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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
Terbit
2023-10-16
Penerbit
Universitas Gadjah Mada
Bahasa
eng
Lisensi
creativecommons.org/licenses/by-sa/4.0

Abstrak

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.

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Aziz PurwantoroAfiliasi tidak diketahui11
Sukarti MoeljopawiroAfiliasi tidak diketahui6
Ari IndriantoAfiliasi tidak diketahui4
Muhammad Dylan LawrieAfiliasi tidak diketahui4
Windi MoseAfiliasi tidak diketahui3
Jose Gutierrez-MarcosAfiliasi tidak diketahui3
Nintya SetiariAfiliasi tidak diketahui2
Jaka WidadaUniversitas Gadjah Mada2
Exsyupransia MursyantiAfiliasi tidak diketahui2
Sismindari SismindariAfiliasi tidak diketahui2
Fitriana PuspitasariAfiliasi tidak diketahui2
Aries Bagus SasongkoUniversitas Gadjah Mada2
Naufal Ghozi Aditya PerdanaAfiliasi tidak diketahui2
Dika SundariAfiliasi tidak diketahui2
Ana AininaAfiliasi tidak diketahui2
Ahmad Yudis MahardhikaAfiliasi tidak diketahui2
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Stalis Norma EthicaAfiliasi tidak diketahui1
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Della Rosiana NingtiasAfiliasi tidak diketahui1
Falah Nur AlifiantoAfiliasi tidak diketahui1
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Sri WahyuningsihAfiliasi tidak diketahui1
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Sumber metadata: OAI-PMH (metadata jurnal) https://jurnal.ugm.ac.id/jtbb/oai, pertama di-harvest 9 Nov 2026, terakhir terlihat 9 Nov 2026.
Metadata asli (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>
	<dc:type xml:lang="en-US"></dc:type>
	<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>
</oai_dc:dc>