PacBio Single-Molecule Long-Read Sequencing Reveals Genes Tolerating Manganese Stress in Schima superba Saplings
文献类型：期刊论文
| 作者 | Liaquat, Fiza; Munis, Muhammad Farooq Hussain1; Arif, Samiah; Haroon, Urooj1; Shi, Jianxin2; Saqib, Saddam3,4; Zaman, Wajid3,4; Che, Shengquan5; Liu, Qunlu5 |
| 刊名 | FRONTIERS IN GENETICS
 |
| 出版日期 | 2021 |
| 卷号 | 12 |
| 关键词 | Schima superba manganese transcriptome full-length transcript alternative splicing |
| DOI | 10.3389/fgene.2021.635043 |
| 文献子类 | Article |
| 英文摘要 | 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. |
| 学科主题 | Genetics & Heredity |
| 出版地 | LAUSANNE |
| 电子版国际标准刊号 | 1664-8021 |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| 语种 | 英语 |
| WOS记录号 | WOS:000641472800001 |
| 出版者 | FRONTIERS MEDIA SA |
| 资助机构 | Shanghai Sciences and Technology Commission [18DZ2283500] |
| 源URL | [http://ir.ibcas.ac.cn/handle/2S10CLM1/26826]  |
| 专题 | 植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文 |
| 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). |
入库方式： OAI收割
来源：植物研究所
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