The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome
Abstract Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. This heterogeneity in assembl...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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BMC
2022-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12864-022-08717-z |
| _version_ | 1828303672099995648 |
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| author | Isaac Adeyemi Babarinde Andrew Paul Hutchins |
| author_facet | Isaac Adeyemi Babarinde Andrew Paul Hutchins |
| author_sort | Isaac Adeyemi Babarinde |
| collection | DOAJ |
| description | Abstract Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. This heterogeneity in assembled transcript sets might be partially explained by sequencing depth. Here, we used real and simulated short-read sequencing data as well as long-read data to systematically investigate the impact of sequencing depths on the accuracy of assembled transcripts. We assembled and analyzed transcripts from 671 human short-read data sets and four long-read data sets. At the first level, there is a positive correlation between the number of reads and the number of recovered transcripts. However, the effect of the sequencing depth varied based on cell or tissue type, the type of read and the nature and expression levels of the transcripts. The detection of coding transcripts saturated rapidly with both short and long-reads, however, there was no sign of early saturation for noncoding transcripts at any sequencing depth. Increasing long-read sequencing depth specifically benefited transcripts containing transposable elements. Finally, we show how single-cell RNA-seq can be guided by transcripts assembled from bulk long-read samples, and demonstrate that noncoding transcripts are expressed at similar levels to coding transcripts but are expressed in fewer cells. This study highlights the impact of sequencing depth on transcript assembly. |
| first_indexed | 2024-04-13T13:57:41Z |
| format | Article |
| id | doaj.art-75ab96b3fdca404c8785f2de95f1a978 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T13:57:41Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-75ab96b3fdca404c8785f2de95f1a9782022-12-22T02:44:08ZengBMCBMC Genomics1471-21642022-07-0123111410.1186/s12864-022-08717-zThe effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genomeIsaac Adeyemi Babarinde0Andrew Paul Hutchins1Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyShenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and TechnologyAbstract Investigating the functions and activities of genes requires proper annotation of the transcribed units. However, transcript assembly efforts have produced a surprisingly large variation in the number of transcripts, and especially so for noncoding transcripts. This heterogeneity in assembled transcript sets might be partially explained by sequencing depth. Here, we used real and simulated short-read sequencing data as well as long-read data to systematically investigate the impact of sequencing depths on the accuracy of assembled transcripts. We assembled and analyzed transcripts from 671 human short-read data sets and four long-read data sets. At the first level, there is a positive correlation between the number of reads and the number of recovered transcripts. However, the effect of the sequencing depth varied based on cell or tissue type, the type of read and the nature and expression levels of the transcripts. The detection of coding transcripts saturated rapidly with both short and long-reads, however, there was no sign of early saturation for noncoding transcripts at any sequencing depth. Increasing long-read sequencing depth specifically benefited transcripts containing transposable elements. Finally, we show how single-cell RNA-seq can be guided by transcripts assembled from bulk long-read samples, and demonstrate that noncoding transcripts are expressed at similar levels to coding transcripts but are expressed in fewer cells. This study highlights the impact of sequencing depth on transcript assembly.https://doi.org/10.1186/s12864-022-08717-zTranscript assemblySequencing depthCoding transcriptsNoncoding transcriptsTransposable elements |
| spellingShingle | Isaac Adeyemi Babarinde Andrew Paul Hutchins The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome BMC Genomics Transcript assembly Sequencing depth Coding transcripts Noncoding transcripts Transposable elements |
| title | The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| title_full | The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| title_fullStr | The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| title_full_unstemmed | The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| title_short | The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| title_sort | effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome |
| topic | Transcript assembly Sequencing depth Coding transcripts Noncoding transcripts Transposable elements |
| url | https://doi.org/10.1186/s12864-022-08717-z |
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