Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.)
Plants are rich in tandem repeats-containing proteins. It is postulated that the occurrence of tandem repeat gene families facilitates the adaptation and survival of plants in adverse environmental conditions. This study intended to identify the tandem repeats in the transcriptome of a high potentia...
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| Format: | Article |
| Language: | English |
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Penerbit Universiti Sains Malaysia
2024
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| Online Access: | http://psasir.upm.edu.my/id/eprint/115213/ http://psasir.upm.edu.my/id/eprint/115213/1/115213.pdf |
| _version_ | 1848866716180807680 |
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| author | Yong, Christina Seok Yien Hamzah, Nur Atheeqah |
| author_facet | Yong, Christina Seok Yien Hamzah, Nur Atheeqah |
| author_sort | Yong, Christina Seok Yien |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Plants are rich in tandem repeats-containing proteins. It is postulated that the occurrence of tandem repeat gene families facilitates the adaptation and survival of plants in adverse environmental conditions. This study intended to identify the tandem repeats in the transcriptome of a high potential tropical horticultural plant, roselle (Hibiscus sabdariffa L.). A total of 92,974 annotated de novo assembled transcripts were analysed using in silico approach, and 6,541 transcripts that encoded proteins containing tandem repeats with length of 20–60 amino acid residues were identified. Domain analysis revealed a total of nine tandem repeat protein families in the transcriptome of roselle, which are the Ankyrin repeats (ANK), Armadillo repeats (ARM), elongation factor-hand domain repeats (EF-hand), Huntingtin, elongation factor 3, protein phosphatase 2A, yeast kinase TOR1 repeats (HEAT), Kelch repeats (Kelch), leucine rich repeats (LRR), pentatricopeptide repeats (PPR), tetratricopeptide repeats (TPR) and WD40 repeats (WD40). Functional annotation analysis further matched 6,236 transcripts to 1,045 known proteins that contained tandem repeats including proteins implicated in plant development, protein-protein interaction, immunity and abiotic stress responses. The findings provide new insights into the occurrence of tandem repeats in the transcriptome and lay the foundation to elucidate the functional associations between tandem peptide repeats (TRs) and proteins in roselle and facilitate the identification of novel biotic and abiotic response related tandem repeats genes that may be useful in breeding improved varieties. |
| first_indexed | 2025-11-15T14:25:01Z |
| format | Article |
| id | upm-115213 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T14:25:01Z |
| publishDate | 2024 |
| publisher | Penerbit Universiti Sains Malaysia |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1152132025-03-04T01:33:32Z http://psasir.upm.edu.my/id/eprint/115213/ Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) Yong, Christina Seok Yien Hamzah, Nur Atheeqah Plants are rich in tandem repeats-containing proteins. It is postulated that the occurrence of tandem repeat gene families facilitates the adaptation and survival of plants in adverse environmental conditions. This study intended to identify the tandem repeats in the transcriptome of a high potential tropical horticultural plant, roselle (Hibiscus sabdariffa L.). A total of 92,974 annotated de novo assembled transcripts were analysed using in silico approach, and 6,541 transcripts that encoded proteins containing tandem repeats with length of 20–60 amino acid residues were identified. Domain analysis revealed a total of nine tandem repeat protein families in the transcriptome of roselle, which are the Ankyrin repeats (ANK), Armadillo repeats (ARM), elongation factor-hand domain repeats (EF-hand), Huntingtin, elongation factor 3, protein phosphatase 2A, yeast kinase TOR1 repeats (HEAT), Kelch repeats (Kelch), leucine rich repeats (LRR), pentatricopeptide repeats (PPR), tetratricopeptide repeats (TPR) and WD40 repeats (WD40). Functional annotation analysis further matched 6,236 transcripts to 1,045 known proteins that contained tandem repeats including proteins implicated in plant development, protein-protein interaction, immunity and abiotic stress responses. The findings provide new insights into the occurrence of tandem repeats in the transcriptome and lay the foundation to elucidate the functional associations between tandem peptide repeats (TRs) and proteins in roselle and facilitate the identification of novel biotic and abiotic response related tandem repeats genes that may be useful in breeding improved varieties. Penerbit Universiti Sains Malaysia 2024 Article PeerReviewed text en cc_by_4 http://psasir.upm.edu.my/id/eprint/115213/1/115213.pdf Yong, Christina Seok Yien and Hamzah, Nur Atheeqah (2024) Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.). Tropical Life Sciences Research, 35 (3). pp. 121-148. ISSN 1985-3718; eISSN: 2180-4249 https://ejournal.usm.my/tlsr/article/view/tlsr_vol35-no-3-2024_6 10.21315/tlsr2024.35.3.6 |
| spellingShingle | Yong, Christina Seok Yien Hamzah, Nur Atheeqah Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title | Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title_full | Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title_fullStr | Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title_full_unstemmed | Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title_short | Transcriptome-wide identification of nine tandem repeat protein families in roselle (Hibiscus sabdariffa L.) |
| title_sort | transcriptome-wide identification of nine tandem repeat protein families in roselle (hibiscus sabdariffa l.) |
| url | http://psasir.upm.edu.my/id/eprint/115213/ http://psasir.upm.edu.my/id/eprint/115213/ http://psasir.upm.edu.my/id/eprint/115213/ http://psasir.upm.edu.my/id/eprint/115213/1/115213.pdf |