Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2022 Jun 29;23:143. doi: 10.1186/s13059-022-02700-3

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 3 — Long-read sequencing is augmented by hybrid assembly. A Artifacts identified in PacBio FLNC reads from two SMRT cells by alignment to the Arabidopsis reference genome. B Nucleotide frequency enrichment in a ± 50 nt window around poly(A) sites (PAS) identified by Direct RNA-seq [30]. C Nucleotide enrichment around 3′ ends of transcripts constructed from PacBio reads by Iso-seq3 (top), StringTie2 (middle), and Bookend (bottom) at sites overlapping a TAIR10 PAS (left), novel PAS at a known gene (middle), and novel antisense or intergenic loci (right); colors and scales as in (B). D Classification against the closest match in TAIR10 or Araport11 of transcripts constructed by four long-read processing strategies: Iso-seq3 clustering, cluster collapse by ToFU, and FLNC assembly by StringTie2 or Bookend. E Effect of long-read assembly on the number of transcripts by class (colored as in D) by StringTie2 (left) or Bookend (right) using hybrid assembly with one or more tissue-matched sequencing libraries. Bars show difference vs. ToFU-collapsed Iso-seq3 clusters. F UpSet plot depicting the number of overlapping transcript isoforms present in TAIR10, Araport11, and the Bookend Floral Bud assembly. G UpSet plot for the union of transcription start site peaks, allowing a ± 50 nt overlap window. H Diagram of floral organs analyzed by nanoPARE (left) and percent change in the number of TSS-overlapping reads for alternative annotations to TAIR10 in 15 tissue-specific nanoPARE libraries (right). I Bar chart of the number of enriched TSSs in each tissue type (≥4-fold mean RPM ingroup vs. outgroup, ANOVA p < 0.01, Benjamini-Hochberg correction). Shaded portions are TSSs exclusive to Bookend Floral Bud. J IGV browser image depicting Bookend Floral Bud assemblies for MPK18 (top) and nanoPARE abundance heatmaps for MPK18 sense and antisense TSSs (bottom). K Architecture and abundance of MPK19 isoforms as in (K). L Full-length and truncated isoforms of SKM1 assembled by Bookend (top). Heatmaps as in (J–K) for SKM1 TSSs (bottomt). TPM, transcripts per million; TSS, transcription start site