,168 Ficus erecta
Moraceae
U
7
light
FRAINS
41,969,926 Fraxinus insularis
Oleaceae
T
6
shade
GARJAS
45,972,670 Gardenia jasminoides
Rubiaceae
S
5
shade
GLOPUB
42,715,126 Glochidion Puberum
Euphorbiaceae
U
7
light
HOVTRI
44,828,684 Hovenia trichocarpa
Rhamnaceae
T
6
shade
HYDCHI
42,739,080 Hydrangea chinensis
Saxifragaceae
S
7
light
IDEPOL
44,151,124 Idesia polycarpa
Flacourtiaceae
T
7
light
ILECHI
35,399,960 Ilex chinensis
Aquifoliaceae
T
6
shade
ILEELM
41,228,236 Ilex elmerriliana
Aquifoliaceae
U
6
shade
ILEFIC
50,883,522 Ilex ficoidea
Aquifoliaceae
U
5
shade
ILEMIC
67,699,244 Ilex micrococca
Aquifoliaceae
T
6
shade
ILESUA
42,012,174 Ilex suaveolens
Aquifoliaceae
T
6
shade
ILEWIL
47,806,762 Ilex wilsonii
Aquifoliaceae
U
6
shade
ILLLAN
42,258,560 Illicium lanceolatum
Magnoliaceae
U
5
shade
ITEOBL
40,985,986 Itea oblonga
Saxifragaceae
U
6
shade
LASJAP
43,362,482 Lasianthus japonicus
Rubiaceae
S
6
shade
LESFOR
30,236,134 Lespedeza Formosa
Leguminosae
S
8
light
LINAGG
62,218,972 Lindera aggregata
Lauraceae
S
5
shade
LINREF
54,780,164 Lindera reflexa
Lauraceae
S
6
shade
LITGLA
41,271,812 Lithocarpus glaber
Fagaceae
T
7
light
LORCHI
35,941,754 Loropetalum chinensis
Hamamelidaceae
U
8
light
LYOOVA
43,811,276 Lyonia ovalifolia
Ericaceae
U
7
light
MACCOC
39,537,382 Maclura cochinchinensis
Moraceae
S
6
shade
MALLEI
41,634,528 Malus leiocalyca
Rosaceae
T
6
shade
MANYUY
38,679,952 Manglietia yuyuanensis
Magnoliaceae
T
6
shade
MICSKI
41,980,454 Michelia skinneriana
Magnoliaceae
U
5
shade
NEOAUR
44,176,162 Neolitsea aurata
Lauraceae
U
6
shade
PHOGLA
38,985,104 Photinia glabra
Rosaceae
U
7
light
PHOPAR
44,345,714 Photinia parvifelia
Rosaceae
U
8
light
PHOSER
43,369,280 Photinia serrulata
Rosaceae
U
7
light
PITILL
43,157,890 Pittosporum illicioides
Pittosporaceae
U
6
shade
PREMIC
52,726,328 Premna microphylla
Verbenaceae
S
7
light
PRUSCH
56,061,612 Prunus schneideriana
Rosaceae
T
7
light
QUESER
43,740,054 Quercus serrata
Fagaceae
U
7
light
RHOLAT
51,026,518 Rhododendron latoucheae
Ericaceae
U
7
light
RHOOVA
49,616,418 Rhododendron ovatum
Ericaceae
U
7
light
RHUHYP
46,867,402 Rhus hypoleuca
Anacardiaceae
U
6
shade
SCHSUP
43,982,524 Schima superba
Theaceae
T
6
shade
SLOSIN
49,853,128 Sloanea sinensis
Elaeocarpaceae
T
6
shade
STYDAS
39,556,810 Styrax dasyanthus
Styracaeae
U
7
light
STYODO
53,857,808 Styrax odoratissimus
Styracaeae
U
7
light
STYSUB
44,860,974 Styrax suberrifolia
Styracaeae
T
6
shade
SYMSUM
40,206,300 Symplocos sumuntia
Symplocaceae
U
6
shade
SYZBUX
37,120,194 Syzygium buxifolium
Myrtaceae
U
6
shade
TERGYM
55,939,194 Ternstroemia gymnanthera
Theaceae
U
6
shade
TOXSUC
45,501,610 Toxicodendron succedaneum
Anacardiaceae
T
7
light
VACBRA
42,393,278 Vaccinium bracteatum
Ericaceae
U
8
light
VACCAR
39,504,028 Vaccinium carlesii
Ericaceae
U
6
shade
VACMAN
64,232,998 Vaccinium mandarimorum
Ericaceae
U
6
shade
VIBERO
47,247,792 Viburnum erosum
Caprifoliaceae
S
6
shade
WIKMON
44,337,410 Wikstroemia monnula
Thvmelaeaceae
S
6
shade
Reference Song, Y.C. (2013) Evergreen Broad-leaved Forests in China, Classification-Ecology-Conservation. Science Press, Beijing [in Chinese]
