Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F22%3A00561822" target="_blank" >RIV/61389030:_____/22:00561822 - isvavai.cz</a>

Result on the web

<a href="https://doi.org/10.1111/pbi.13816" target="_blank" >https://doi.org/10.1111/pbi.13816</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/pbi.13816" target="_blank" >10.1111/pbi.13816</a>

Result language

angličtina

Original language name

Prospects of telomere-to-telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome

Original language description

The first gapless, telomere-to-telomere (T2T) sequence assemblies of plant chromosomes were reported recently. However, sequence assemblies of most plant genomes remain fragmented. Only recent breakthroughs in accurate long-read sequencing have made it possible to achieve highly contiguous sequence assemblies with a few tens of contigs per chromosome, that is a number small enough to allow for a systematic inquiry into the causes of the remaining sequence gaps and the approaches and resources needed to close them. Here, we analyse sequence gaps in the current reference genome sequence of barley cv. Morex (MorexV3). Optical map and sequence raw data, complemented by ChIP-seq data for centromeric histone variant CENH3, were used to estimate the abundance of centromeric, ribosomal DNA, and subtelomeric repeats in the barley genome. These estimates were compared with copy numbers in the MorexV3 pseudomolecule sequence. We found that almost all centromeric sequences and 45S ribosomal DNA repeat arrays were absent from the MorexV3 pseudomolecules and that the majority of sequence gaps can be attributed to assembly breakdown in long stretches of satellite repeats. However, missing sequences cannot fully account for the difference between assembly size and flow cytometric genome size estimates. We discuss the prospects of gap closure with ultra-long sequence reads.

Czech name

—

Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10603 - Genetics and heredity (medical genetics to be 3)

Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2022

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Plant Biotechnology Journal

ISSN

1467-7644

e-ISSN

1467-7652

Volume of the periodical

20

Issue of the periodical within the volume

7

Country of publishing house

US - UNITED STATES

Number of pages

14

Pages from-to

1373-1386

UT code for WoS article

000780977300001

EID of the result in the Scopus database

2-s2.0-85127550817