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 May 21;23:120. doi: 10.1186/s13059-022-02685-z

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. 2 — sRNA analysis of lyc homozygous transcribed regions in hybrids: a S. lycopersicum genome is divided into 200-nt bins (sRNA loci). Percentage of sRNA loci in each group (F4s vs lyc parent) calculated from the total number of sRNA loci in lyc homozygous transcribed regions. Groups are sRNA loci upregulated (+ DESL, red), downregulated (− DESL, blue), “in-between” (lilac), and non-differentially expressed (non-DESL, yellow). The right-hand panel shows an expanded view of the + DESL (red) and − DESL (blue). Thresholds: DESL, FDR < 0.05; “in-between,” 0.05 < FDR < 0.9; non-DESL, FDR > 0.9. b Overlap matrix showing the number of lyc DESL shared among the F4 hybrids. The color scale shows the ratio of observed vs expected sRNA loci shared in a pairwise combination. c–e Box plot showing the percentage of lyc sRNA loci that map c genome-wide, d to each genomic feature, e to TE order that are + DESL or − DESL. The ratio of + DESL/ − DESL is shown at the bottom. Each plant is represented by different symbols. Box plot elements: box limits, upper and lower quartiles; center line, median; whiskers, from each quartile to the minimum or maximum. For comparison, colored lines are the genome percentage values for + DESL (red) and − DESL (blue) (from c). f, g Genome browser snapshots of two genomic regions with f sRNA loci upregulated in the F4 and downregulated in dcl2 (+ DESL/ − D2SL) and g sRNA loci downregulated in the F4 and dcl2 (− DESL/ − D2SL). Tracks show sRNA mapping (blue) and filtered for 21 nt (red), 22 nt (purple), and 24 nt (green) for lyc and P4042 (top tracks) and WT and dcl2 (bottom tracks). The numbers in brackets show the scale (normalized number of reads) for each track. The P4042 data are from this paper and dcl2 raw data from [18]