Abstract
BACKGROUND: Trees such as Populus are planted extensively for reforestation and afforestation. However, their successful establishment greatly depends upon ambient environmental conditions and their relative resistance to abiotic and biotic stresses. Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. Additionally, there is a paucity of information regarding hormonal responses at the whole genome level. RESULTS: A genome-wide analysis of the poplar PPO family was performed in the present study, and 18 PtrPPO genes were identified. Bioinformatics and qRT-PCR were then used to analyze the gene structure, phylogeny, chromosomal localization, gene replication, cis-elements, and expression patterns of PtrPPOs. Sequence analysis revealed that two-thirds of the PtrPPO genes lacked intronic sequences. Phylogenetic analysis showed that all PPO genes were categorized into 11 groups, and woody plants harbored many PPO genes. Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes, and 3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars. Cis-acting element analysis identified numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members. Furthermore, PtrPPO genes were expressed preferentially in the tissues and fruits of young plants. In addition, the expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate, thereby revealing their potential role in regulating the stress response. Currently, we identified potential upstream TFs of PtrPPOs using bioinformatics. CONCLUSIONS: Comprehensive analysis is helpful for selecting candidate PPO genes for follow-up studies on biological function, and progress in understanding the molecular genetic basis of stress resistance in forest trees might lead to the development of genetic resources.
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Claims 13
Claim · model-written summary
Eighteen PtrPPO genes were identified.
- Taxon
- Populus trichocarpa
Populus trichocarpat0 - Gene
- PtrPPOe0
- Outcome
- 18 PtrPPO genese0
- Value
- 18e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“18 PtrPPO genes were identified”
Claim · model-written summary
Two-thirds of PtrPPO genes lacked introns.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Gene
- PtrPPOe0
- Outcome
- lacked intronic sequencese0
- Value
- two-thirdse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“two-thirds of the PtrPPO genes lacked intronic sequences”
Claim · model-written summary
PPO genes were classified into 11 phylogenetic groups.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Gene
- PPOe0
- Outcome
- categorized into 11 groupse0
- Value
- 11e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“all PPO genes were categorized into 11 groups”
Claim · model-written summary
Woody plants harbored many PPO genes.
Verbatim
t0“Populus trichocarpa”
e0“woody plants harbored many PPO genes”
Claim · model-written summary
Eighteen PtrPPO genes were distributed disproportionately across 19 chromosomes.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Gene
- PtrPPOe0
- Outcome
- disproportionally localized on 19 chromosomese0
- Value
- 19 chromosomese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“Eighteen PtrPPO genes were disproportionally localized on 19 chromosomes”
Claim · model-written summary
Three pairs of segmented replication genes were detected in poplars.
PopulusOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars”
Claim · model-written summary
Four tandem repeat genomes were detected in poplars.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“3 pairs of segmented replication genes and 4 tandem repeat genomes were detected in poplars”
Claim · model-written summary
PPO promoters contained growth, secondary metabolism, and stress related cis elements.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Gene
- PPOe0
- Outcome
- growth and developmental elements, secondary metabolism processes, and stress-related elementse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“numerous growth and developmental elements, secondary metabolism processes, and stress-related elements in the promoters of different PPO members”
Claim · model-written summary
PtrPPO genes were expressed preferentially in young tissues and fruits.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Organ / stage
- tissues and fruits of young plantse0
- Gene
- PtrPPOe0
- Outcome
- expressed preferentiallye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“PtrPPO genes were expressed preferentially in the tissues and fruits of young plants”
Claim · model-written summary
Polyethylene glycol significantly induced expression of some PtrPPO genes.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Treatment
- polyethylene glycole0
- Gene
- PtrPPOse0
- Outcome
- expression of some PtrPPOse0
- Direction
- inducede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate”
Claim · model-written summary
Abscisic acid significantly induced expression of some PtrPPO genes.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Treatment
- abscisic acide0
- Gene
- PtrPPOse0
- Outcome
- expression of some PtrPPOse0
- Direction
- inducede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate”
Claim · model-written summary
Methyl jasmonate significantly induced expression of some PtrPPO genes.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Treatment
- methyl jasmonatee0
- Gene
- PtrPPOse0
- Outcome
- expression of some PtrPPOse0
- Direction
- inducede0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“expression of some PtrPPOs could be significantly induced by polyethylene glycol, abscisic acid, and methyl jasmonate”
Claim · model-written summary
Potential upstream transcription factors of PtrPPOs were identified bioinformatically.
- Taxon
- Populus trichocarpaPopulus trichocarpat0
- Gene
- PtrPPOse0
- Outcome
- potential upstream TFse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Populus trichocarpa”
e0“identified potential upstream TFs of PtrPPOs using bioinformatics”
The same questions in other papers
(-)-methyl jasmonate · molecular: expression · Populus trichocarpa (black cottonwood)Results agree
1 paper in the same direction as this paper
- 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.