干旱区生态环境知识资源中心(Arid): Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss

Arid

DOI	10.3390/plants11182365
	Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss
	Sheikh-Assadi, Morteza; Naderi, Roohangiz; Salami, Seyed Alireza; Kafi, Mohsen; Fatahi, Reza; Shariati, Vahid; Martinelli, Federico; Cicatelli, Angela; Triassi, Maria; Guarino, Francesco; Improta, Giovanni; Claros, Manuel Gonzalo
通讯作者	Sheikh-Assadi, M ; Naderi, R
来源期刊	PLANTS-BASEL
ISSN	2223-7747
出版年	2022
卷号	11 期号:18
英文摘要	A high-quality transcriptome is required to advance numerous bioinformatics workflows. Nevertheless, the effectuality of tools for de novo assembly and real precision assembled transcriptomes looks somewhat unexplored, particularly for non-model organisms with complicated (very long, heterozygous, polyploid) genomes. To disclose the performance of various transcriptome assembly programs, this study built 11 single assemblies and analyzed their performance on some significant reference-free and reference-based criteria. As well as to reconfirm the outputs of benchmarks, 55 BLAST were performed and compared using 11 constructed transcriptomes. Concisely, normalized benchmarking demonstrated that Velvet-Oases suffer from the worst results, while the EvidentialGene strategy can provide the most comprehensive and accurate transcriptome of Lilium ledebourii (Baker) Boiss. The BLAST results also confirmed the superiority of EvidentialGene, so it could capture even up to 59% more (than Velvet-Oases) unique gene hits. To promote assembly optimization, with the help of normalized benchmarking, PCA and AHC, it is emphasized that each metric can only provide part of the transcriptome status, and one should never settle for just a few evaluation criteria. This study supplies a framework for benchmarking and optimizing the efficiency of assembly approaches to analyze RNA-Seq data and reveals that selecting an inefficient assembly strategy might result in less identification of unique gene hits.
英文关键词	transcriptomics de novo assembly hybrid transcriptome normalized comparison optimization non-model organisms
类型	Article
语种	英语
开放获取类型	gold, Green Published
收录类别	SCI-E
WOS记录号	WOS:000857110400001
WOS关键词	QUALITY ASSESSMENT ; GENE-EXPRESSION ; GENOME ; ANNOTATION
WOS类目	Plant Sciences
WOS研究方向	Plant Sciences
资源类型	期刊论文
条目标识符	http://119.78.100.177/qdio/handle/2XILL650/394003
推荐引用方式 GB/T 7714	Sheikh-Assadi, Morteza,Naderi, Roohangiz,Salami, Seyed Alireza,et al. Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss[J],2022,11(18).
APA	Sheikh-Assadi, Morteza.,Naderi, Roohangiz.,Salami, Seyed Alireza.,Kafi, Mohsen.,Fatahi, Reza.,...&Claros, Manuel Gonzalo.(2022).Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss.PLANTS-BASEL,11(18).
MLA	Sheikh-Assadi, Morteza,et al."Normalized Workflow to Optimize Hybrid De Novo Transcriptome Assembly for Non-Model Species: A Case Study in Lilium ledebourii (Baker) Boiss".PLANTS-BASEL 11.18(2022).