Jax Labs eBook - 18

IMPACTFUL SOLUTIONS CREATE INNOVATIVE SCIENCE

non-genic sequences, sequencing errors, and suspect variation.
These types of assembly issues inflate false positive rates in
reference-based variant calling.
In general, the preference is to use the latest version of a
given species reference genome, except where bioinformatics
processing tools or resources are not compatible, or to keep
consistency in a long-term project and for comparison purposes.
"EVE" HAS BEEN SEQUENCED
JAX researchers recently provided an update to the mouse
reference genome that more accurately represents the genome
of today's C57BL/6J mice, using long read, short read, and
optical mapping technologies to generate a de novo assembly
of the C57BL/6J Eve genome. They have identified structural
variations, closed gaps in the mouse reference assembly, and
revealed previously unannotated coding sequences (Sarsani
et al., 2019). To generate data for their de novo assembly of
the C57BL/6J Eve genome, they used a range of technologies,
including; Pacific BioSciences long read technology at 66X whole
genome coverage, Illumina short read at 32X whole genome
coverage, and Bionano Genomics optical maps.
Eve's genome is very different from the 2002 mouse reference
genome. The authors found over 500 high quality, recurring
variants (SNP/Indels) and over 40 structural variants (inversions,
deletions, and duplications) involving protein-coding genes
compared to the prior reference genome GRCm38.p6 (Figure 1).
18 | GENengnews.com

Figure 1. Ideogram of GRCm38 assembly annotated to highlight resolved gaps
(vs. current reference), structural variants, and fixed variation using B6J Eve data.
Adapted from Sarsani et al 2019.


http://www.GENengnews.com

Jax Labs eBook

Table of Contents for the Digital Edition of Jax Labs eBook

Contents
Jax Labs eBook - 1
Jax Labs eBook - 2
Jax Labs eBook - 3
Jax Labs eBook - Contents
Jax Labs eBook - 5
Jax Labs eBook - 6
Jax Labs eBook - 7
Jax Labs eBook - 8
Jax Labs eBook - 9
Jax Labs eBook - 10
Jax Labs eBook - 11
Jax Labs eBook - 12
Jax Labs eBook - 13
Jax Labs eBook - 14
Jax Labs eBook - 15
Jax Labs eBook - 16
Jax Labs eBook - 17
Jax Labs eBook - 18
Jax Labs eBook - 19
Jax Labs eBook - 20
Jax Labs eBook - 21
Jax Labs eBook - 22
Jax Labs eBook - 23
Jax Labs eBook - 24
Jax Labs eBook - 25
Jax Labs eBook - 26
Jax Labs eBook - 27
Jax Labs eBook - 28
Jax Labs eBook - 29
Jax Labs eBook - 30
Jax Labs eBook - 31
Jax Labs eBook - 32
Jax Labs eBook - 33
Jax Labs eBook - 34
Jax Labs eBook - 35
Jax Labs eBook - 36
https://www.nxtbookmedia.com