Bulletin of Botanical Research ›› 2021, Vol. 41 ›› Issue (2): 251-261.doi: 10.7525/j.issn.1673-5102.2021.02.013
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Yi-Ping GUO, Jia-Xin LIU, Ying YU, Chao WANG, Chuan-Ping YANG()
Received:
2020-06-17
Online:
2021-03-20
Published:
2021-01-05
Contact:
Chuan-Ping YANG
E-mail:yangcp@nefu.edu.cn
About author:
GUO Yi-Ping(1994—),female,master,major in molecular mechanism of wood formation.
Supported by:
CLC Number:
Yi-Ping GUO, Jia-Xin LIU, Ying YU, Chao WANG, Chuan-Ping YANG. Expression Profile Analysis ofXylem Development Regulated by BpNAC012 Gene from Betula platyphylla[J]. Bulletin of Botanical Research, 2021, 41(2): 251-261.
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URL: https://bbr.nefu.edu.cn/EN/10.7525/j.issn.1673-5102.2021.02.013
Table 1
List of data output quality
样本 Sample | 原始序列 Original sequence | 过滤数据 Filter data | 测序量 Sequencing volume | 错误率 Error rate(%) | Q20(%) | Q30(%) | GC(%) |
---|---|---|---|---|---|---|---|
WT_1 | 56242018 | 55322414 | 8.3G | 0.03 | 97.48 | 92.81 | 46.34 |
WT_2 | 58518124 | 56683910 | 8.5G | 0.03 | 97.55 | 92.97 | 46.30 |
WT_3 | 52203502 | 50544932 | 7.58G | 0.03 | 97.42 | 92.71 | 46.30 |
OE_1 | 58644414 | 57292724 | 8.59G | 0.03 | 97.81 | 93.58 | 46.46 |
OE_2 | 59189588 | 57679272 | 8.65G | 0.03 | 97.34 | 92.52 | 46.55 |
OE_3 | 56973490 | 56366534 | 8.45G | 0.03 | 97.81 | 93.59 | 46.45 |
RS_1 | 51023786 | 50389048 | 7.56G | 0.03 | 97.52 | 92.95 | 46.56 |
RS_2 | 54950226 | 54540828 | 8.18G | 0.03 | 97.33 | 92.47 | 46.51 |
RS_3 | 57784458 | 57021886 | 8.55G | 0.03 | 97.26 | 92.35 | 46.37 |
Table 3
Gene annotation success rate statistics
基因数量 Number of genes | 百分率 Percentage(%) | |
---|---|---|
NR数据库所占比例Proportion of NR database | 117 364 | 65.57 |
NT数据库所占比例Proportion of NT database | 92 957 | 51.93 |
KO数据库所占比例Proportion of KO database | 44 707 | 24.97 |
SwissProt数据库所占比例Proportion of SwissProt database | 86 603 | 48.38 |
PFAM数据库所占比例Proportion of PFAM database | 84 724 | 47.33 |
GO数据库所占比例Proportion of GO database | 86 008 | 48.05 |
KOG数据库所占比例Proportion of KOD database | 29 536 | 16.50 |
7大数据库共同出现的比例The proportion of 7 major databases | 18 243 | 10.19 |
至少一个数据库注释成功的比例Proportion of at least one database annotation success | 129 213 | 72.19 |
总基因数Total genes | 178 983 | 100.00 |
Table 4
Gene Ontology classification of differential gene enrichment in samples
数据库中唯一的标号信息 GO accession gene ontology | 功能的描述信息 Description gene ontology | 为该GO的类别 Term type | 富集分析统计学显著水平 Over represented p-value | 校正后的p-value Corrected p-value | DEG item | DEG list |
---|---|---|---|---|---|---|
GO:0001071 | nucleic acid binding transcription factor activity | molecular_function | 5.8636e-17 | 1.7558e-13 | 60 | 581 |
GO:0003700 | transcription factor activity, sequence-specific DNA binding | molecular_function | 5.8636e-17 | 1.7558e-13 | 60 | 581 |
GO:0005667 | transcription factor complex | cellular_component | 7.2294e-14 | 1.4432e-10 | 66 | 581 |
GO:0006355 | regulation of transcription, DNA-templated | biological_process | 1.0952e-08 | 1.3118e-05 | 85 | 581 |
Fig.3
Differential gene GO enrichmentA.Histogram of GO enrichment of differential genes,the abscissa is the GO term of the next three levels of GO, and the ordinate is the number of differential genes annotated under the term(including subterms of the term).The three different classifications represent the three basic classifications of Go term(from left to right are biological processes, cellular components,and molecular functions);B.For GO in Fig.1,according to biological processes,cellular components, and molecular functions,three Histograms of large categories and differential genes up and down classification
Fig.4
KEGG pathway enrichment scatter plotThe vertical axis represents the name of the pathway,and the horizontal axis represents the Rich factor corresponding to the pathway.The size of qvalue is represented by the color of the dot. The smaller the qvalue,the closer the color is to red.To represent.OEvsWT,RSvsWT
Table 5
Top 10 genes with the highest differential expression fold in overexpressing lines
基因ID Gene_id | log2倍数变化log2 fold change | 基因长度 Gene length | NR GI | NR ID | NR评估 NR evalue | NR注释 NR description |
---|---|---|---|---|---|---|
Cluster-12857.66427 | 13.492 | 2 378 | 118132570 | ABK60177.1 | 4.80E-16 | conserved hypothetical protein[Streptomyces ghanaensis ATCC 14672] |
Cluster-12857.79868 | 11.786 | 4 286 | 645227348 | XP_008220472.1 | 0.00E+00 | PREDICTED: glycine dehydrogenase(decarboxylating),mitochondrial[Prunus mume] |
Cluster-12857.83191 | 11.500 | 3 565 | 802581682 | XP_012069851.1 | 2.40E-205 | PREDICTED:probable methyltransferase PMT3[Jatropha curcas] |
Cluster-12857.66430 | 11.254 | 2 133 | 566183478 | XP_002311438.2 | 8.50E-190 | DNA-binding protein RAV2[Populus trichocarpa] |
Cluster-12857.97128 | 10.632 | 2 699 | 720084019 | XP_010243074.1 | 2.60E-159 | PREDICTED:probable phenylalanine--tRNA ligase alpha subunit[Nelumbo nucifera] |
Cluster-12857.60814 | 10.592 | 8 563 | 645275167 | XP_008242682.1 | 0.00E+00 | PREDICTED:dnaJ homolog subfamily C GRV2 isoform X2[Prunus mume] |
Cluster-12857.62522 | 10.323 | 3 186 | 590658081 | XP_007034748.1 | 1.50E-294 | No lysine kinase 1 isoform 1[Theobroma cacao] |
Cluster-12857.109476 | 10.191 | 1 118 | 590634122 | XP_007028287.1 | 3.30E-116 | 2,4-dienoyl-CoA reductase isoform 2[Theobroma cacao] |
Cluster-12857.80721 | 9.689 3 | 2 946 | 645260833 | XP_008236004.1 | 1.20E-197 | PREDICTED: amino acid permease 3-like[Prunus mume] |
Cluster-12857.54251 | 9.565 4 | 945 | 723712802 | XP_010323300.1 | 1.50E-21 | PREDICTED: cucumber peeling cupredoxin-like[Solanum lycopersicum] |
Table 6
The top 10 genes with the highest differential expression folds in the suppressed expression lines
基因ID Gene_id | log2倍数变化 log2 fold change | 基因长度 Gene length | NR GI | NR ID | NR评估 NR evalue | NR说明 NR description |
---|---|---|---|---|---|---|
Cluster-12857.25938 | -11.44 8 | 2 910 | 645278673 | XP_008244338.1 | 4.70E-183 | PREDICTED:kinesin-3[Prunus mume] |
Cluster-12857.85041 | -9.912 4 | 4 383 | 449456208 | XP_004145842.1 | 1.60E-126 | PREDICTED:UTP--glucose-1-phosphate uridylyltransferase[Cucumis sativus] |
Cluster-12857.98081 | -9.167 2 | 4 075 | 297745750 | CBI15806.3 | 3.60E-35 | unnamed protein product[Vitis vinifera] |
Cluster-12857.25935 | -9.037 2 | 2 757 | 645278673 | XP_008244338.1 | 4.50E-183 | PREDICTED:kinesin-3[Prunus mume] |
Cluster-12857.74657 | -8.754 7 | 2 186 | 719976857 | XP_010248668.1 | 1.90E-112 | PREDICTED:uncharacterized protein LOC104591513[Nelumbo nucifera] |
Cluster-12857.45080 | -8.609 6 | 3 854 | 645230669 | XP_008222040.1 | 2.60E-277 | PREDICTED:ankyrin repeat and sterile alpha motif domain-containing protein 1B-like[Prunus mume] |
Cluster-12857.58236 | -8.509 5 | 3 080 | 590658081 | XP_007034748.1 | 1.40E-294 | No lysine kinase 1 isoform 1[Theobroma cacao] |
Cluster-12857.27318 | -8.495 4 | 2 146 | 596174565 | XP_007223177.1 | 5.00E-105 | hypothetical protein PRUPE_ppa009157mg[Prunus persica] |
Cluster-12857.135896 | -8.463 2 | 1 217 | 590566763 | XP_007010326.1 | 4.60E-132 | Catalytic,putative isoform 1[Theobroma cacao] |
Cluster-12857.69484 | -8.311 2 | 2 496 | 567877953 | XP_006431535.1 | 1.20E-38 | hypothetical protein CICLE_v10003979mg,partial[Citrus clementina] |
Table 7
Genes related to up-regulated expression of xylem development in overexpressing lines
基因ID Gene_id | log2倍数变化 log2 fold change | 基因长度 Gene length | NR GI | NR ID | NR评估 NR Evalue | NR说明 NR Description |
---|---|---|---|---|---|---|
Cluster-12857.118958 | 4.8343 | 1483 | 359497539 | XP_003635559.1 | 1.90E-159 | PREDICTED:cellulose synthase-like protein E6 isoform X1[Vitis vinifera] |
Cluster-12857.76168 | 2.3144 | 2522 | 225457723 | XP_002277713.1 | 1.70E-274 | PREDICTED: probable cellulose synthase A catalytic subunit 5 [UDP-forming][Vitis vinifera] |
Cluster-12857.74320 | 3.2946 | 681 | 571534195 | XP_003549490.2 | 5.30E-93 | PREDICTED: probable xyloglucan endotransglucosylase/hydrolase protein 23-like[Glycine max] |
Cluster-12857.86571 | 3.5818 | 375 | 590661748 | XP_007035759.1 | 1.10E-60 | Xyloglucan endotransglucosylase/hydrolase family protein [Theobroma cacao] |
Cluster-12857.94374 | 3.8561 | 1450 | 590683434 | XP_007041599.1 | 7.30E-108 | Fructose-1,6-bisphosphatase, cytosolic[Theobroma cacao] |
Cluster-12857.94375 | 6.9966 | 1771 | 590683434 | XP_007041599.1 | 7.20E-118 | Fructose-1,6-bisphosphatase, cytosolic[Theobroma cacao] |
Cluster-12857.76506 | 2.2768 | 2951 | 567877365 | XP_006431272.1 | 1.20E-266 | hypothetical protein CICLE_v10011622mg[Citrus clementina] |
Cluster-12857.90286 | 5.2815 | 1523 | 645249297 | XP_008230687.1 | 4.90E-155 | PREDICTED:probable galacturonosyltransferase-like 10[Prunus mume] |
Cluster-12857.59289 | 1.0271 | 7112 | 658001427 | XP_008393176.1 | 9.70E-222 | PREDICTED:galactoside 2-alpha-L-fucosyltransferase-like[Malus domestica] |
Cluster-12857.85038 | 2.3215 | 3248 | 694386135 | XP_009368869.1 | 5.40E-151 | PREDICTED:glucan endo-1,3-beta-glucosidase 14-like[Pyrus x bretschneideri] |
Cluster-12857.105697 | 1.9631 | 2202 | 802652705 | XP_012080173.1 | 7.50E-181 | PREDICTED:probable beta-1,3-galactosyltransferase 19[Jatropha curcas] |
Cluster-12857.77676 | 3.1264 | 1772 | 645247636 | XP_008229928.1 | 3.70E-69 | PREDICTED:fasciclin-like arabinogalactan protein 2[Prunus mume] |
Cluster-12857.82137 | 8.2031 | 1984 | 166209291 | ABY85195.1 | 2.50E-268 | p-coumaryl-CoA 3'-hydroxylase[Populus alba×Populus grandidentata] |
Cluster-12857.97128 | 10.632 | 2699 | 720084019 | XP_010243074.1 | 2.60E-159 | PREDICTED:probable phenylalanine—tRNA ligase alpha subunit[Nelumbo nucifera] |
Cluster-12857.41401 | 4.3742 | 1547 | 854930414 | AKN79297.1 | 8.70E-67 | peroxidase 4[Betula platyphylla] |
Cluster-12857.76083 | 9.0528 | 1305 | 470108362 | XP_004290489.1 | 5.90E-141 | PREDICTED:peroxidase 12[Fragaria vesca subsp.vesca] |
Cluster-12857.113235 | 5.9308 | 1124 | 255542656 | XP_002512391.1 | 6.40E-35 | serine-threonine protein kinase,plant-type, putative[Ricinus communis] |
Cluster-8794.3 | 6.5661 | 2512 | 255555051 | XP_002518563.1 | 3.40E-105 | serine-threonine protein kinase, plant-type, putative[Ricinus communis] |
Cluster-12857.119083 | 2.6264 | 1800 | 225452312 | XP_002272486.1 | 3.40E-38 | PREDICTED: serine/threonine-protein kinase HT1[Vitis vinifera] |
Cluster-12857.118054 | 4.7784 | 2738 | 645224059 | XP_008218928.1 | 6.30E-270 | PREDICTED: serine/threonine-protein kinase-like protein CCR4[Prunus mume] |
Cluster-12857.61436 | 5.542 | 320 | 568883219 | XP_006494380.1 | 6.20E-28 | PREDICTED: wall-associated receptor kinase-like 8-like[Citrus sinensis] |
Cluster-12857.80854 | 1.1382 | 3198 | 590591190 | XP_007016945.1 | 1.40E-143 | Leucine-rich repeat protein kinase family protein, putative isoform 1[Theobroma cacao] |
Cluster-12857.46913 | 2.5993 | 1991 | 590640151 | XP_007029875.1 | 2.40E-178 | Leucine-rich repeat containing protein, putative isoform 1[Theobroma cacao] |
Table 8
Genes related to down-regulated expression of xylem development-inhibited expression lines
基因ID gene_id | log2倍数变化 log2 fold change | 基因长度 Gene Length | NR GI | NR ID | NR评估 NR cvalue | NR说明 NR description |
---|---|---|---|---|---|---|
Cluster-12857.3401 | -3.592 8 | 2 347 | 590679436 | XP_007040580.1 | 1.10E-299 | Cellulose synthase like G3,putative[Theobroma cacao] |
Cluster-12857.79817 | -1.296 6 | 3 177 | 541135587 | AGV22123.1 | 3.90E-239 | endo-1,4-beta-glucanase 1[Betula luminifera] |
Cluster-12857.85041 | -9.912 4 | 4 383 | 449456208 | XP_004145842.1 | 1.60E-126 | PREDICTED:UTP—glucose-1-phosphate uridylyltransferase[Cucumis sativus] |
Cluster-12857.147630 | -6.796 5 | 494 | 566186337 | XP_002314111.2 | 3.00E-21 | UDP-glucoronosyl/UDP-glucosyl transferase family protein[Populus trichocarpa] |
Cluster-12857.88974 | -2.119 6 | 1 519 | 702434862 | XP_010069751.1 | 2.30E-165 | PREDICTED:galactinol synthase 2-like[Eucalyptus grandis] |
Cluster-12857.75094 | -8.027 0 | 5 417 | 470102424 | XP_004287654.1 | 9.40E-92 | PREDICTED: probable polygalacturonase[Fragaria vesca subsp. vesca] |
Cluster-12857.92483 | -7.776 6 | 5 415 | 470102424 | XP_004287654.1 | 9.40E-92 | PREDICTED:probable polygalacturonase[Fragaria vesca subsp. vesca] |
Cluster-12857.154648 | -2.077 7 | 837 | 645235470 | XP_008224286.1 | 1.90E-68 | PREDICTED:non-specific lipid-transfer protein-like protein At2g13820[Prunus mume] |
Cluster-12857.52725 | -7.975 1 | 3 230 | 720011916 | XP_010259705.1 | 7.60E-57 | PREDICTED:probable pectinesterase 29[Nelumbo nucifera] |
Cluster-12857.57875 | -6.393 4 | 1 137 | 571537497 | XP_003550077.2 | 6.10E-126 | PREDICTED:serine/threonine-protein kinase SRK2I-like isoform 1[Glycine max] |
Cluster-12857.105258 | -2.206 6 | 1 465 | 645216354 | XP_008220732.1 | 5.60E-100 | PREDICTED:dehydrodolichyl diphosphate synthase 2[Prunus mume] |
Cluster-12857.122193 | -7.172 0 | 2 231 | 702507890 | XP_010040057.1 | 2.50E-14 | PREDICTED:extensin-like[Eucalyptus grandis] |
Cluster-12857.20627 | -2.917 3 | 2 070 | 225440560 | XP_002276415.1 | 3.20E-258 | PREDICTED:laccase-7[Vitis vinifera] |
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