Literature summary for 3.5.1.98 extracted from

Yang, C.; Shen, W.; Chen, H.; Chu, L.; Xu, Y.; Zhou, X.; Liu, C.; Chen, C.; Zeng, J.; Liu, J.; Li, Q.; Gao, C.; Charron, J.B.; Luo, M.
Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean (2018), BMC Plant Biol., 18, 226 .

Cloned(Commentary)

Cloned (Comment)	Organism
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA1 is located on chromosome 1	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA10 is located on chromosome 6	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA11 is located on chromosome 11	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA12 is located on chromosome 11	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA13 is located on chromosome 12	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA14 is located on chromosome 12	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA15 is located on chromosome 17	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA16 is located on chromosome 17	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA17 is located on chromosome 17	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA18 is located on chromosome 17	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA2 is located on chromosome 4	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA3 is located on chromosome 4	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA4 is located on chromosome 4	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA5 is located on chromosome 5	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA6 is located on chromosome 5	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA7 is located on chromosome 5	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA8 is located on chromosome 5	Glycine max
28 HDAC genes from soybean genome are identified, which are asymmetrically distributed on 12 chromosomes, genotyping and phylogenetic analysis, genetic structure, real-time quantitative PCR enzyme expression analysis, recombinant expression of YFP-tagged isozymes in transgenic Glycine max, gene GmHDA9 is located on chromosome 6	Glycine max

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
chloroplast	isozyme GmHDA10	Glycine max	9507	-
chloroplast	isozyme GmHDA14	Glycine max	9507	-
chloroplast	isozyme GmHDA16	Glycine max	9507	-
chloroplast	isozyme GmHDA3	Glycine max	9507	-
chloroplast	isozyme GmHDA8	Glycine max	9507	-
cytoplasm	isozyme GmHDA1	Glycine max	5737	-
cytoplasm	isozyme GmHDA10	Glycine max	5737	-
cytoplasm	isozyme GmHDA11	Glycine max	5737	-
cytoplasm	isozyme GmHDA12	Glycine max	5737	-
cytoplasm	isozyme GmHDA13	Glycine max	5737	-
cytoplasm	isozyme GmHDA14	Glycine max	5737	-
cytoplasm	isozyme GmHDA15	Glycine max	5737	-
cytoplasm	isozyme GmHDA17	Glycine max	5737	-
cytoplasm	isozyme GmHDA18	Glycine max	5737	-
cytoplasm	isozyme GmHDA2	Glycine max	5737	-
cytoplasm	isozyme GmHDA3	Glycine max	5737	-
cytoplasm	isozyme GmHDA4	Glycine max	5737	-
cytoplasm	isozyme GmHDA5	Glycine max	5737	-
cytoplasm	isozyme GmHDA6	Glycine max	5737	-
cytoplasm	isozyme GmHDA9	Glycine max	5737	-
mitochondrion	isozyme GmHDA13	Glycine max	5739	-
additional information	GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2	Glycine max	-	-
nucleus	isozyme GmHDA1	Glycine max	5634	-
nucleus	isozyme GmHDA11	Glycine max	5634	-
nucleus	isozyme GmHDA12	Glycine max	5634	-
nucleus	isozyme GmHDA15	Glycine max	5634	-
nucleus	isozyme GmHDA16	Glycine max	5634	-
nucleus	isozyme GmHDA17	Glycine max	5634	-
nucleus	isozyme GmHDA18	Glycine max	5634	-
nucleus	isozyme GmHDA2	Glycine max	5634	-
nucleus	isozyme GmHDA5	Glycine max	5634	-
nucleus	isozyme GmHDA6	Glycine max	5634	-
nucleus	isozyme GmHDA7	Glycine max	5634	-
nucleus	isozyme GmHDA8	Glycine max	5634	-
nucleus	isozyme GmHDA9	Glycine max	5634	-

Organism

Organism	UniProt	Comment	Textmining
Glycine max	A0A0R0FIH2	-	-
Glycine max	A0A0R0H2W2	-	-
Glycine max	A0A0R0JU82	-	-
Glycine max	A0A0R0K0I2	-	-
Glycine max	I1JB12	-	-
Glycine max	I1JZJ1	-	-
Glycine max	I1K037	-	-
Glycine max	I1LFN1	-	-
Glycine max	I1LKU7	-	-
Glycine max	I1LTZ2	-	-
Glycine max	I1LWR2	-	-
Glycine max	I1MTD8	-	-
Glycine max	I1MUF8	-	-
Glycine max	I1MXC3	-	-
Glycine max	K7K0Q1	-	-
Glycine max	K7KKZ9	-	-
Glycine max	K7KL00	-	-
Glycine max	K7KR69	-	-

Source Tissue

Source Tissue	Comment	Organism	Textmining
cotyledon	of 5-day-old plants	Glycine max	-
epicotyl	of 5-day-old plants	Glycine max	-
flower	young	Glycine max	-
hypocotyl	of 5-day-old plants	Glycine max	-
leaf	of 14-day-old plants	Glycine max	-
additional information	GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Real-time quantitative PCR tissue distribution analysis, differential expression across various tissues	Glycine max	-
root	of 5-day-old plants	Glycine max	-
seed	-	Glycine max	-
seedling	-	Glycine max	-
stem	of 14-day-old plants	Glycine max	-

Subunits

Subunits	Comment	Organism
?	x * 41180, sequence calculation	Glycine max
?	x * 22260, sequence calculation	Glycine max
?	x * 26740, sequence calculation	Glycine max
?	x * 38500, sequence calculation	Glycine max
?	x * 45280, sequence calculation	Glycine max
?	x * 45540, sequence calculation	Glycine max
?	x * 48940, sequence calculation	Glycine max
?	x * 52180, sequence calculation	Glycine max
?	x * 52920, sequence calculation	Glycine max
?	x * 53300, sequence calculation	Glycine max
?	x * 55950, sequence calculation	Glycine max
?	x * 55960, sequence calculation	Glycine max
?	x * 56120, sequence calculation	Glycine max
?	x * 56280, sequence calculation	Glycine max
?	x * 59600, sequence calculation	Glycine max
?	x * 72990, sequence calculation	Glycine max
?	x * 73040, sequence calculation	Glycine max
More	domain architecture of HDACs in soybean, overview	Glycine max

Synonyms

Synonyms	Comment	Organism
Glyma.01 g245100	locus name	Glycine max
Glyma.04 g000200	locus name	Glycine max
Glyma.04 g187000	locus name	Glycine max
Glyma.04 g187100	locus name	Glycine max
Glyma.05 g012900	locus name	Glycine max
Glyma.05 g021400	locus name	Glycine max
Glyma.05 g040600	locus name	Glycine max
Glyma.05 g192600	locus name	Glycine max
Glyma.06 g000100	locus name	Glycine max
Glyma.06 g178700	locus name	Glycine max
Glyma.11 g000300	locus name	Glycine max
Glyma.11 g187800	locus name	Glycine max
Glyma.12 g086700	locus name	Glycine max
Glyma.12 g188200	locus name	Glycine max
Glyma.17 g078000	locus name	Glycine max
Glyma.17 g085700	locus name	Glycine max
Glyma.17 g120900	locus name	Glycine max
Glyma.17 g229600	locus name	Glycine max
GmHDA1	-	Glycine max
GmHDA10	-	Glycine max
GmHDA11	-	Glycine max
GmHDA12	-	Glycine max
GmHDA13	-	Glycine max
GmHDA14	-	Glycine max
GmHDA15	-	Glycine max
GmHDA16	-	Glycine max
GmHDA17	-	Glycine max
GmHDA18	-	Glycine max
GmHDA2	-	Glycine max
GmHDA3	-	Glycine max
GmHDA4	-	Glycine max
GmHDA5	-	Glycine max
GmHDA6	-	Glycine max
GmHDA7	-	Glycine max
GmHDA8	-	Glycine max
GmHDA9	-	Glycine max
GmHDAC	-	Glycine max
HDAC	-	Glycine max

pI Value

Organism	Comment	pI Value Maximum	pI Value
Glycine max	sequence calculation	-	4.98
Glycine max	sequence calculation	-	5.04
Glycine max	sequence calculation	-	5.06
Glycine max	sequence calculation	-	5.22
Glycine max	sequence calculation	-	5.24
Glycine max	sequence calculation	-	5.25
Glycine max	sequence calculation	-	5.26
Glycine max	sequence calculation	-	5.28
Glycine max	sequence calculation	-	5.3
Glycine max	sequence calculation	-	5.35
Glycine max	sequence calculation	-	5.44
Glycine max	sequence calculation	-	5.91
Glycine max	sequence calculation	-	6.09
Glycine max	sequence calculation	-	6.29
Glycine max	sequence calculation	-	6.31
Glycine max	sequence calculation	-	7.39
Glycine max	sequence calculation	-	8.88

Expression

Organism	Comment	Expression
Glycine max	responses of GmHDACs to abscisic acid (ABA) treatment, which is the most important stress-protective phytohormone, differ. Two HD2 family genes (GmHDT2 and GmHDT4) are induced and two RPD3/HDA1 family genes (GmHDA8 and GmHDA16) are markedly suppressed, the expression of five other HDAC genes (GmHDA6, 13, 14, GmSRT2 and GmSRT4) is only slightly modulated. The status of H3K4me2 and H3K4me3 is also modulated by the both cold and heat treatments. High levels of H3K4me2 and low levels of H3K4me3 are observed following cold treatment. The level of H3K4me2 is upregulated in response to heat stress, while this treatment only has a mild effect on H3K4me3 levels	additional information

General Information

General Information	Comment	Organism
evolution	GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2, phylogenetic analysis. Chromosomal localization and duplications of HDAC genes in soybean, overview	Glycine max
physiological function	histone deacetylases play roles in response to abiotic stresses in soybean. Histone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. Differential changes in GmHDACs transcripts accumulation occur in response to several abiotic cues, indicating that these epigenetic modifiers might potentially be part of a dynamic transcriptional response to stress in soybean. The levels of histone marks associated with plant HDACs are modulated by cold and heat in this legume	Glycine max