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In Silico Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid

Journal of Tropical Biodiversity and Biotechnology · Vol. 8 No. 3 (2023)

DOI
10.22146/jtbb.83934
ISSN
2540-9581, 2540-9573
Published
2023-10-16
Publisher
Universitas Gadjah Mada
Language
eng
License
creativecommons.org/licenses/by-sa/4.0

Abstract

The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved. Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11.

Keywords

Collaboration network of the authors

40 authors · 125 co-authorship links · showing the 40 most connected

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  • Universitas Gadjah Mada
  • Affiliation unknown
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Co-authorOrganisationJoint articles
Aziz PurwantoroAffiliation unknown11
Sukarti MoeljopawiroAffiliation unknown6
Ari IndriantoAffiliation unknown4
Muhammad Dylan LawrieAffiliation unknown4
Windi MoseAffiliation unknown3
Jose Gutierrez-MarcosAffiliation unknown3
Nintya SetiariAffiliation unknown2
Jaka WidadaUniversitas Gadjah Mada2
Exsyupransia MursyantiAffiliation unknown2
Sismindari SismindariAffiliation unknown2
Fitriana PuspitasariAffiliation unknown2
Aries Bagus SasongkoUniversitas Gadjah Mada2
Naufal Ghozi Aditya PerdanaAffiliation unknown2
Dika SundariAffiliation unknown2
Ana AininaAffiliation unknown2
Ahmad Yudis MahardhikaAffiliation unknown2
Ni Putu Ayu Erninda Oktaviani SuputriAffiliation unknown2
Tri Joko RaharjoAffiliation unknown1
Stalis Norma EthicaAffiliation unknown1
Oedjijono OedjijonoAffiliation unknown1
Triono Bagus SaputroAffiliation unknown1
Zulfa LayinaAffiliation unknown1
Della Rosiana NingtiasAffiliation unknown1
Falah Nur AlifiantoAffiliation unknown1
Budi Setiadi DaryonoAffiliation unknown1
Rina ArimarsetiowatiAffiliation unknown1
Yohana Theresia Maria AstutiAffiliation unknown1
Ixora Sartika MercurianiAffiliation unknown1
Seonghoe JangAffiliation unknown1
Sri WahyuningsihAffiliation unknown1
Budi Setiadi DaryonoAffiliation unknown1
Soenghoe JangAffiliation unknown1
Sri NopitasariAffiliation unknown1
Yuli SetiawatiAffiliation unknown1

Affiliations come from OpenAlex; journal OAI-PMH metadata carries none. Authors without an OpenAlex ID are matched by name, which can merge or split people.

Metadata source: OAI-PMH (metadata jurnal) https://jurnal.ugm.ac.id/jtbb/oai, first harvested 9 Nov 2026, last seen 9 Nov 2026.
Original metadata (oai_dc) 
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	<dc:title xml:lang="en-US">In Silico Analysis of Phalaenopsis Orchid Homeobox1 (POH1) Functional Gene for Shoot Development in Phalaenopsis Orchid</dc:title>
	<dc:creator>Rasjid, Nuzlan</dc:creator>
	<dc:creator>Kurniawan, Febri Yuda</dc:creator>
	<dc:creator>Putri, Saifa Usni</dc:creator>
	<dc:creator>Linggabuwana, Aviesta</dc:creator>
	<dc:creator>Prasojo, Ireneus Seno</dc:creator>
	<dc:creator>Semiarti, Endang</dc:creator>
	<dc:subject xml:lang="en-US">Biology</dc:subject>
	<dc:subject xml:lang="en-US">POH1; Conserved Domain; Transcription Factor; Protein Modelling; Phalaenopsis</dc:subject>
	<dc:description xml:lang="en-US">The most favorite ornamental crop in Indonesia is orchid which benefited as floriculture. Therefore, the quality of this crop must be improved.  Biotechnology is appropriate to be used to improve the quality and quantity of orchid plants. To conduct this method, researchers must know what genes function in plant development. In Phalaenopsis orchids, the gene has been identified as homeobox genes called Phalaenopsis Orchid Homeobox1 (POH1). This research aims to conduct in silico analysis of the gene. The materials were retrieved from mRNA and amino acid databases. Then, the materials are aligned, visualized, motif location analysis, motif function discovery, phylogenetic construction, and protein 3D structural modelling. Based on mRNA and amino acid alignment, there are 4 domain regions that are conserved in POH1 and other homologous genes, such as KNOX1, KNOX2, ELK Domain, and Homeobox KN Domain, which roles as a transcription factor involved in plant development. SWISS-MODEL and ColabFold were used in protein modelling of the protein. By ColabbFold modelling, the modelling prediction uses 325 residues, higher than SWISS-MODEL in 59 residues. ColabFold validation by Ramachandra Plot depicts having the most favourite regions is 68.6%, while SWISS-MODEL is 92.3%. Another validation parameter is overall quality factor and QMEAN Score. Protein modelling by ColabFold has overall quality factor 89.252 and QMEAN Score 0.41 ± 0.05. However, SWISS-MODEL 3D prediction has overall quality factor 98.039 and QMEAN score of 0.71 ± 0.11. </dc:description>
	<dc:publisher xml:lang="en-US">Universitas Gadjah Mada</dc:publisher>
	<dc:contributor xml:lang="en-US">Universitas Gadjah Mada</dc:contributor>
	<dc:date>2023-10-16</dc:date>
	<dc:type>info:eu-repo/semantics/article</dc:type>
	<dc:type>info:eu-repo/semantics/publishedVersion</dc:type>
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	<dc:format>application/pdf</dc:format>
	<dc:identifier>https://journal.ugm.ac.id/jtbb/article/view/83934</dc:identifier>
	<dc:identifier>10.22146/jtbb.83934</dc:identifier>
	<dc:source xml:lang="en-US">Journal of Tropical Biodiversity and Biotechnology; Vol 8, No 3 (2023): December; jtbb83934</dc:source>
	<dc:source>2540-9581</dc:source>
	<dc:source>2540-9573</dc:source>
	<dc:language>eng</dc:language>
	<dc:relation>info:eu-repo/grantAgreement/EC/FP7/003550</dc:relation>
	<dc:relation>https://journal.ugm.ac.id/jtbb/article/view/83934/37149</dc:relation>
	<dc:relation>https://journal.ugm.ac.id/jtbb/article/downloadSuppFile/83934/26393</dc:relation>
	<dc:relation>https://journal.ugm.ac.id/jtbb/article/downloadSuppFile/83934/26394</dc:relation>
	<dc:coverage xml:lang="en-US">Indonesia</dc:coverage>
	<dc:coverage xml:lang="en-US">In silico POH1 gene</dc:coverage>
	<dc:coverage xml:lang="en-US">Bioinformatics</dc:coverage>
	<dc:rights xml:lang="en-US">info:eu-repo/semantics/openAccess</dc:rights>
	<dc:rights xml:lang="en-US">Copyright (c) 2023 Journal of Tropical Biodiversity and Biotechnology</dc:rights>
	<dc:rights xml:lang="en-US">http://creativecommons.org/licenses/by-sa/4.0</dc:rights>
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