Open AccessProspects of telomere‐to‐telomere assembly in barley: Analysis of sequence gaps in the MorexV3 reference genome
Author(s) -
Navrátilová Pavla,
Toegelová Helena,
Tulpová Zuzana,
Kuo YiTzu,
Stein Nils,
Doležel Jaroslav,
Houben Andreas,
Šimková Hana,
Mascher Martin
Publication year - 2022
Publication title -
plant biotechnology journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.525
H-Index - 115
eISSN - 1467-7652
pISSN - 1467-7644
DOI - 10.1111/pbi.13816
Subject(s) - biology , contig , genetics , genome , telomere , sequence (biology) , sequence assembly , chromosome , reference genome , computational biology , whole genome sequencing , subtelomere , dna sequencing , dna , gene , gene expression , transcriptome
Summary 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.