Genome Assembly of the Canadian two-row Malting Barley cultivar AAC Synergy

Abstract

Barley (Hordeum vulgare L.) is one of the most important global crops. The six-row barley cultivar Morex reference genome has been used by the barley research community worldwide. However, this reference genome can have limitations when used for genomic and genetic diversity analysis studies, gene discovery, and marker development when working in two-row germplasm that is more common to Canadian barley. Here we assembled, for the first time, the genome sequence of a Canadian two-row malting barley, cultivar AAC Synergy. We applied deep Illumina paired-end reads, long mate-pair reads, PacBio sequences, 10X chromium linked read libraries, and chromosome conformation capture sequencing (Hi-C) to generate a contiguous assembly. The genome assembled from super-scaffolds had a size of 4.85 Gb, N50 of 2.32 Mb and an estimated 93.9% of complete genes from a plant database (BUSCO, benchmarking universal single-copy orthologous genes). After removal of small scaffolds (< 300 Kb), the assembly was arranged into pseudomolecules of 4.14 Gb in size with seven chromosomes plus unanchored scaffolds. The completeness and annotation of the assembly were assessed by comparing it with the updated version of six-row Morex and recently released two-row Golden Promise genome assemblies.

A Novel Mutator-Like Transposable Elements With Unusual Structure and Recent Transpositions in Barley (Hordeum vulgare)

“…The complete Hvu-Abermu elements in barley was compared and found that they can share more than 95% sequence identity suggesting that Hvu-Abermu may be an active mutator. To detect its transpositional activity, the 600-bp flanking sequences (300-bp for each side) of the 284 Hvu_Abermu transposons with well-defined boundaries in the reference barley genome from the malting barley cultivar “Morex” ( Mascher et al, 2017 ) were used to search against the genomes of 22 cultivated and wild barley accessions, including 18 cultivated barley genotypes and one accession of wild barley (B1K-04-12) generated by the barley pan-genome project ( Jayakodi et al, 2020 ; Schreiber et al, 2020 ), one Canadian malting barley cultivar “AAC Synergy” ( Xu et al, 2021 ), one Tibetan hulless barley “Lasa Goumang” ( Zeng et al, 2020 ) and another wild barley accession AWCS276 (WB1; Liu et al, 2020 ). No hits or multiple highly identical hits were detected for the flanking sequences of 160 Hvu_Abermu transposons suggesting that these Hvu_Abermu elements were either inserted into highly repetitive regions or the flanking regions were not sequenced and/or assembled in the 22 genomes.…”

“…To validate the computational analyses performed, 16 barley genotypes were collected for PCR analysis including “Morex,” “Golden Promise” and other five cultivated barley varieties that genomes have been sequenced by the barley pan-genome and other projects ( Jayakodi et al, 2020 ; Schreiber et al, 2020 ; Xu et al, 2021 ). We were not able to obtain the seeds or DNAs for “Lasa Goumang” and two wild barley B1K-04-12 and AWCS276 (WB1) but we collected four Tibetan hulless varieties and five wild barley accessions from the National Small Grains Collection (NSGC) at the USDA ( Supplementary Table 1 ).…”

“…All hits were manually inspected to identify complete transposons and typical derivative elements and determine their exact boundaries based on the TIRs, flanking TSDs and sequence comparisons with the representative element. The 600-bp flanking sequence (300-bp for each side) for each transposon with well-defined boundaries was used to search against the genomes of 20 cultivated barley varieties and two wild barley accessions ( Liu et al, 2020 ; Jayakodi et al, 2020 ; Schreiber et al, 2020 ; Zeng et al, 2020 ; Xu et al, 2021 ) and to detect its presence/absence in other 22 barley genomes based on the sequence alignment.…”

“…Due to its diploid genome structure, close evolutionary relationships with the polyploidy wheat, and other unique features, barley has emerged as a model system for characterizing molecular functions of agronomically important genes in cereal crops ( Carciofi et al, 2012 ). Thus far, over 20 genomes of cultivated barley and its wild progenitor, Hordeum spontaneum , have been sequenced and high repetitive fractions (over 80%) were detected in these genomes ( Mascher et al, 2017 ; Jayakodi et al, 2020 ; Liu et al, 2020 ; Schreiber et al, 2020 ; Zeng et al, 2020 ; Xu et al, 2021 ). MULEs were identified in both cultivated and wild barley genomes ( Mascher et al, 2017 ; Liu et al, 2020 ; Xu et al, 2021 ).…”

“…Thus far, over 20 genomes of cultivated barley and its wild progenitor, Hordeum spontaneum , have been sequenced and high repetitive fractions (over 80%) were detected in these genomes ( Mascher et al, 2017 ; Jayakodi et al, 2020 ; Liu et al, 2020 ; Schreiber et al, 2020 ; Zeng et al, 2020 ; Xu et al, 2021 ). MULEs were identified in both cultivated and wild barley genomes ( Mascher et al, 2017 ; Liu et al, 2020 ; Xu et al, 2021 ). However, the transposition and evolution of mutator transposons in barley is still poorly understood.…”