Knowledge Management System Of Institute Of Botany,CAS
| PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings | |
| Liaquat, Fiza; Munis, Muhammad Farooq Hussain1; Arif, Samiah; Haroon, Urooj1; Shi, Jianxin2; Saqib, Saddam3,4; Zaman, Wajid3,4; Che, Shengquan5; Liu, Qunlu5 | |
| 2021 | |
| 发表期刊 | FRONTIERS IN GENETICS
 |
| 卷号 | 12 |
| 摘要 | Schima superba (Theaceae) is a subtropical evergreen tree and is used widely for forest firebreaks and gardening. It is a plant that tolerates salt and typically accumulates elevated amounts of manganese in the leaves. With large ecological amplitude, this tree species grows quickly. Due to its substantial biomass, it has a great potential for soil remediation. To evaluate the thorough framework of the mRNA, we employed PacBio sequencing technology for the first time to generate S. Superba transcriptome. In this analysis, overall, 511,759 full length non-chimeric reads were acquired, and 163,834 high-quality full-length reads were obtained. Overall, 93,362 open reading frames were obtained, of which 78,255 were complete. In gene annotation analyses, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Genes (COG), Gene Ontology (GO), and Non-Redundant (Nr) databases were allocated 91,082, 71,839, 38,914, and 38,376 transcripts, respectively. 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 8,551, 9,174, 20,720, and 18,669 lncRNAs, respectively. Moreover, nine genes were randomly selected for the expression analysis, which showed the highest expression of Gene 6 (Na_Ca_ex gene), and CAX (CAX-interacting protein 4) was higher in manganese (Mn)-treated group. This work provided significant number of full-length transcripts and refined the annotation of the reference genome, which will ease advanced genetic analyses of S. superba. |
| 关键词 | Schima superba manganese transcriptome full-length transcript alternative splicing |
| 学科领域 | Genetics & Heredity |
| DOI | 10.3389/fgene.2021.635043 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000641472800001 |
| 出版者 | FRONTIERS MEDIA SA |
| 文献子类 | Article |
| 出版地 | LAUSANNE |
| EISSN | 1664-8021 |
| 资助机构 | Shanghai Sciences and Technology Commission [18DZ2283500] |
| 作者邮箱 | liuql@sjtu.edu.cn |
| 作品OA属性 | Green Published, gold |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/26826 |
| 专题 | 系统与进化植物学国家重点实验室 |
| 作者单位 | 1.Shanghai Jiao Tong Univ, Sch Agr & Biol, Shanghai, Peoples R China 2.Quaid I Azam Univ, Fac Biol Sci, Dept Plant Sci, Islamabad, Pakistan 3.Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci, Shanghai, Peoples R China 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 5.Univ Chinese Acad Sci, Beijing, Peoples R China 6.Shanghai Jiao Tong Univ, Sch Design, Dept Landscape Architecture, Shanghai, Peoples R China |
| 推荐引用方式 GB/T 7714 | Liaquat, Fiza,Munis, Muhammad Farooq Hussain,Arif, Samiah,et al. PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings[J]. FRONTIERS IN GENETICS,2021,12. |
| APA | Liaquat, Fiza.,Munis, Muhammad Farooq Hussain.,Arif, Samiah.,Haroon, Urooj.,Shi, Jianxin.,...&Liu, Qunlu.(2021).PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings.FRONTIERS IN GENETICS,12. |
| MLA | Liaquat, Fiza,et al."PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings".FRONTIERS IN GENETICS 12(2021). |
| 条目包含的文件 | ||||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| _Applet_2022-10-14_b（1995KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。
修改评论