Menara Perkebunan 2025, 93.
, 135-147 p-ISSN: 0125-9318/ e-ISSN: 1858-3768 http://dx.
org/10.
22302/iribb.
Accreditation Number: 177/E/KPT/2024 In silico study: identification and characterization of heat shock protein 90 (HSP.
in Arabica coffee (Coffea arabica L.
QoriAoatul MUSTAFIDAH & Mukhamad SUAoUDI*) Department of Biology.
Faculty of Mathematics and Natural Science.
University of Jember.
Indonesia 68121 Received 5 Aug 2025 / Revised 11 Oct 2025 / Accepted 20 Oct 2025 Abstract The use of low-quality planting material and extreme weather conditions caused by global warming are major factors contributing to low Arabica coffee productivity in Indonesia.
The development of new cultivars and the improvement of Arabica coffee adaptability play crucial roles in preventing productivity decline.
This study aims to identify and characterize HSP90 proteins in Arabica coffee through in silico analysis, focusing on their adaptability to biotic and abiotic stress conditions.
This study was conducted using DNA and HSP90 protein sequences from Arabica coffee retrieved from various databases.
The analysis included assessments of physicochemical properties, gene structure analysis, protein subcellular localization prediction, cis-acting element analysis, protein interaction analysis, and phylogenetic analysis.
The results identified a total of twenty CaHSP90 genes distributed across 11 Arabica coffee chromosomes.
Characterization revealed that the HSP90 protein family has diverse physicochemical properties, with varying sequence lengths and molecular weights.
Most members are acidic, hydrophilic proteins localized in the cytoplasm.
Analysis of the CaHSP90 gene expression based on cis-acting elements and phylogenetics showed that HSP90 in Arabica coffee is expressed in response to biotic and abiotic stresses as well as defense against pathogens.
The results of this study provide a foundation for the development of new Arabica coffee cultivars with improved resistance to biotic and abiotic stresses, and support the selection of candidate CaHSP90 genes for breeding programs.
[Keywords: bioinformatics, biotic and abiotic stress.
C3 plant, heat stres.
Introduction Indonesia is one of the world's top four coffee producers, after Brazil.
Vietnam, and Colombia.
This position is largely supported by the productivity of its coffee plantations.
Data from the Central Statistics Agency (Badan Pusat Statisti.
in 2023 indicated that the area of coffee plantations in Indonesia increased by 0.
05% between 2022 and However, this increase in plantation area was not accompanied by a corresponding increase in coffee production.
Coffee production declined by 43% from 786.
19 tons in 2021 to 774.
96 thousand tons in 2022.
This decline continued in 2023 at a greater rate of 2.
10% bringing total production down 73 thousand tons.
This figure represents the largest decline in the last five years, surpassing the decline in the 2018-2019 period, which was only 47% (Badan Pusat Statistik, 2.
The use of low-quality planting materials and various biotic and abiotic factors, such as pest and disease attacks, temperature, and altitude, have contributed to reduced Arabica coffee productivity.
The decline in coffee productivity in Indonesia may also be attributed to extreme weather conditions caused by global warming.
Extreme weather can affect plant growth and development due to the inhibition of starch biosynthesis (Oldroyd & Leyser.
Tigchelaar et al.
, 2.
Global warming can also cause protein denaturation due to an increase in temperature of 10-15AC above optimal plant growth.
These conditions allow plants to develop adaptive mechanisms to tolerate high temperatures by producing stress-related proteins known as heat shock proteins (Peng et al.
, 2.
Heat shock proteins (HSP.
regulate responses to heat stress and are highly conserved across both cellular and organismal levels (Appiah et al.
, 2.
In C3 plants such as coffee.
HSP production is particularly important for supporting photosynthesis by maintaining and protecting heat-sensitive proteins, including PSII (Chauhan et al.
, 2023.
et al.
, 2.
HSPs are classified into five families based on their molecular weight: HSP20.
HSP60.
HSP70/DnaK.
HSP90, and HSP100/ClpB (Donato & Geisler, 2019.
Wasilah et al.
, 2.
Accounting for 1-2% of total cellular proteins.
HSP90 is the most abundant HSP family found in prokaryotic and eukaryotic cytoplasm.
This family Corresponding author: msuudi.
fmipa@unej.
0125-9318/ 1858-3768 A2025 Authors This is an open-access article under the CC BY license .
ttps://creativecommons.
org/licenses/by/4.
Menara Perkebunan is a DOAJ-indexed journal and accredited as Sinta 2 Journal .
ttps://sinta.
id/journals/profile/3.
How to Cite: Mustafidah.
& SuAoudi.
In silico study: identification and characterization of heat shock protein 90 (HSP.
in Arabica coffee (Coffea Arabica L.
Menara Perkebunan, 93.
, 135-147.
http://dx.
org/10.
22302/iribb.
In silico study of heat shock protein 90 (HSP.
in Arabica coffee .
(Mustafidah et al.
is involved in several physiological processes, including plant growth and development, biotic and abiotic stress responses, and the repair of damaged HSP90 supports normal cell survival under stress, maintains the conformation of other proteins, and acts as a negative feedback regulator of the heat stress response (Peng et al.
, 2.
Structurally, consists of three domains: an N-terminal ATPbinding domain, an M domain, and a C-terminal substrate-binding domain (Chiosis et al.
, 2.
HSP90 is abundantly expressed in the plant cytoplasm under normal physiological conditions but rapidly accumulates in the nucleus under heat stress (Appiah et al.
, 2.
HSP90 has been identified in several plants, including Arabidopsis thaliana with seven HSP90 genes (Krishna & Gloor, 2.
Oryza sativa with nine genes (Hu et al.
, 2.
Zea mays with eleven genes (Magnard & Vergne, 1.
, and Solanum lycopersicum with six genes (Liu et al.
, 2.
These studies, conducted using both in silico bioinformatics analyses and in vitro validation, have provided valuable insights into the functional mechanisms of HSP90 proteins in various plants.
However, similar studies have not yet been conducted in Arabica coffee, despite its economic importance and vulnerability to temperature-related Accordingly, this study aims to identify and characterize HSP90 genes in Arabica coffee through in silico analysis, focusing on their potential roles in adaptation to biotic and abiotic stress conditions.
Materials and Methods This research was conducted in silico using DNA and protein sequences of HSP90 from Arabica coffee, obtained from the Phytozome database (Coffea arabica Geisha v1.
(Goodstein et al.
HSP90 sequences from A.
(AtHSP.
were also retrieved from the National Center for Biotechnology Information (NCBI) .
ttps://w.
gov/protein/) and used for motif analysis using the MOTIF tool .
ttps://w.
jp/tools/motif/).
The resulting motifs served as queries for BLAST searches .
ith E-value cutoff 10e-.
against the Arabica coffee Subsequent analyses included HSP90 assessment, gene structure and chromosomal localization, cis-acting element analysis, protein interactions and subcellular localization prediction, and phylogenetic analysis.
Data extraction and identification of HSP90 From BLAST search results, transcript ID, chromosome number, chromosome location data, base pair length of coding sequence (CDS), protein length, and Phytozome annotations were collected.
When identical transcript IDs were detected, redundant or incomplete sequences were removed.
The candidate HSP90 genes were named CaHSP90 (Coffea arabica HSP.
and numbered sequentially according to their chromosomal position.
The genome.
CDS, and peptide sequences of each gene were then retrieved from the Phytozome database for further analysis.
Physicochemical properties analysis The physicochemical properties of CaHSP90 proteins were analyzed using the Expasy ProtParam .
ttps://web.
org/protparam/) (Gasteiger et , 2.
Parameters included molecular weight .
, isoelectric point .
I), and Grand Average of Hydropathicity (GRAVY).
Negative GRAVY values indicate hydrophilic proteins, whereas positive values indicate hydrophobic proteins.
Gene structure analysis Gene structure analysis was performed by aligning the genomic and CDS sequences of each CaHSP90 gene using the Gene Structure Display Server 2.
ttps://gsds.
gao-lab.
org/) (Hu et al.
This analysis was performed to determine the number of exons and introns and the completeness of each CaHSP90 gene.
Chromosomal localization analysis HSP90 gene locations and distribution within chromosomes were visualized using the PhenoGram Plot .
ttps://visualization.
phenograms/plo.
Input data included chromosome number, gene location, and the length of each chromosome in the Arabica coffee genome.
This analysis was conducted to determine the distribution of the HSP90 gene within each chromosome in Arabica coffee.
Cis-acting element analysis Cis-acting element analysis was performed by retrieving the promoter regions .
0 bp upstream of the start codo.
of each CaHSP90 gene from the Phytozome database.
The obtained sequences were then analyzed using the PlantCARE database .
ttps://bioinformatics.
be/webtools/plant care/html/) (Lescot et al.
, 2.
The results were visualized with TBtools-II (Chen et al.
, 2.
to predict the regulation of HSP90 gene expression in Arabica coffee.
Protein interaction analysis Analysis of CaHSP90 protein interactions was performed using STRING software .
ttps://stringdb.
org/) (Szklarczyk et al.
, 2.
based on the CaHSP90 protein sequences.
Menara Perkebunan 2025, 93.
, 135-147 Protein subcellular localization prediction Subcellular localization of CaHSP90s was predicted using CELLO v.
ttp://cello.
tw/) (Yu et al.
, 2004.
Yu et al.
, 2.
and WoLF PSORT .
ttps://wolfpsort.
jp/) (Horton et , 2.
CELLO results marked with an asterisk were retained, while all WoLF PSORT data and predicted values were included.
Data were visualized as a heat map using TBtools-II (Chen et , 2.
Phylogenetic analysis Evolutionary relationships of Arabica coffee HSP90s were analyzed through multiple sequence alignment with HSP90s from A.
mays, and O.
Sequence alignment was performed using ClustalW (Thompson et al.
, 1.
and MEGA11 (Tamura et , 2.
Phylogenetic trees were constructed using the maximum likelihood method with partial deletion parameters and a 1000-fold bootstrap The phylogenetic tree construction provides information on the evolutionary relationships of Arabica coffee HS90 with several other plants to identify orthologs between species and paralogs within species.
Results and Discussion Identification of the HSP90 gene in Arabica coffee (Coffea arabica L.
BLAST results on the AtHSP90 motif against the Arabica coffee genome sequence identified 20 HSP90 genes, designated CaHSP90-1 to CaHSP9020 (Table .
The twenty CaHSP90 genes have varying sequence lengths with CDS ranging from 306 bp (CaHSP90-.
to 2466 bp (CaHSP90-.
(Table .
The identified genes encode proteins ranging from 102 to 822 amino acids .
, corresponding molecular weights range from 11.
525 kDa, and isoelectric points .
I) ranging 86 to 9.
Based on the pI values, fifteen CaHSP90 proteins .
I < .
were acidic and five were basic .
I > .
The basic CaHSP90 proteins have different properties compared to HSP90s found in A.
thaliana, tomatoes, and several other acidic plants (Sajad et al.
, 2.
The GRAVY index of CaHSP90s ranged from 0.
896 to -0.
332, indicating that all members of CaHSP90 are hydrophilic (Zhang et al.
, 2.
Protein localization predictions indicate that most CaHSP90 proteins are localized in the cytoplasm, with several also detected in the nucleus and endoplasmic reticulum.
This is consistent with the results of Appiah et al.
, which reported that HSP90 is mainly accumulated in the cytoplasm and plays an important role in regulating the response to heat stress.
CaHSP90 protein motif Motif analysis of the 20 CaHSP90 genes showed that all contained a histidine kinase-like ATPase or HATPase_c domain (Figure .
The HATPase_c is a conserved protein domain found in several ATPbinding proteins, including histidine kinase.
DNA gyrase B (GyrB), topoisomerase (Bellon et al.
, molecular chaperones HSP90 (Immormino et , 2.
DNA mismatch repair protein, and phytochrome-like ATPase (Bettaieb et al.
, 2.
Based on research by Zhang et al.
, it was stated that protein sequences containing both HSP90 and HATPase_c domains were identified as HSP90.
HSP90 interacts with HATPase to bind and hydrolyze ATP (Bettaieb et al.
, 2.
Motif analysis revealed that the longest HSP90 domain was present in CaHSP90-18, spanning 540 aa, while the shortest was in CaHSP90-15, comprising only 40 aa (Figure CaHSP90 gene structure Gene structure analysis was done to further investigate the structural characteristics of the CaHSP90 gene family.
Variations in gene structure between HSP90 groups are associated with differences in their function in subcellular compartments (Bettaieb et al.
, 2.
Among the twenty identified CaHSP90 genes, each exhibits a distinct exon-intron pattern (Figure .
Genes with complete structures consist of upstream, exon, intron, and downstream regions.
Among the 20 CaHSP90 genes, nine possess complete structures, while eleven are incomplete.
The largest gene.
CaHSP90-6, spans around 9 kb, whereas the smallest gene.
CaHSP90-12, is only 315 The largest number of exons is found in CaHSP90-5 and CaHSP90-6, with a total of twenty exons, while the fewest are found in CaHSP90-2.
CaHSP90-7.
CaHSP90-9.
CaHSP90-10.
CaHSP9012, and CaHSP90-13, each with only a single exon.
Exon-intron organization provides insights into gene evolution (Wang et al.
, 2.
In Arabica coffee, the variation in the gene structure among CaHSP90 genes suggests possible evolutionary divergence within the family.
The number of introns is largely related to the sensitivity of gene transcription regulation.
Genes with fewer introns usually respond more rapidly to environmental stimuli (Appiah et al.
, 2021.
Sajad et al.
, 2.
In silico study of heat shock protein 90 (HSP.
in Arabica coffee .
(Mustafidah et al.
Table 1.
HSP90s in Coffea arabica L.
Transcript ID Gene name Chr Location Molecular .
GRAVY Exon.
Intron
Protein localization Phytozome annotations CAG017222
CaHSP90-1
11,641
Heat shock protein 90 // Heat
shock protein 90-1
CAG017223
CaHSP90-2
26,047
Heat shock protein Hsp90 family // Ribosomal protein S5 domain
2-type fold
CAG027009
CaHSP90-3
81,000
Molecular chaperone HtpG
HSP90A) CAG020662
CaHSP90-4
80,997
Molecular chaperone HtpG
HSP90A) CAG031359
CaHSP90-5
90,847
Heat shock protein 90kDa beta (HSP90B.
TRA.
CAG025028
CaHSP90-6
90,797
Heat shock protein 90kDa beta (HSP90B.
TRA.
Heat shock protein Hsp90 family // Concanavalin A-like lectin/glucanase domain // Ribosomal protein S5 domain 2type fold
Heat shock protein Hsp90 family // Ribosomal protein S5 domain
2-type fold
CAG038127
CaHSP90-7
45,042
CAG048341
CaHSP90-8
44,622
CAG051226
CaHSP90-9
40,616
Heat shock protein 90 // Subfamily not named CAG051227
CaHSP90-10
18,795
Heat shock protein 90 // Heat shock protein 90-2-related Menara Perkebunan 2025, 93.
, 135-147 Table 1.
Transcript ID Gene name Chr Location Molecular .
GRAVY Exon.
Intron
Protein localization Phytozome annotations CAG047913
CaHSP90-11
80,063
Heat shock protein 90 // Subfamily not named CAG062435
CaHSP90-12
11,791
Heat shock protein 90 // Heat
shock protein 90-1
CAG062436
CaHSP90-13
27,994
Heat shock protein 90 // Subfamily not named CAG069612
CaHSP90-14
80,948
Molecular chaperone HtpG
HSP90A) CAG072725
CaHSP90-15
41,163
, nuclear .
Heat shock protein Hsp90
family // Ribosomal protein S5
domain 2-type fold
CAG072730
CaHSP90-16
76,721
Molecular chaperone HtpG
HSP90A) CAG000807
CaHSP90-17
88,457
ER .
Heat shock protein 90 // Endoplasmin homolog
CAG003938
CaHSP90-18
93,525
ER .
Heat shock protein 90 // Endoplasmin homolog
CAG008931
CaHSP90-19
93,387
Heat shock protein 90kDa beta (HSP90B.
TRA.
CAG011964
CaHSP90-20
90,665
Heat shock protein 90kDa beta (HSP90B.
TRA.
In silico study of heat shock protein 90 (HSP.
in Arabica coffee .
(Mustafidah et al.
Figure 1.
CaHSP90 protein motif Figure 2.
CaHSP90 gene structure Chromosomal localization of CaHSP90 genes Arabica coffee has a tetraploid genome with 11 pairs of chromosomes.
Localization data showed that one CaHSP90 gene was located on chromosome two genes each on chromosomes 1, 7, 10, and 11.
three genes on chromosome 8.
and four genes each on chromosomes 2 and 5.
No genes were located on chromosomes 4 and 9 (Figure .
Compared to other species in the same subclass as Arabica coffee, the Asteridae, the distribution of HSP90 genes in tobacco (Nicotiana tabacu.
The tobacco genome has nine HSP90s randomly distributed on its 12 chromosomes, while the remaining 12 HSP90s remain unassigned (Song et al.
, 2.
Cis-acting element analysis of CaHSP90 Cis-acting element analysis was conducted to understand the regulation of CaHSP90 expression in response to stress conditions under abiotic stress.
The results revealed 51 types of cis-acting elements in the promoter regions of CaHSP90 genes (Figure Among them, the TATA box was detected across all CaHSP90 promoters.
This element plays a central role in transcription initiation by facilitating the binding of RNA polymerase II to the promoter via interaction with the TATA-binding protein (Savinkova et al.
, 2.
Several light-responsive cis-acting elements were also identified, including MRE.
G-box.
ACE.
Box 4.
ATCT motif.
GT1 motif, and GATA motif Menara Perkebunan 2025, 93.
, 135-147 (Bettaieb et al.
, 2020.
Zhang et al.
, 2.
The MRE element was detected in CaHSP90-7.
CaHSP90-9.
CaHSP90-13, and CaHSP90-15, located 1,480 bp upstream of the start codon in CaHSP90-15.
The ACE element was detected only in CaHSP90-15 and CaHSP90-18, located 890 bp and 420 bp upstream of the start codon, respectively (Figure .
Other cis-acting elements identified in CaHSP90 were LTR.
ARE.
MBS, and TC-rich repeats.
LTR is known to be responsive to drought, salinity, and low temperature (Bettaieb et al.
, 2020.
Xue et al.
, 2.
The element was found in CaHSP90-3.
CaHSP904.
CaHSP90-5.
CaHSP90-6.
CaHSP90-19, and CaHSP90-20.
The ARE elements were detected in 18 CaHSP90 genes, excluding CaHSP90-3 and CaHSP90-4.
The element is known to play an important role in responding to oxygen limitation.
Additionally.
TC-rich repeats, associated with defense and stress response, and the MYB Binding Site (MBS), involved in drought induction, were also present in several CaHSP90 promoters (Bettaieb et al.
, 2020.
Xue et al.
, 2.
The promoter region analysis also revealed the presence of phytohormone-responsive elements, including AuxRR-core and TGA element .
, the GARE motif and P-box .
ibberellin-responsiv.
ABRE .
bscisic acidresponsiv.
TCA element .
alicylic acidresponsiv.
, and CGTCA and TGACG motifs .
oth methyl jasmonate-responsiv.
(Bettaieb et al.
Overall, the total of 51 cis-acting elements identified play key roles in growth, development, and abiotic or hormonal stress responses, suggesting the complex functions of CaHSP90s.
The ABRE responsiveness, has been identified in A.
thaliana to regulate lignin deposition and secondary cell wall formation through phosphorylation of the NST1 wall protein (Liu et al.
, 2.
Collectively, these diverse regulatory elements may contribute to tissue-specific and stress-responsive expression patterns of CaHSP90 genes in Arabica coffee, influencing both developmental processes and adaptive stress responses (Bettaieb et al.
, 2.
Interactions between proteins in CaHSP90 The protein-protein interaction (PPI) network of HSP90s in Arabica coffee (Figure .
, showed that CaHSP90-1.
CaHSP90-4.
CaHSP90-12.
CaHSP9015, and CaHSP90-16 interact with CaHSP90-5.
CaHSP90-6.
CaHSP90-7.
CaHSP90-17.
CaHSP9018.
CaHSP90-19, and CaHSP90-20.
Additionally.
HSP90 proteins interact with several other proteins, including the cysteine- and histidine-rich domaincontaining protein RAR1, the heat shock factor binding protein, the Aha1_N domain-containing protein, and the cochaperone protein p23 (Figure .
The RAR1 .
equired for Mla12 resistanc.
protein is involved in the plant immune response to In plants.
RAR1 plays a crucial role in R protein activity and facilitates he interaction between SGT1 and HSP90.
RAR1 interacts with the N-terminal portion of HSP90, which contains the ATPase domain (Niikura & Kitagawa, 2.
The observation that RAR1 interacts with all CaHSP90 proteins suggests a conserved role for Arabica coffee HSP90s in pathogen defense and immune Figure 3.
Chromosomal distribution of CaHSP90 genes In silico study of heat shock protein 90 (HSP.
in Arabica coffee .
(Mustafidah et al.
Figure 4.
Cis-acting element CaHSP90.
The most common cis-acting elements are marked with red boxes.
HSP90 proteins in Coffea arabica Protein interactions Figure 5.
CaHSP90 protein interactions In plants, the heat shock factor binding protein (HSBP) regulates the expression of the heat shock factor (HSF) gene under normal and recovery Based on the PPI analysis.
HSBP interacts with all CaHSP90 proteins because it is related to HSF, which regulates HSP90 gene The Arabica coffee HSP90 proteins also interact with Aha1 .
ctivator of HSP90 ATPase .
as the only co-chaperone that accelerates the formation of its closed conformation.
Aha1 comprises two domains, the C-terminal (Aha1_C) and N-terminal (Aha1_N), which interact with the HSP90 center domain of HSP90 proteins (Albakova, 2024.
Mondol et al.
, 2.
Aha1_N (Figure .
interacts with all CaHSP90 proteins because it is the main activator in increasing ATPase activity.
Another important interacting partner identified was p23/PTGES3, a co-chaperone that stabilizes the closed conformation of HSP90 and suppresses ATPase activity to regulate its chaperone cycle (Schopf et al.
, 2.
The interaction of p23 with all CaHSP90 proteins suggests its critical role in fine142 Menara Perkebunan 2025, 93.
, 135-147 tuning HSP90Aos conformational dynamics during stress response and protein folding.
Subcellular localization of CaHSP90 proteins The predicted subcellular localization of HSP90 proteins in Arabica coffee showed that most of the CaHSP90 proteins were localized in the nucleus with lower prediction scores, while a smaller proportion were detected in the cytoplasm with higher prediction scores (Figure .
This is consistent with the study by Appiah et al.
which stated that HSP90 is expressed in the This was also shown in A.
(Sarkar et al.
, 2.
Brachypodium distachyon (L.
Beauv (Zhang et al.
, 2.
, which also indicates that the cytoplasm is the site of protein assembly, which may be the main site of HSP90 protein activity (Bettaieb et al.
, 2.
Phylogenetic Analysis of CaHSP90 Phylogenetic analysis was conducted to examine evolutionary relationships among HSP90 proteins in arabica and other plant species, and to identify potential orthologous and paralogous relationships.
The resulting tree grouped the proteins into five clades, with Group I having the largest number of members .
and Group i the fewest .
hree Group I comprised four genes from Z.
three from O.
sativa, two each from A.
thaliana and lycopersicum, and four genes from C.
Arabica.
Group i contained two genes from C.
Arabica and one from O.
Several orthologous relationships were identified between C.
arabica and other species, including CaHSP90-5 and CaHSP90-6 with AtHSP90-6.
CaHSP90-17 and CaHSP90-18 with AtHSP90-7.
CaHSP90-1 and CaHSP90-15 with Os09g36420.
CaHSP90-11 Solycl2g015880.
1 (SlHSP90-.
and CaHSP90-3 and CaHSP90-4.
CaHSP90-9 and CaHSP90-13 with AtHSP90-1.
Eight pairs of paralogous genes were also identified within C.
arabica: CaHSP90-19 and CaHSP90-20.
CaHSP90-5 and CaHSP90-6.
CaHSP90-17 and CaHSP90-18.
CaHSP90-8 and CaHSP90-10.
CaHSP90-2 and CaHSP90-7.
CaHSP90-14 and CaHSP90-16.
CaHSP90-3 and CaHSP90-4, and CaHSP90-9 and CaHSP90-13.
The phylogenetic clustering revealed clear separation between dicots (C.
and S.
and monocots (O.
sativa and may.
, consistent with their taxonomic The presence of multiple paralogous pairs within C.
arabica indicates gene duplication events during the evolution of the HSP90 family, contributing to species-specific diversification (Song et al.
, 2.
Figure 6.
Prediction of the subcellular localization of CaHSP90 proteins In silico study of heat shock protein 90 (HSP.
in Arabica coffee .
(Mustafidah et al.
Figure 7.
Evolutionary relationships of HSP90 in C.
Arabica.
sativa, and Z.
CaHSP90 is written in red.
Furthermore, several orthologous CaHSP90 genes showed similarities to stress-responsive homologs in other species.
CaHSP90-19 and CaHSP90-20 share similarity with AtHSP90-5 and Solyc05g010670.
1 (SlHSP90-.
, which are associated with both drought and salinity tolerance (Song et al.
, 2.
CaHSP90-5 and CaHSP90-6 cluster with AtHSP90-6, which is linked to plant development (Luo et al.
, 2019.
Zai et al.
, 2.
CaHSP90-17 and CaHSP90-18 share similarity with AtHSP90-7, which is associated with drought and salt stress tolerance (Song et al.
, 2.
Finally.
CaHSP90-3 and CaHSP90-4.
CaHSP90-9, and CaHSP90-13 group with AtHSP90-1, associated with osmotic stress response and ABA responses (Zai et al.
, 2015.
Zhang et al.
, 2.
Conclusion This in silico study identified twenty HSP90 genes in the Coffea arabica genome, providing the first comprehensive characterization of the HSP90 gene family in this species.
The identified CaHSP90 proteins displayed distinct physicochemical properties, reflecting functional diversity among family members.
Most were found to be acidic, hydrophilic, and predominantly localized in the cytoplasm, consistent with their roles as molecular Cis-acting element and phylogenetic analyses indicated that CaHSP90 genes are regulated in response to various biotic and abiotic stresses, including light, drought, salinity, low temperature, and pathogen attack.
These findings highlight the importance of the HSP90 family in stress adaptation and defense mechanisms in Arabica coffee.
Overall, this study provides a molecular foundation for understanding the structure, regulation, and potential function of HSP90 genes in C.
The identified candidate genes offer valuable targets for future breeding programs aimed at developing stress-tolerant Arabica coffee cultivars through molecular-assisted selection or genetic improvement strategies.
References