Performance of gene expression analyses using<i>de novo</i>assembled transcripts in polyploid species
Abstract Motivation Quality of gene expression analyses usingde novoassembled transcripts in species experienced recent polyploidization is yet unexplored.Results Five plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses usingde novoassembled transcriptome identified 50–76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7–30%. In addition, 7–89% of differentially expressed genes fromde novoassembly are contaminations. Gene co-expression network analyses usingde novoassemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.Availability and Implementation Commands and scripts used in this study are available at<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/">https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/</jats:ext-link>; Analysis files are available at Dryad doi: XXXXXX.Contact <jats:email>lychen83qq.com</jats:email><jats:sec sec-type="supplementary-material">Supplementary information Supplementary data are available atBioinformaticsonline.
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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 04. Sept. Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Chen, Ling-Yun [VerfasserIn] |
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| doi: |
10.1101/380063 |
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| PPN (Katalog-ID): |
XBI000324485 |
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| 520 | |a Abstract Motivation Quality of gene expression analyses usingde novoassembled transcripts in species experienced recent polyploidization is yet unexplored.Results Five plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses usingde novoassembled transcriptome identified 50–76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7–30%. In addition, 7–89% of differentially expressed genes fromde novoassembly are contaminations. Gene co-expression network analyses usingde novoassemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.Availability and Implementation Commands and scripts used in this study are available at<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/">https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/</jats:ext-link>; Analysis files are available at Dryad doi: XXXXXX.Contact <jats:email>lychen83qq.com</jats:email><jats:sec sec-type="supplementary-material">Supplementary information Supplementary data are available atBioinformaticsonline | ||
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| 700 | 1 | |a Yang, Ya |4 aut | |
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