FIGURE SUMMARY
Title

Long-read sequencing of the zebrafish genome reorganizes genomic architecture

Authors
Chernyavskaya, Y., Zhang, X., Liu, J., Blackburn, J.
Source
Full text @ BMC Genomics
Fig. 1

Curated current assembly issues with zebrafish reference genome GRCz11 as reported by the Genome Research Consortium
Fig. 2

Long-read library run metrics. A Distribution of read lengths from one representative library (L194) relative to number of bases sequenced within that library. Read length distribution for additional libraries can be found in Supplemental Fig. 1. B Histogram of read depth and coverage across individual chromosomes at 50Kbp intervals. Chromosomes are depicted on the y-axis with maximum depth cut off at 50X. Telomeres (red caps) extend the first 20Kbp into each chromosome. Red box on Chr 6 emphasizes a region of low coverage. C Cumulative average depth across all chromosomes of long-read assembly. D Magnification of low coverage region depicted in B (red box) to show continuous nanopore reads spanning across the zero-coverage section of GRCz11
Fig. 3

Comparison of total assembly size (Gbp) versus number of contigs generated when using Canu and Miniasm with and without polishing steps. Contigs are ordered largest to smallest, left to right
Fig. 4

Association plots of similarities and differences between ZF1 assembly and GRCz11 primary assembly. A Entire de novo generated ZF1 assembly compared to GRCz11. Center, diagonal line marks strong association and alignments with shorter indels placed off-center of the diagonal (B) Magnified area on Chr 2 showing an 8.5Mbp inversion (red box) in ZF1 deviating from GRCz11. C Chromosomal placement of unlocalized contigs of GRCz11 bearing at least 99% similarity to ZF1. Color scale indicates percent similarity between alignments
Fig. 5

Novel indel distribution in ZF1 assembly. A Frequency of insertions (yellow) and deletions (blue) identified in ZF1 assembly across all chromosomes. B-C Dot plots showing lack of correlation between indel frequency and chromosome length. R value cutoff for correlation was set to 0.6

Fig. 6

Identification of active retrotransposons in ZF1 assembly. A Results of gene prediction software reveals 23 novel insertions of LTR retrotransposons in the de novo assembly. B Expression by RT-qPCR of select retrotransposons compared to ctslb, which is silenced, and a negative control amplified with primers meant to pick up genomic DNA contamination

Acknowledgments
This image is the copyrighted work of the attributed author or publisher, and ZFIN has permission only to display this image to its users. Additional permissions should be obtained from the applicable author or publisher of the image. Full text @ BMC Genomics
Your Input Welcome
We welcome your input and comments. Please use this form to recommend updates to the information in ZFIN. We appreciate as much detail as possible and references as appropriate. We will review your comments promptly.
Please check the highlighted fields and try again.
Thank you for submitting comments. Your input has been emailed to ZFIN curators who may contact you if additional information is required.
Oops. Something went wrong. Please try again later.