0215-0212 / e-ISSN: 2406-9574 Pelita Perkebunan 41.
2025, 73 85 gene family in Theobroma cacao L.
inISSN:
Identification ofAi
HSP90
silico study DOI: 10.
22302/iccri.
Identification of Heat Shock Protein 90 (HSP.
Gene Family in Cocoa (Theobroma cacao L.
) in Silico Study QoriAoatul Mustafidah.
Mukhamad SuAoudi.
, and Sulistyani Pancaningtyas.
Department of Biology.
Faculty of Mathematics and Natural Science.
University of Jember.
Jl.
Kalimantan No.
Jember.
Indonesia Indonesian Coffee and Cocoa Research Institute (ICCRI).
Kaliwining.
Jember.
Indonesia Corresponding author: msuudi.
fmipa@unej.
Received: March 1, 2025 / Accepted: July 6, 2025 Abstract Heat Shock Protein 90 (HSP.
has an important role in regulating heat stress response, plant development control, and defense reactions.
The HSP90 gene family has been extensively reported in numerous plant species, but studies on the HSP90 gene in cocoa (Theobroma cacao L.
) remain lacking.
Continuous global warming and the use of low-grade quality planting materials are the reasons for low cocoa productivity in Indonesia.
Based on this, it is necessary to have good adaptability in cocoa as well as the development of new cultivars so that there is no decrease in cocoa productivity.
This study aims to identify the HSP90 gene family in cocoa to recognize the HSP90 functioning in cocoa and provide the necessary information to characterize HSP90 at the genome level.
Identification of the HSP90 gene family in T.
cacao was carried out through analysis of TcHSP90 sequences obtained from various related databases.
The results showed that a total of seven TsHSP90 genes are distributed into ten T.
cacao chromosomes.
Analysis of the TcHSP90 motif showed that HSP90 is conserved in each T.
Cis-acting element analysis showed that TcHSP90 has important roles in growth and development as well as abiotic and hormonal stress responses including defense against pathogens.
Phylogenetic analysis showed that TcHSP90 has a similar evolutionary distribution to A.
thaliana and S.
The results of this study can be used as a scientific foundation and basic knowledge for the development of new T.
cacao cultivars that are resistant to biotic and abiotic stresses by selecting suitable candidate genes for T.
cacao breeding.
Keywords:
Ab iotic s tress , genome-wide st ud y.
Heat Sh ock P r ot ein ( HSP 90 ).
Theobroma cacao L.
INTRODUCTION
Plant growth and development are influenced by various factors including interrelated biotic and abiotic stresses.
Abiotic stresses such as temperature, salinity, high light intensity, heavy metal toxicity and other abiotic stresses can cause stress conditions in plants.
Global warming that has occurred in recent decades is the main factor that causes extreme weather.
Extreme weather conditions will have a detri- mental impact that can affect plant growth and development and reduce crop quality and quantity (Guihur et al.
, 2.
Extreme weather due to prolonged global warming has a major impact on plants because it can inhibit starch synthesis, carbon assimilation, and cause a decrease in crop yields which then presents a new challenge to food security (Oldroyd & Leyser, 2020.
Tigchelaar et al.
, 2.
These conditions allow plants to develop adapta- PELITA PERKEBUNAN.
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August 2025 Edition Mustafidah et al.
tion to high temperatures through regulatory mechanisms to overcome heat stress by producing stress proteins, namely Heat Shock Protein (HSP) (Peng et al.
, 2.
HSP is one of the proteins that has an important role in regulating the response to heat stress and is highly conserved at the cellular and organismal levels (Appiah et al.
The mechanism of HSPs in stress response in plants works by helping to refold unfolded or misfolded proteins due to the disruption of cell homeostasis after experiencing stress (Bettaieb et al.
, 2.
HSPs can be divided into five families based on molecular weight and sequence homogeneity, namely HSP20.
HSP60.
HSP70/DnaK.
HSP90, and HSP100/ClpB .
i Donato & Geisler, 2019.
Wasilah et al.
, 2.
One of the most abundant proteins in the prokaryotic and eukaryotic cytoplasm is the HSP90 family which makes up 1-2% of the cellular protein level.
HSP90 is generally composed of three structural domains namely N-terminal ATP-binding domain.
M domain, and C-terminal substrate-binding domain (Chiosis et al.
, 2.
HSP90 is directly or indirectly involved in several physiological processes ranging from plant growth and development to abiotic and biotic stress responses (Peng et al.
, 2.
HSP90 will be abundantly expressed in the plant cytoplasm under normal physiological conditions but will accumulate rapidly in the nucleus under heat stress conditions (Appiah et al.
, 2.
The function of HSP90 is to regulate and maintain the conformation of various proteins, assist normal cell survival under stress, and act as a negative feedback regulator of the heat stress response (Peng et al.
, 2.
HSP90
along with other molecular chaperones will function in protein folding, prevent protein aggregation, and facilitate the folding of inactive proteins to increase resistance to certain cells.
HSP90 expression is regulated when plants experience stress by joining nonprotein substances to allow the repair of damaged proteins (Li et al.
, 2.
Protein damage can be caused by heat stress because it can cause Rubisco inactivation and increased oxygen affinity for Rubisco.
This condition can have more harmful effects, especially in C3 plants such as soybean, coffee, and cocoa because it can reduce photosynthetic efficiency (Arachchige et al.
, 2.
Cocoa (Theobroma cacao L.
) is one of the leading plantation commodities in Indonesia that has high potential and has a large contribution to the countryAos economy through export activities.
The number of people interested in processed cocoa products has increased the demand for cocoa to 380.
thousand tons of cocoa per year (Larasati et al.
, 2.
Indonesia is the largest cocoa producer in Asia and ranks seventh among the worldAos largest cocoa producers (ICCO.
The area of cocoa plantations in Indonesia is known to continue to decline every year, resulting in cocoa productivity also continuing to decline.
The cocoa plantation area in Indonesia in 2020 was recorded at around 1,5 million hectares but this condition continued to decline to 1,39 million hectares in 2023 (BPS, 2.
Cocoa productivity will be indirectly affected by global warming.
The producing Heat Shock Protein (HSP) in response toheat stress is a mechanism that this condition enables cocoa to develop into more adaptable, preventing a decline in output and ensuring that the demand for cocoa exports is continuously fulfilled.
HSP production in cocoa plants which are C3 plants has an important role especially in supporting the photosynthesis process by maintaining and protecting the proteins involved in it.
Heat stress in plants will respond to the thylakoid membrane protein complex in chloroplasts by producing a large number of companion proteins to protect PELITA PERKEBUNAN.
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August 2025 Edition Identification of HSP90 gene family in Theobroma cacao L.
in silico study PSII which is the most sensitive target to heat stress and other abiotic stresses (Chauhan et al.
, 2023.
Hu et al.
, 2.
One of these companion proteins is HSP90C, which is a member of HSP90 that has a function in maintaining protein homeostasis and chloroplast protein transport (Mu et al.
, 2.
HSP90 has been identified and found in several plants including Arabidopsis thaliana with seven HSP90 genes (Krishna & Gloor, 2.
Solanum lycopersicum with six HSP90 genes (Liu et al.
, 2.
Oryza sativa with nine HSP90 genes (Hu et al.
, and Zea mays with eleven HSP90 genes (Magnard & Vergne, 1.
The identification of HSP90 in Theobroma cacao related to adaptability to extreme weather conditions due to global warming has not yet been reported.
These extreme weather conditions will certainly affect the growth and development of cocoa plants so that it will have an impact on the productivity produced.
Therefore, identification of the HSP90 gene family in Theobroma cacao is very important to understand the HSP90 family that works in Theobroma cacao and provides the necessary information to characterize HSP90 at the whole genome level of T.
MATERIALS AND METHODS
Cocoa genome database This study used the HSP90 protein sequence from Arabidopsis thaliana (AtHSP.
obtained from the National Center for Biotechnology Information (NCBI) .
ttps:// gov/protein/).
The protein sequences were then used for domain or motif analysis of AtHSP90 protein sequences using MOTIF tools .
ttps://w.
tools/motif/).
The cocoa genome to be identified was obtained from the Phytozome database (Goodstein et al.
, 2012.
https://phyto- zome-next.
gov/) with annotation version v1.
1 or Theobroma cacao v1.
Identification of the HSP90 gene family in T.
The identification of the HSP90 gene in T.
cacao was carried out by performing BLASTP on the AtHSP90 motif against the cacao genome in the Phytozome database (Goodstein et al.
, 2012.
https://phytozomenext.
gov/).
Data extraction of T.
HSP90 was carried out by searching for information including transcript ID, chromosome number, chromosome location data, strand.
CDS .
oding sequenc.
base pair length and protein length (AA), and phytozome annotation.
The T.
cacao HSP90 chromosome number was obtained from the NCBI protein database and then used to determine the name of the HSP90 gene in T.
cacao based on the sequenced chromosome number.
Based on the sequence of chromosome numbers, seven HSP90 genes in T.
cacao were obtained, so they were named TcHSP90-1 to TcHSP90-7.
Data extraction was also carried out on the genomic sequence.
CDS sequence, and peptide sequence of TcHSP90-1 to TcHSP90-7 in the Phytozome database.
Analysis of physicochemical properties including molecular weight .
, isoelectric point .
I), and Grand Average of Hydropathicity (GRAVY) was carried out through the Expasy ProtParam tool software (Gasteiger et al.
, 2005.
/web.
org/protparam/) using the obtained cacao HSP90 protein sequence.
Analysis of gene structure The exon-intron structures of TcHSP90-1 to TcHSP90-7 were analyzed through genomic sequence alignment with the corresponding CDS and genomic sequences using Genes Structure Display Server 2.
0 software (Hu et al.
, 2015.
https://gsds.
gao-lab.
org/).
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6 8 7
25 23 84 1
Thecc1EG034 246 t1 TcHSP90-7 20 9029 4.
2 0971 75
-0 ,3 2 4
18 78 62 6
Thecc1EG034 239 t1 TcHSP90-6 20 5424 2.
2 0630 21
-0 .
5 8 3
21 00 70 0
Thecc1EG030 579 t1 TcHSP90-5 39 895 8.
4 029 67
-0 .
5 7 1
21 18 70 6
Thecc1EG016 330 t1 TcHSP90-4 32399 517 forward -0 .
6 1 0
21 12 70 4
Thecc1EG015 252 t1 TcHSP90-3 27009 274 forward -0 .
5 6 4
-0 .
5 3 0
24 45 81 5
23 70 79 0
40050 867 reverse Strand Location Gene Name Chromosome BLAST results between seven AtHSP90 genes and the T.
cacao genome for the identification of HSP90 proteins in T.
Thecc1EG011 421 t1 TcHSP90-2
Identification of HSP90 genes in Theobroma cacao
Transcript ID
RESULT AND DISCUSSION
Table 1.
Analysis of the evolutionary relationships of HSP90 members of T.
cacao was carried out through protein sequence alignment with thaliana.
mays, and Sequence alignment was performed using ClustalW (Thompson et al.
, 1.
with MEGA11 software (Tamura et al.
, 2.
while the phylogenetic tree was constructed using the maximum likelihood method with partial deletion parameters and the bootstrap method with 1000 bootstrap replications.
List of Heat Shock Protein 90 gene family in Theobroma cacao L.
Phylogenetic tree
CDS
Molecular .
Sub-cellular localization of proteins was predicted using CELLO v.
5 software (Yu et al.
, 2004.
Yu et al.
, 2006.
http://cello.
tw/) and WoLF PSORT (Horton et al.
, 2007.
https://wolfpsort.
and the heat-map illustration were visualized with TBtools-II software (Chen et al.
, 2.
13196 723 reverse Sub-cellular localization GRAVY Exon Intron Protein Localization Prediction Analysis of cis-acting elements from the promoter region of the TcHSP90-1 to TcHSP90-7 genes was carried out by searching 2000 bp genomic sequence before the start codon from the Phytozome database.
The data obtained were then analyzed using the plantCARE software (Lescot et al.
, 2002.
https://bioinformatics.
be/webtools/ plantcare/html/) and visualized with TBtools-II software (Chen et al.
, 2.
Thecc1EG002 328 t1 TcHSP90-1 Phytozome Annotations Promoter analysis of HSP90 gene families Heat shock protein 90 // .
, nuclear Heat shock protein 89.
4 05 )
Heat shock protein 90 // .
6 70 )
Heat shock protein 89.
cytoplasmic Molecular chaperone HtpG .
9 36 )
HSP90A) cytoplasmic Molecular chaperone HtpG .
0 53 )
HSP90A) Heat shock protein 90 // .
8 12 )
Subfamily not named ER .
Heat shock protein 90 .
0 85 )
ER .
Heat shock protein 90 Mustafidah et al.
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in silico study showed that there were seven HSP90 genes that were successfully selected from the cacao genome.
HSP90 genes in T.
(TcHSP.
were renamed according to the order of chromosomal location, resulting in genes TcHSP90-1 to TcHSP90-7 (Table .
Data extraction of TcHSP90 showed that of the 10 chromosomes in the T.
genome, two genes were located on chromosomes 3 and 8, one gene on chromosomes 1, 2, and 7 and no genes were located on chromosomes 4, 5, 6, 9, and 10.
The seven TcHSP90 genes have varying sequence lengths with Coding Sequence (CDS) ranging from 1878 bp (TcHSP90-.
to 2523 bp (TcHSP90-.
while amino acids range from 626 aa (TcHSP90-.
to 841 aa (TcHSP90-.
The molecular weight of the seven TcHSP90s ranged from 69,739 kDa (TcHSP.
to 95,408 kDa (TcHSP90-.
The isoelectric point .
I) of the seven TcHSP90s showed values varying from 4.
84 (TcHSP90-.
to 49 (TcHSP90-.
These pI values indicate that all HSP90 proteins of T.
cacao are acidic .
I < 7.
and these results are similar to those found in A.
thaliana, tomato and some other plants (Sajad et al.
, 2.
The Grand Average of Hydropathicity (GRAVY) also showed values varying between -0.
687 (TcHSP90-.
324 (TcHSP90-.
The GRAVY values obtained indicate that all T.
cacao HSP90 proteins are negative, so the T.
cacao HSP90 proteins are hydrophilic (Zhang et al.
, 2.
Protein localization prediction shows that most of the TcHSP90 are located in cytoplasmic with TcHSP90-1 located in cytoplasmic and nuclear.
TcHSP90-2 to TcHSP90-4 and TcHSP90-6 located in cytoplasmic.
TcHSP905 located in cytoplas-mic and ER (Endoplasmic Reticulu.
, and TcHSP90-7 located in ER (Endoplasmic Reticulu.
This is in accordance with the research of Appiah et al.
2021 which states that HSP90 is expressed in the cytoplasm and has an important role in regulating the response to heat stress.
Motif and gene structure analysis of TcHSP90 Based on motif analysis of seven HSP90 in T.
TcHSP90-1 to TcHSP90-7 contain histidine kinase-like ATPase (HATPase_.
The HATPase_c domain is an evolutionarily conserved protein domain found in several ATP-binding proteins including histidine kinase.
DNA gyrase B, topoisomerase (Bellon et al.
, 2.
HSP90 molecular chaperones (Immormino et al.
, 2.
, phytochromelike ATPase and DNA mismatch repair protein (Bettaieb et al.
, 2.
The longest HSP90 motif is found in TcHSP90-7 with a length range from 252 to 835 aa while the shortest HSP90 motif is found in TcHSP90-6 with a length range from 266 to 525 (Figure 1A).
Zhang et al.
2021 stated that the protein sequence containing HSP90 and the domain structure of HATPase_c were identified as HSP90.
HATPase_c together with HSP90 is known to have an important role in ATP binding and hydrolysis and as a binding site for ATP/ ADP with ATPase activity (Bettaieb et al.
Gene structure was used to further investigate the structural characteristics of the HSP90 gene family in T.
Differences in gene structure between HSP90 groups are related to differences in gene function in subcellular compartments (Bettaieb et al.
, 2.
Based on seven TcHSP90 genes (Figure 1B), it shows that from TcHSP90-1 to TcHSP90-7 have different exon-intron distribution patterns.
The largest genome size is found in TcHSP90-6 with a length of around 8.
8 kb while the smallest genome size is found in TcHSP90-4 with a length of around 3.
3 kb with an average genome size between the seven TcHSP90 genes are 5.
76 kb.
The highest number of exons is found in TcHSP90-1 with 20 exons while the least is found in TcHSP90-5 which only has 3 exons.
Additionally, the highest PELITA PERKEBUNAN.
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TcHSP90 -1 TcHSP90 -2 TcHSP90 -3 TcHSP90 -4 TcHSP90 -5 TcHSP90 -6 TcHSP90 -7 Legend:
E xo n Up stream/downstream - Intron Figure 1.
Motif and gene structure of TcHSP90 number of introns is found in TcHSP90-1 with 19 introns while the least is found in TcHSP90-5 which only has 2 introns.
TcHSP90-6 has the longest gene structure due to the length of introns although it does not have the highest number of introns.
The gene structure also shows that all TcHSP90 genes have an upstream that leads to the 5' end and a downstream that leads to the 3' end.
Analysis of the gene structure showing the exon-intron structure can be important evidence of the evolution of a gene (Wang et al.
, 2.
Analysis of the exon-intron structure of the HSP90 sequence from cacao will show information about the evolution of the TcHSP90 gene family.
The number of introns is largely related to the sensitivity of gene transcription regulation.
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in silico study so the fewer the number of introns, the more likely the plant will have the ability to respond to various environmental stimuli and developmental processes (Appiah et al.
, 2021.
Sajad et al.
, 2.
Cis-acting element analysis in the promoter of TcHSP90 genes Analysis of cis-acting elements in the promoter region was carried out to find out more about the regulation of TcHSP90 gene expression as a reaction to stress conditions under abiotic pressure (Peng et al.
, 2.
Based on this analysis, there are about 35 types of cis-acting elements that can be identified in the promoter sequence (Figure 2.
Some of the cis-acting elements found in TcHSP90 are ACE.
G-box.
MRE.
ATCTmotif.
Box 4.
GATA-motif.
GT1-motif which are known to be responsive to light (Bettaieb et al.
, 2020.
Zhang et al.
, 2.
The ACE cis element in the TcHSP90 gene is only present in TcHSP90-1 with locations around 820 bp and 1,320 bp before the start codon ATG.
Cis element ATCT-motif and GATA-motif are also only found in one TcHSP90 gene, namely in TcHSP90-7 with the location of ATCT-motif around 1,180 bp and GATA-motif around 1,480 bp before the start codon.
In addition, there is also Box 4 which is spread throughout the TcHSP90 genes (Figure 2.
Another cis-acting element found in TcHSP90 is the LTR which is associated with responsiveness to drought, low temperature, and salt stress (Bettaieb et al.
, 2020.
Xue et al.
, 2.
The gene associated with this response is found in TcHSP90-2.
TcHSP90-4, and TcHSP90-5 with the location being around 580 bp before the start codon in TcHSP90-4.
The TcHSP90 promoter also contains anaerobic responsive elements (ARE) which are scattered throughout the TcHSP90 genes and are known to have an important role in responding to oxygen limi- Other cis-acting elements found in TcHSP90 are MYB Binding Site (MBS) involved in drought induction and TC-rich repeats involved in defense and stress responsiveness (Bettaieb et al.
, 2020.
Xue et al.
Some TcHSP90 promoters also contain elements induced by phytohormones, such as GARE-motif and P-box that are responsive to gibberellin.
AuxRR-core and TGAelement that are responsive to auxin, and ABRE that is responsive to abscisic acid.
In addition, there are CGTCA-motifs and TGACG-motifs that are responsive to Me-JA and TCA-elements that are responsive to salicylic acid (Bettaieb et al.
, 2.
Other elements such as O2-site and GCN4-motif are known to be found only on specific promoters, suggesting that the corresponding genes will be controlled only under certain conditions (Xue et al.
, 2.
The analysis of the cis-acting element showed that abiotic stress and hormone regulation can regulate the expression of the TcHSP90 genes.
A total of 38 cis-acting elements that are randomly distributed in the TcHSP90 genes have important roles in growth and development as well as abiotic and hormonal stress responses, thus showing the complex function of TcHSP90.
Abiotic stress will increase the expression of the TcHSP90 gene to maintain protein stability and function, thereby increasing its tolerance to environmental stress conditions.
The HSP90 mechanism play a role in regulating and maintaining the conformation of various proteins and binds with non-protein substances to enable the repair of proteins damaged by stress (Li et al.
, 2.
Abiotic stress will be related to the function of hormones in plants such as auxin, gibberellin, methyl-jasmonic, and abscisic acid.
Cis acting ABRE related to abscisic acid responsiveness has been identified in A.
thaliana and showed its function in the regulation of lignin deposition and PELITA PERKEBUNAN.
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CAAT-box
ABRE
TGA-element
LTR
3-AF3 binding site
GA-motif
TC-rich repeats l-box
MRE
GARE-motif
Sp1
AT1-motif
A-box
ATCT-motif
GATA-motif
ATC-motif
CAT-box
GCN4_motif Box 4
MBS
CGTCA-motif
ACE
G-box
ARE
chs-CMA1a AE-box TCA-element P-box GT1-motif TGACG-motif AuxRR-core O2-site TATA-box TcHSP90 -7 TcHSP90 -6 TcHSP90 -5 TcHSP90 -4 TcHSP90 -3 TcHSP90 -2 TcHSP90 -1 secondary cell wall formation through phosphorylation of wall NST1 (Liu et al.
, 2.
Auxin and gibberellin identified in cotton fiber cells function as promoters of cell elongation while jasmonic acid functions as a response to plant pathogen defense.
The various cis-acting types found in the TcHSP90 gene can show different and specific expression patterns in various tissues including the function and regulation of the genes contained therein.
The gene expression pattern is involved in the growth of T.
cacao and the development of various tissues and organs (Bettaieb et al.
Subcellular localization of TcHSP90 Figure 2.
Cis-acting element of TcHSP90
TCT-motif
Tc-motif
800 1,000 1,200 1,400 1,600 1,800 2,000
CCAAT-box G-box Mustafidah et al.
The subcellular localization of proteins is used to predict TcHSP90 members in different cellular compartments indicating the involvement and function of each gene in various subcellular processes (Bettaieb et al.
, 2020.
Zhang et al.
, 2.
The expression of ABAresponsive genes is known to be inhibited by overexpression of AtHSP90-2 in the cytosol but not affected by overexpression of AtHSP90-5 and AtHSP90-7 under drought and salt stress This suggests that the cellular compartment that localizes Arabidopsis thaliana HSP90 protein respond to abiotic stresses with different functional mechanisms (Appiah et al.
, 2.
The subcellular localization of HSP90 proteins in T.
cacao (Figure 3.
) showed that six of the seven proteins were predicted to be localized in the nucleus and none of the proteins were predicted to be localized in the From the various predictions of HSP90 protein localization in T.
cacao, it shows that the cytoplasm has the highest prediction value.
This is in accordance with the research of Appiah et al.
, 2021, that HSP90 is expressed in the cytoplasm.
The highest predicted subcellular localization of TcHSP90 protein is also in the mitochondria, namely in TcHSP901, chloroplast in TcHSP90-2, and cytoplasm PELITA PERKEBUNAN.
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August 2025 Edition Chlo_Mito Ex tr Pe ro Golg Plas Chlo Cysk Vacu Mito Cyto Nucl Identification of HSP90 gene family in Theobroma cacao L.
in silico study TcHSP90 -1 TcHSP90 -2 TcHSP90 -3 TcHSP90 -4 TcHSP90 -5 TcHSP90 -6 TcHSP90 -7 Figure 3.
Heat map of TcHSP90 in TcHSP90-6.
Between TcHSP90-1 in the mitochondria.
TcHSP90-2 in the chloroplast, and TcHSP90-6 in the cytoplasm shows that the highest subcellular localization is in TcHSP90-6 in the cytoplasm.
This was also shown in A.
thaliana (Sarkar et al.
, 2.
and Brachypodium distachyon (Zhang et al.
, 2.
and indicates that the cytoplasm is the site of protein assembly which may be the main site of HSP90 protein activity (Bettaieb et al.
Phylogenetic analysis Phylogenetic analysis is used to obtain information on the evolutionary relationships of species and to help identify orthologs between species and paralogs within species.
Construction of a phylogenetic tree on T.
HSP90 (Figure 4.
) is aimed at determining the evolutionary relationships and classification of T.
cacao HSP90 proteins.
cacao HSP90 phylogenetic tree construction was formed through the alignment of HSP90 protein sequences from several plants such as thaliana with 7 sequences.
Solanum lycopersicum with 6 sequences.
Oryza sativa with 9 sequences, and Zea mays with 11 Based on the results of the phylogenetic tree construction obtained, 6 groups were formed which showed that group I was the largest group with 13 genes consisting of 4 genes from Z.
mays, 3 genes from O.
2 genes from S.
lycopersicum, 2 genes from thaliana, and 2 genes from T.
cacao while group 5 was the smallest group because it only consisted of 2 genes from Z.
The phylogenetic tree construction shows that each clade has a close relationship based on the grouping of closed seed plants, namely dicots in T.
thaliana, and S.
and monocots in Z.
mays and O.
Different HSP90 protein families have different biophysical properties, suggesting that there is diversity among HSP90 members for further study.
The results of the phylogenetic tree construction showed that there were 3 orthologous genes among species, namely TcHSP90-2 and AtHSP90-5.
TcHSP90-1 with AtHSP90-6 and Solyc07g047790.
(SlHSP90-.
and TcHSP90-5 and Solyc12g 1 (SlHSP90-.
The phylogenetic tree construction results also showed the presence of 9 pairs of paralogs within species.
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Figure 4.
Phylogenetic tree of the HSP90 protein from T.
mays, and O.
one of them from A.
thaliana (AtHSP90-3 and AtHSP90-.
, 2 pairs from T.
(TcHSP90-6 and TcHSP907.
TcHSP90-3 and TcHSP90-.
, 2 pairs from S.
(Solyc03g 007890.
1 and Solyc06g036290.
Solyc07g 065840.
1 and Solyc12g .
, and 4 pairs from Z.
The nine pairs of paralogous genes in the phylogenetic tree construction indicated that most species evolved according to their own speciesspecific approaches during the evolution of the HSP90 gene family (Song et al.
, 2.
The analysis of orthologous and paralogous genes in the phylogenetic tree can be used to predict the characteristics and functions of TcHSP90 genes in evolutionary relationships with A.
and O.
sativa (Appiah et al.
, 2.
Based on the analysis of genes that are orthologous to TcHSP90, the evolutionary distribution of TcHSP90-2 is similar to that of AtHSP90-5, indicating a degree of sensitivity to drought and salt stress (Song et al.
TcHSP90-1 has an evolutionary distribution similar to AtHSP90-6 and Solyc07g047790.
1 (SlHSP90-.
which are associated with plant development (Luo et al.
, 2019.
Zai et al.
, 2.
TcHSP90-5 has a similar evolutionary distribution to Solyc12g 015880.
1 (SlHSP90-.
which is also involved in plant development (Zai et al.
Based on the analysis of paralogous genes in TcHSP90.
TcHSP90-6 and TcHSP90-7 are in a clade with AtHSP90-7, which shows a level of sensitivity to drought and salt stress (Song et al.
, 2.
Other paralogs in TcHSP90 PELITA PERKEBUNAN.
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August 2025 Edition Identification of HSP90 gene family in Theobroma cacao L.
in silico study are found in TcHSP90-3 and TcHSP90-4 which are in one clade with Solyc03g 1 (SlHSP90-.
and Solyc06g 1 (SlHSP90-.
and AtHSP90-1 which are related to plant development and osmotic stress responses from ABA signaling (Zai et al.
, 2015.
Zhang et al.
, 2.
CONCLUSIONS
The identification and characterization of seven HSP90 gene families found in Theobroma cacao were successfully analysed related to the motif and structure of the TcHSP90 genes, the cis element in the promoter, the prediction of subcellular localization, and the phylogenetic tree.
Different HSP90 protein families have different biophysical properties, indicating diversity among HSP90 members.
Analysis of the expression pattern of T.
HSP90 family genes showed that TcHSP90-1.
TcHSP90-3, and TcHSP90-5 were expressed in response to biotic and abiotic stresses, which means that the three genes have an important role in T.
cacao development.
Analysis of the expression patterns of TcHSP90-2.
TcHSP90-4.
TcHSP90-6, and TcHSP90-7 was related to the response to drought and salt This study not only provides a scientific basis for HSP90 in T.
cacao but can also be used as basic knowledge for the development of new T.
cacao cultivars that are resistant to biotic and abiotic stresses and can help in the selection of candidate genes for T.
REFERENCES