Abstract
PP2C phosphatases regulate key physiological processes in plants, essential for growth, development, and stress responses. Sugarcane, a vital crop for many economies, faces severe abiotic stress, which negatively impacts production. Given the role of the PP2C gene family in stress tolerance and the recent publication of the genome sequence of the modern polyploid sugarcane cultivar R570, this study conducted genome-wide identification and characterization of the PP2C gene family in sugarcane. The analysis includes genome-wide identification, phylogenetic analysis, gene structure, conserved motif and domain analysis, synteny analysis, evolutionary selection pressure (Ka/Ks) estimation, gene ontology annotation, and RT-qPCR based expression profiling of selected PP2C genes. A total of 500 PP2C genes were identified, distributed across all 10 chromosomes and their subgenomes. Phylogenetic analysis, using Arabidopsis, S. spontaneum , maize, and wheat as references, classified these genes into 13 subfamilies. The results showed that, similar to S. spontaneum , where the largest subfamily is F with 37 members, the largest subfamily in the sugarcane hybrid cultivar was also F, with 74 members, followed by subfamily A with 69 members. The exon and motif distribution were found to be highly conserved within the same subfamily. Tandem duplication was prominent, with 107 genes identified as paralogs, indicating their role in gene expansion. The chromosomal distribution of SoffiXPP2C genes was partially biased, as approximately 50% of the genes were located on chromosomes 1, 2, and 3, along with their respective subgenomes. Synteny analysis revealed a strong conservation of the protein phosphatase domain between modern hybrid and wild sugarcane ( S. spontaneum ). Additionally, the synteny association of SoffiXPP2C genes with two potential cold stress-responsive genes, SsPP2C27 and SsPP2C64, suggests a possible role of SoffiXPP2C genes in abiotic stress regulation. The observed downregulation of certain SoffiXPP2C genes in waterlogging-tolerant genotypes further supports their potential function as negative regulators, particularly under waterlogging stress conditions. The domain architecture analysis further emphasizes the multifaceted roles of sugarcane PP2Cs, particularly in stress signaling, protein phosphorylation regulation, and membrane-associated functions. Furthermore, the strong alignment of 34 SoffiXPP2C genes with differentially expressed contigs of sugarcane under oxidative stress conditions reinforces insights into the potential role of SoffiXPP2Cs in stress response. These findings provide valuable insights into the evolutionary conservation of PP2C genes in sugarcane hybrid cultivar and their critical role in abiotic stress responses.
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Claims 12
Claim · model-written summary
The sugarcane genome contained 500 PP2C genes across 10 chromosomes and subgenomes.
Verbatim
e0“A total of 500 PP2C genes were identified, distributed across all 10 chromosomes and their subgenomes.”
t0“sugarcane”
Claim · model-written summary
PP2C genes were classified into 13 subfamilies.
Verbatim
e0“classified these genes into 13 subfamilies”
t0“sugarcane”
Claim · model-written summary
Subfamily F was largest with 74 members.
Verbatim
e0“largest subfamily in the sugarcane hybrid cultivar was also F, with 74 members”
Claim · model-written summary
Subfamily A had 69 members.
Verbatim
e0“followed by subfamily A with 69 members”
t0“sugarcane”
Claim · model-written summary
Exon and motif distributions were conserved within subfamilies.
Verbatim
e0“The exon and motif distribution were found to be highly conserved within the same subfamily.”
t0“sugarcane”
Claim · model-written summary
Tandem duplication included 107 paralogous genes.
Verbatim
e0“Tandem duplication was prominent, with 107 genes identified as paralogs”
t0“sugarcane”
Claim · model-written summary
About half of SoffiXPP2C genes lay on chromosomes 1, 2 and 3.
Verbatim
e0“approximately 50% of the genes were located on chromosomes 1, 2, and 3”
t0“sugarcane”
Claim · model-written summary
The phosphatase domain was conserved between modern hybrid and wild sugarcane.
Verbatim
e0“strong conservation of the protein phosphatase domain between modern hybrid and wild sugarcane ( S. spontaneum )”
Claim · model-written summary
SoffiXPP2C synteny with SsPP2C27 and SsPP2C64 suggested a cold stress role.
- Taxon
- sugarcanet0
- Gene
- SoffiXPP2Ce0
- Outcome
- possible role of SoffiXPP2C genes in abiotic stress regulatione0
Not reportedDirection
Verbatim
e0“synteny association of SoffiXPP2C genes with two potential cold stress-responsive genes, SsPP2C27 and SsPP2C64, suggests a possible role of SoffiXPP2C genes in abiotic stress regulation”
t0“sugarcane”
Claim · model-written summary
Some SoffiXPP2C genes were downregulated in waterlogging-tolerant genotypes.
Verbatim
e0“downregulation of certain SoffiXPP2C genes in waterlogging-tolerant genotypes”
t0“sugarcane”
Claim · model-written summary
Domain architecture suggested roles in stress signalling, phosphorylation and membrane functions.
Verbatim
e0“multifaceted roles of sugarcane PP2Cs, particularly in stress signaling, protein phosphorylation regulation, and membrane-associated functions”
Claim · model-written summary
Thirty-four SoffiXPP2C genes aligned with oxidative stress responsive contigs.
Not reportedDirection
Verbatim
e0“strong alignment of 34 SoffiXPP2C genes with differentially expressed contigs of sugarcane under oxidative stress conditions”