Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae)
<i>Rhododendron</i><i>simsii</i> is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in <i>Rhododendron L</i>. The understanding...
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| Format: | Article |
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MDPI AG
2021-03-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/4/649 |
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| author | Qunlu Liu Fiza Liaquat Yefeng He Muhammad Farooq Hussain Munis Chunying Zhang |
| author_facet | Qunlu Liu Fiza Liaquat Yefeng He Muhammad Farooq Hussain Munis Chunying Zhang |
| author_sort | Qunlu Liu |
| collection | DOAJ |
| description | <i>Rhododendron</i><i>simsii</i> is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in <i>Rhododendron L</i>. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in <i>Rhododendron L</i>. To generate the <i>R.</i><i>simsii</i> transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3′H and ANS showed an upward trend in the developmental stages of <i>R. simsii</i>. The highest expression of F3′5′H and FLS in the petal color formation of <i>R. simsii</i> was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of <i>R.</i><i>simsii</i>. native, which is a semi-deciduous shrub. |
| first_indexed | 2024-03-10T12:48:23Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-10T12:48:23Z |
| publishDate | 2021-03-01 |
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| record_format | Article |
| series | Plants |
| spelling | doaj.art-6ddb17788682466a838d3be6dca6eaa62023-11-21T13:17:21ZengMDPI AGPlants2223-77472021-03-0110464910.3390/plants10040649Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae)Qunlu Liu0Fiza Liaquat1Yefeng He2Muhammad Farooq Hussain Munis3Chunying Zhang4Department of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai 200240, ChinaSchool of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, ChinaDepartment of Landscape Architecture, School of Design, Shanghai Jiao Tong University, Shanghai 200240, ChinaDepartment of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, PakistanShanghai Engineering Research Center of Sustainable Plant Innovation, Shanghai Botanical Garden, Shanghai 200231, China<i>Rhododendron</i><i>simsii</i> is one of the top ten famous flowers in China. Due to its historical value and high aesthetic, it is widely popular among Chinese people. Various colors are important breeding objectives in <i>Rhododendron L</i>. The understanding of the molecular mechanism of flower color formation can provide a theoretical basis for the improvement of flower color in <i>Rhododendron L</i>. To generate the <i>R.</i><i>simsii</i> transcriptome, PacBio sequencing technology has been used. A total of 833,137 full-length non-chimeric reads were obtained and 726,846 high-quality full-length transcripts were found. Moreover, 40,556 total open reading frames were obtained; of which 36,018 were complete. In gene annotation analyses, 39,411, 18,565, 16,102 and 17,450 transcriptions were allocated to GO, Nr, KEGG and COG databases, correspondingly. To identify long non-coding RNAs (lncRNAs), we utilized four computational methods associated with Protein families (Pfam), Cooperative Data Classification (CPC), Coding Assessing Potential Tool (CPAT) and Coding Non Coding Index (CNCI) databases and observed 6170, 2265, 4084 and 1240 lncRNAs, respectively. Based on the results, most genes were enriched in the flavonoid biosynthetic pathway. The eight key genes on the anthocyanin biosynthetic pathway were further selected and analyzed by qRT-PCR. The F3′H and ANS showed an upward trend in the developmental stages of <i>R. simsii</i>. The highest expression of F3′5′H and FLS in the petal color formation of <i>R. simsii</i> was observed. This research provided a huge number of full-length transcripts, which will help to proceed genetic analyses of <i>R.</i><i>simsii</i>. native, which is a semi-deciduous shrub.https://www.mdpi.com/2223-7747/10/4/649<i>Rhododendron simsii</i>transcriptomefull length transcriptalternative splicing |
| spellingShingle | Qunlu Liu Fiza Liaquat Yefeng He Muhammad Farooq Hussain Munis Chunying Zhang Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) Plants <i>Rhododendron simsii</i> transcriptome full length transcript alternative splicing |
| title | Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) |
| title_full | Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) |
| title_fullStr | Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) |
| title_full_unstemmed | Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) |
| title_short | Functional Annotation of a Full-Length Transcriptome and Identification of Genes Associated with Flower Development in <i>Rhododendron simsii</i> (Ericaceae) |
| title_sort | functional annotation of a full length transcriptome and identification of genes associated with flower development in i rhododendron simsii i ericaceae |
| topic | <i>Rhododendron simsii</i> transcriptome full length transcript alternative splicing |
| url | https://www.mdpi.com/2223-7747/10/4/649 |
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