Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i>
<i>Cephalotaxus oliveri</i> is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In vie...
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| Format: | Article |
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MDPI AG
2021-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/22/2/787 |
| _version_ | 1797411552067846144 |
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| author | Ziqing He Yingjuan Su Ting Wang |
| author_facet | Ziqing He Yingjuan Su Ting Wang |
| author_sort | Ziqing He |
| collection | DOAJ |
| description | <i>Cephalotaxus oliveri</i> is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of <i>C. oliveri</i>. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for <i>C. oliveri</i>, and this resource will facilitate further studies on the functional genomics and adaptive evolution of <i>C. oliveri</i>. |
| first_indexed | 2024-03-09T04:47:45Z |
| format | Article |
| id | doaj.art-44ca08c6da864320bbb25641aa8f7bec |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T04:47:45Z |
| publishDate | 2021-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-44ca08c6da864320bbb25641aa8f7bec2023-12-03T13:13:35ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672021-01-0122278710.3390/ijms22020787Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i>Ziqing He0Yingjuan Su1Ting Wang2School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaSchool of Life Sciences, Sun Yat-sen University, Guangzhou 510275, ChinaCollege of Life Sciences, South China Agricultural University, Guangzhou 510642, China<i>Cephalotaxus oliveri</i> is a tertiary relict conifer endemic to China, regarded as a national second-level protected plant in China. This species has experienced severe changes in temperature and precipitation in the past millions of years, adapting well to harsh environments. In view of global climate change and its endangered conditions, it is crucial to study how it responds to changes in temperature and precipitation for its conservation work. In this study, single-molecule real-time (SMRT) sequencing and Illumina RNA sequencing were combined to generate the complete transcriptome of <i>C. oliveri</i>. Using the RNA-seq data to correct the SMRT sequencing data, the four tissues obtained 63,831 (root), 58,108 (stem), 33,013 (leaf) and 62,436 (male cone) full-length unigenes, with a N50 length of 2523, 3480, 3181, and 3267 bp, respectively. Additionally, 35,887, 11,306, 36,422, and 25,439 SSRs were detected for the male cone, leaf, root, and stem, respectively. The number of long non-coding RNAs predicted from the root was the largest (11,113), and the other tissues were 3408 (stem), 3193 (leaf), and 3107 (male cone), respectively. Functional annotation and enrichment analysis of tissue-specific expressed genes revealed the special roles in response to environmental stress and adaptability in the different four tissues. We also characterized the gene families and pathways related to abiotic factors. This work provides a comprehensive transcriptome resource for <i>C. oliveri</i>, and this resource will facilitate further studies on the functional genomics and adaptive evolution of <i>C. oliveri</i>.https://www.mdpi.com/1422-0067/22/2/787<i>Cephalotaxus oliveri</i>SMRTtranscriptomemultiple tissuesgene familiespathways |
| spellingShingle | Ziqing He Yingjuan Su Ting Wang Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> International Journal of Molecular Sciences <i>Cephalotaxus oliveri</i> SMRT transcriptome multiple tissues gene families pathways |
| title | Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> |
| title_full | Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> |
| title_fullStr | Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> |
| title_full_unstemmed | Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> |
| title_short | Full-Length Transcriptome Analysis of Four Different Tissues of <i>Cephalotaxus oliveri</i> |
| title_sort | full length transcriptome analysis of four different tissues of i cephalotaxus oliveri i |
| topic | <i>Cephalotaxus oliveri</i> SMRT transcriptome multiple tissues gene families pathways |
| url | https://www.mdpi.com/1422-0067/22/2/787 |
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