Plant Transcriptome Assembly: Review and Benchmarking

Behera, Sairam; Voshall, Adam; Moriyama, Etsuko N.

doi:10.36255/exonpublications.bioinformatics.2021.ch7

Cited by 4 publications

(13 citation statements)

References 63 publications

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“…As a matter of fact, genome assembly and transcriptome analysis are complementary and these procedures do not take place of each other 29 . The genome assembly encompasses the structural data, information on chromosomes, SNPs, and haplotypes 6 – 9 .…”

Section: Discussionmentioning

confidence: 99%

“…To benefit from each assembler, one common method is to combine (concatenate) the outputs of multiple assemblers 29 , 30 . However, this approach may result in lengthy, poorly assembled transcripts 31 .…”

Section: Introductionmentioning

confidence: 99%

“…This package intends to eliminate redundancy and exclude misassembled transcripts by focusing on coding regions (CDS) 32 . CAP3, another useful tool used in the ensemble approach, has been mainly applied to cluster and fuse similar isoforms into a consensual sequence 29 .…”

Section: Introductionmentioning

confidence: 99%

“…The root can be traced back to the lack of a comprehensive method for benchmarking and quality assessment of assembly datasets 33 . Numerous reference-based and reference-free metrics have already been evolved to control the quality of a transcriptome assembly 29 . Users typically evaluate the outputs of these programs by estimating the number of complete transcripts, Nx statistics, mapping rates, and benchmarking of single-copy orthologs (BUSCO) 33 .…”

Section: Introductionmentioning

confidence: 99%

“…The main algorithm behind the basis of developed assemblers (such as Trinity, IDBA-Trans, rnaSPAdes, BinPacker, Velvet-Oases) is de Bruijn graphs algorithm, but each has its own focus and variations on greedy k-mer extension, overlap-layout-consensus, exhaustive enumeration and other statistical strategies. Additionally, CAP3 follows the overlap-layout-consensus (OLC) algorithm, and EvidentialGene employs sequence alignment and homology search 17 – 20 , 27 , 29 , 32 . The current work addresses the following questions: (1) What parameters should be considered in a standard quality control pipeline?…”

Section: Introductionmentioning

confidence: 99%

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Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Ahmadi,

Sheikh-Assadi,

Fatahi

et al. 2023

Sci Rep

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Non-erroneous and well-optimized transcriptome assembly is a crucial prerequisite for authentic downstream analyses. Each de novo assembler has its own algorithm-dependent pros and cons to handle the assembly issues and should be specifically tested for each dataset. Here, we examined efficiency of seven state-of-art assemblers on ~ 30 Gb data obtained from mRNA-sequencing of Thymus daenensis. In an ensemble workflow, combining the outputs of different assemblers associated with an additional redundancy-reducing step could generate an optimized outcome in terms of completeness, annotatability, and ORF richness. Based on the normalized scores of 16 benchmarking metrics, EvidentialGene, BinPacker, Trinity, rnaSPAdes, CAP3, IDBA-trans, and Velvet-Oases performed better, respectively. EvidentialGene, as the best assembler, totally produced 316,786 transcripts, of which 235,730 (74%) were predicted to have a unique protein hit (on uniref100), and also half of its transcripts contained an ORF. The total number of unique BLAST hits for EvidentialGene was approximately three times greater than that of the worst assembler (Velvet-Oases). EvidentialGene could even capture 17% and 7% more average BLAST hits than BinPacker and Trinity. Although BinPacker and CAP3 produced longer transcripts, the EvidentialGene showed a higher collinearity between transcript size and ORF length. Compared with the other programs, EvidentialGene yielded a higher number of optimal transcript sets, further full-length transcripts, and lower possible misassemblies. Our finding corroborates that in non-model species, relying on a single assembler may not give an entirely satisfactory result. Therefore, this study proposes an ensemble approach of accompanying EvidentialGene pipelines to acquire a superior assembly for T. daenensis.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Ahmadi,

Sheikh-Assadi,

Fatahi

et al. 2023

Sci Rep

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Bioinformatic Resources for Plant Genomic Research

Valsala Sudarsanan,

Sreekumar

2024

CBIO

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Genome assembly and annotation are crucial steps in plant genomics research as they provide valuable insights into plant genetic makeup, gene regulation, evolutionary history, and biological processes. In the emergence of high-throughput sequencing technologies, a plethora of genome assembly tools have been developed to meet the diverse needs of plant genome researchers. Choosing the most suitable tool to suit a specific research need can be daunting due to the complex and varied nature of plant genomes and reads from the sequencers. To assist informed decision-making in selecting the appropriate genome assembly and annotation tool(s), this review offers an extensive overview of the most widely used genome and transcriptome assembly tools. The review covers the specific information on each tool in tabular data, and the data types it can process. In addition, the review delves into transcriptome assembly tools, plant resource databases, and repositories (12 for Arabidopsis, 9 for Rice, 5 for Tomato, and 8 general use resources), which are vital for gene expression profiling and functional annotation and ontology tools that facilitate data integration and analysis.

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Integrative metabolomic and transcriptomic reveals potential mechanism for promotion of ginsenoside synthesis in Panax ginseng leaves under different light intensities

Di,

Yang,

Wan

et al. 2023

Front. Bioeng. Biotechnol.

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Panax ginseng C.A. Meyer is a shade plant, and its leaves are an important medicinal part of P. ginseng. Light intensity plays a crucial role in physiological activities and metabolite accumulation in P. ginseng. Currently, little is known about the molecular mechanisms underlying physiological changes and quality under different light intensities in P. ginseng leaves. Therefore, we investigated the changes in photosynthetic physiology, secondary metabolism, transcriptomics, and metabolomics of P. ginseng leaves under different light intensities [T20 (20 µmol m-2·s-1), T50 (50 µmol m-2·s−1), T100 (100 μmol m−2·s−1)]]. Higher light intensity positively influenced the yield, photosynthesis, and accumulation of polysaccharides, soluble sugars, terpenoids, and ginsenosides in P. ginseng leaves. The T100 treatment notably promoted the accumulation of ginsenosides in the leaves, resulting in a 68.32% and 45.55% increase in total ginsenosides compared to the T20 and T50 treatments, respectively. Ginsenosides Rg1, Re, Rb1, Rc, Rg2, Rb2, Rb3, and Rd were 1.28-, 1.47-, 2.32-, 1.64-, 1.28-, 2.59-, 1.66-, and 2.28-times higher than in the T20 treatment. Furthermore, 285 differentially accumulated metabolites (DAMs) and 4218 differentially expressed genes (DEGs) in the metabolome and transcriptome of P. ginseng leaves, respectively, were identified. 13 triterpenoid saponins were significantly upregulated, and three were downregulated. The expression of genes encoding photosystem II reaction center proteins was upregulated under the T100 treatment, thereby increasing photosynthetic activity. The T100 treatment enhanced the expression of genes involved in photosynthetic carbon and energy metabolism in P. ginseng. The expression of antenna protein synthesis genes was upregulated under the T20, which increased the ability to capture light in P. ginseng leaves. T100 upregulated the expression of HMGR, SS, CYP716A53v2, UGT74AE, PgUGT1, and UGTPg45, thereby promoting terpene and ginsenoside synthesis. In summary, 100 µmol m−2·s−1 was conducive to quality formation of P. ginseng leaves. This study elucidates molecular mechanisms underlying the photosynthetic physiology and ginsenoside synthesis in P. ginseng under varying light intensities and provides a theoretical basis for the P. ginseng cultivation and its industrial production of secondary metabolites.

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Plant Transcriptome Assembly: Review and Benchmarking

Cited by 4 publications

References 63 publications

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Optimizing an efficient ensemble approach for high-quality de novo transcriptome assembly of Thymus daenensis

Bioinformatic Resources for Plant Genomic Research

Integrative metabolomic and transcriptomic reveals potential mechanism for promotion of ginsenoside synthesis in Panax ginseng leaves under different light intensities

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