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A Comprehensive transcriptome assembly of Pigeonpea （Cajanus cajan L.） using Sanger and Second-Generation Sequencing Platforms

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Molecular Plant 2012年第5期5卷 1020-1028页

作者： Himabindu Kudapa Arvind K. Bharti Steven B. Cannon Andrew D. Farmer Benjamin Mulaosmanovi Robin Kramer Abhishek Bohra Nathan T. Weeks John A. Crow Reetu Tuteja Trushar Shah Sutapa Dutta Deepak K. Gupta Archana Singh Kishor Gaikwad Tilak R. Sharma Gregory D. May Nagendra K. Singh Rajeev K. Varshney International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) Patancheru 502324 india National Center for Genome Resources (NCGR) Santa Fe NM 87505 USA United States Department of Agriculture-Agricultural Research Service (USDA-ARS) Corn Insects and Crop Genetics Research Unit Ames IA USA National Research Centre on Plant Biotechnology (NRCPB) Indian Agricultural Research Institute New Delhi 110 012 India Department of Agronomy Iowa State University Amens IA USA CGIAR Generation Challenge Programme (GCP) c/o ClMMYT 06600 Mexico DF Mexico

A comprehensive transcriptome assembly for pigeonpea has been developed by analyzing 128.9 million short Illumina GA IIx single end reads, 2.19 million single end FLX/454 reads, and 18 353 Sanger expressed sequenced tags from more than 16 genotypes. The resultant transcriptome assembly, referred to as CcTA v2, comprised 21 434 transcript as- sembly contigs （TACs） with an N50 of 1510 bp, the largest one being -8 kb. Of the 21 434 TACs, 16 622 （77.5%） could be mapped on to the soybean genome build 1.0.9 under fairly stringent alignment parameters. Based on knowledge of intron junctions, 10 009 primer pairs were designed from 5033 TACs for amplifying intron spanning regions （ISRs）. By using in silico mapping of BAC-end-derived SSR loci of pigeonpea on the soybean genome as a reference, putative mapping posi- tions at the chromosome level were predicted for 6284 ISR markers, covering all 11 pigeonpea chromosomes. A subset of 128 ISR markers were analyzed on a set of eight genotypes. While 116 markers were validated, 70 markers showed one to three alleles, with an average of 0.16 polymorphism information content （PIC） value. In summary, the CcTA v2 transcript assembly and ISR markers will serve as a useful resource to accelerate genetic research and breeding applications in pigeonpea.

关键词： Cajanus cajan (L.) second-generation sequencing transcriptome assembly intron spanning region (ISR)markers.

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Comparative analysis of de novo transcriptome assembly

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Science China(Life Sciences) 2013年第2期56卷 156-162页

作者： CLARKE Kaitlin YANG Yi MARSH Ronald XIE LingLin ZHANG Ke K. Bioinformatics Core Department of PathologyUniversity of North Dakota Department of Computer Science University of North Dakota Department of Biochemistry and Molecular Biology University of North Dakota

The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis.A fast algorithm,de Bruijn graph has been successfully used for genome DNA de novo assembly;nevertheless,its performance for transcriptome assembly is *** this study,we used both simulated and real RNA-Seq data,from either artificial RNA templates or human transcripts,to evaluate five de novo assemblers,ABySS,Mira,Trinity,Velvet and *** these assemblers,ABySS,Trinity,Velvet and Oases are all based on de Bruijn graph,and Mira uses an overlap graph *** numbers of RNA short reads were selected from the External RNA Control Consortium(ERCC) data and human chromosome 22.A number of statistics were then calculated for the resulting contigs from each *** experiment was repeated multiple times to obtain the mean statistics and standard error *** had relative good performance for both ERCC and human data,but it may not consistently generate full length *** was the fastest method but its assembly quality was *** gave a good rate for mapping its contigs onto human chromosome 22,but its computational speed is not *** results suggest that transcript assembly remains a challenge problem for bioinformatics ***,a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

关键词： transcriptome assembly next-generation sequencing RNA-Seq De Bruijn graph overlap graph

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r＇ranscriptome assembly strategies for ）recision medicine

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Frontiers of Electrical and Electronic Engineering in China 2017年第4期5卷 280-290页

作者： Lu Wang Lipi Acharya Changxin Bai Dongxiao Zhu Department of Computer Science Wayne State University Detroit MI 48202 USA DOW AgroSciences lndianapolis IN 46268 USA

Background： Precision medicine approach holds great promise to tailored diagnosis, treatment and prevention. Individuals can be vastly different in their genomic information and genetic mechanisms hence having unique transcriptomic signatures. The development of precision medicine has demanded moving beyond DNA sequencing （DNA-Seq） to much more pointed RNA-sequencing （R_NA-Seq） [Cell, 2017, 168： 584--599]. Results： Here we conduct a brief survey on the recent methodology development of transcriptome assembly approach using RNA-Seq. Conclusions： Since transcriptomes in human disease are highly complex, dynamic and diverse, transcriptome assembly is playing an increasingly important role in precision medicine research to dissect the molecular mechanisms of the human diseases.

关键词： precision medicine transcriptome assembly RNA-Seq de novo De Bruijn

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Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 377-393页

作者： Haitao Luo Dechao Bu Lijuan Shao Yang Li Liang Sun Ce Wang Jing Wang Wei Yang Xiaofei Yang Jun Dong Yi Zhao Furong Li Translational Medicine Collaborative Innovation Center The Second Clinical Medical College(Shenzhen People’s Hospital)Jinan UniversityShenzhen 518020China Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation Shenzhen 518020China Integrated Chinese and Western Medicine Postdoctoral Research Station Jinan UniversityGuangzhou 510632China Bioinformatics Research Group Key Laboratory of Intelligent Information ProcessingAdvanced Computing Research CenterInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Department of Gastrointestinal Surgery The Second Clinical Medical College(Shenzhen People’s Hospital)Jinan UniversityShenzhen 518020China

The development of new biomarkers or therapeutic targets for cancer immunotherapies requires deep understanding of *** date,the complete landscape and systematic characterization of long noncoding RNAs(lncRNAs)in T cells in cancer immunity are ***,by systematically analyzing full-length single-cell RNA sequencing(scRNA-seq)data of more than 20,000 libraries of T cells across three cancer types,we provided the first comprehensive catalog and the functional repertoires of lncRNAs in human T ***,we developed a custom pipeline for de novo transcriptome assembly and obtained a novel lncRNA catalog containing 9433 *** increased the number of current human lncRNA catalog by 16%and nearly doubled the number of lncRNAs expressed in T *** found that a portion of expressed genes in single T cells were lncRNAs which had been overlooked by the majority of previous *** on metacell maps constructed by the MetaCell algorithm that partitions scRNA-seq datasets into disjointed and homogenous groups of cells(metacells),154 signature lncRNA genes were *** were associated with effector,exhausted,and regulatory T cell ***,84 of them were functionally annotated based on the co-expression networks,indicating that lncRNAs might broadly participate in the regulation of T cell *** findings provide a new point of view and resource for investigating the mechanisms of T cell regulation in cancer immunity as well as for novel cancer-immune biomarker development and cancer immunotherapies.

关键词： Long non-coding RNA transcriptome assembly Metacell Immune regulation Functional annotation

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