The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome

Babarinde，Isaac Adeyemi; Hutchins，Andrew Paul

2022-07-04

10.1186/s12864-022-08717-z

BMC GENOMICS   Impact Factor & Quartile

1471-2164

1471-2164

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.

Transcript assembly Sequencing depth Coding transcripts Noncoding transcripts Transposable elements

SCI

English

First ; Corresponding

National Natural Science Foundation of China["31970589","32150710521"] ; Shenzhen Innovation Committee of Science and Technology[ZDSYS20200811144002008] ; Stable Support Plan Program of the Shenzhen Natural Science Fund[20200925153035002]

Biotechnology & Applied Microbiology ; Genetics & Heredity

Biotechnology & Applied Microbiology ; Genetics & Heredity

WOS:000820645100004

BMC

MOLECULAR BIOLOGY & GENETICS

2-s2.0-85133279796

Web of Science

Shenzhen Key Laboratory of Gene Regulation and Systems Biology,Department of Biology,School of Life Sciences,Southern University of Science and Technology,Shenzhen,518055,China

Babarinde，Isaac Adeyemi,Hutchins，Andrew Paul. The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome[J]. BMC GENOMICS,2022,23(1).

Babarinde，Isaac Adeyemi,&Hutchins，Andrew Paul.(2022).The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome.BMC GENOMICS,23(1).

Babarinde，Isaac Adeyemi,et al."The effects of sequencing depth on the assembly of coding and noncoding transcripts in the human genome".BMC GENOMICS 23.1(2022).