Abstract
The APETALA2/Ethylene Responsive Factor (AP2/ERF) gene family has been shown to play a crucial role in plant growth and development, stress responses and secondary metabolite biosynthesis. Nevertheless, little is known about the gene family in ginseng (Panax ginseng C.A. Meyer), an important medicinal herb in Asia and North America. Here, we report the systematic analysis of the gene family in ginseng using several transcriptomic databases. A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts. The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist. The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana. Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity. The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes. The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily. This result suggests that the DREB subfamily genes play an important role in plant response to cold stress. Finally, we studied the responses of the PgERF genes to methyl jasmonate (MeJA). We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment, with 136 up-regulated and 152 down-regulated, indicating that most members of the PgERF gene family are responsive to MeJA. These results, therefore, provide new resources and knowledge necessary for family-wide functional analysis of the PgERF genes in ginseng and related species.
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Claims 9
Claim · model-written summary
Ginseng has 189 putative AP2/ERF genes yielding 397 transcripts.
- Taxon
- ginseng
Panax ginsenge1 - Gene
- PgERF genese0
- Outcome
- 189 putative AP2/ERF genese0
- Value
- 189e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“A total of 189 putative AP2/ERF genes, defined as PgERF001 through PgERF189, were identified and these PgERF genes were spliced into 397 transcripts.”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
The 93 complete-domain PgERF genes were classified into five subfamilies.
- Taxon
- ginsengPanax ginsenge1
- Gene
- PgERF genese0
- Outcome
- five subfamiliese0
- Value
- 93e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The 93 PgERF genes that have complete AP2 domains in open reading frame were classified into five subfamilies, DREB, ERF, AP2, RAV and Soloist.”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
DREB and ERF formed four and six groups, compared with 12 groups in Arabidopsis.
- Taxon
- ginsengPanax ginsenge1
- Gene
- DREB subfamily and ERF subfamilye0
- Outcome
- four and six groupse0
- Value
- four and six groupse0
- Comparator
- Arabidopsis thalianae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The DREB subfamily and ERF subfamily were further clustered into four and six groups, respectively, compared to the 12 groups of these subfamilies found in Arabidopsis thaliana.”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
Gene ontology placed the 397 transcripts into eight functional subcategories, especially nucleic acid binding transcription factor activity.
- Taxon
- ginsengPanax ginsenge1
- Gene
- PgERF genese0
- Outcome
- eight functional subcategoriese0
- Value
- eighte0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Gene ontology categorized these 397 transcripts of the 189 PgERF genes into eight functional subcategories, suggesting their functional differentiation, and they have been especially enriched for the subcategory of nucleic acid binding transcription factor activity.”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
PgERF transcript expression activity and networks diversified across tissues, stages and genotypes.
- Taxon
- ginsengPanax ginsenge1
- Gene
- PgERF transcriptse0
- Outcome
- expression activity and networkse0
- Direction
- diversifiede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expression activity and networks of the 397 PgERF transcripts have substantially diversified across tissues, developmental stages and genotypes.”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
Six sampled DREB PgERF genes varied significantly in expression under cold stress.
- Taxon
- ginsengPanax ginsenge0
- Treatment
- cold stresse0
- Gene
- PgERF genese0
- Outcome
- expressions of the PgERF genese0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The expressions of the PgERF genes also significantly varied, when ginseng was subjected to cold stress, as tested using six PgERF genes, PgERF073, PgERF079, PgERF110, PgERF115, PgERF120 and PgERF128, randomly selected from the DREB subfamily.”
Claim · model-written summary
Of 397 PgERF transcripts, 288 responded to MeJA.
- Taxon
- ginsengPanax ginsenge1
- Treatment
- MeJA treatmente0
- Gene
- PgERF gene transcriptse0
- Outcome
- PgERF gene transcripts respondede0
- Value
- 288 (72.5%)e0
Not reportedComparatorDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We found that 288 (72.5%) of the 397 PgERF gene transcripts responded to the MeJA treatment”
e1“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
MeJA up-regulated 136 PgERF transcripts.
- Taxon
- ginsengPanax ginsenge2
- Treatment
- MeJA treatmente1
- Gene
- PgERF gene transcriptse1
- Outcome
- PgERF gene transcriptse1
- Direction
- up-regulatede0
- Value
- 136e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“with 136 up-regulated and 152 down-regulated”
e1“PgERF gene transcripts responded to the MeJA treatment”
e2“ginseng (Panax ginseng C.A. Meyer)”
Claim · model-written summary
MeJA down-regulated 152 PgERF transcripts.
- Taxon
- ginsengPanax ginsenge2
- Treatment
- MeJA treatmente1
- Gene
- PgERF gene transcriptse1
- Outcome
- PgERF gene transcriptse1
- Direction
- down-regulatede0
- Value
- 152e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“with 136 up-regulated and 152 down-regulated”
e1“PgERF gene transcripts responded to the MeJA treatment”
e2“ginseng (Panax ginseng C.A. Meyer)”
The same questions in other papers
(-)-methyl jasmonate · molecular: expression · Panax ginseng (ginseng)Positive and negative results
2 papers in the same direction as this paper · 1 in the opposite direction
- negative
- positive
- positive
Claims are grouped by organism, treatment and what was measured or targeted. A paper counts as positive when any of its claims in the group is positive.