Whole-genome assembly of Corylus avellana cv “Tonda Gentile delle Langhe” using linked-reads (10X Genomics)

Abstract

The European hazelnut (Corylus avellana L.; 2n=2x=22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv ‘Tonda Gentile delle Langhe’ (‘TGdL’) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of ′TGdL′ with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv ′Tombul′ genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤ 0.4 and 92% of BUSCO completeness), whose function was analysed with BlastP and InterProScan software. To characterise ‘TGdL’ specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The ‘TGdL’ genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.

Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L.

“…The second most represented superfamily (6.19%) was SSF52540 (P-loop containing nucleoside triphosphate hydrolase) which is involved in several UniPathways, such as chlorophyll or CoA biosynthesis, followed by SSF48264 (4.10%-Cytochrome P450). These superfamilies have been previously reported as highly abundant in various genomic backgrounds [ 25 , 26 , 27 , 28 , 29 ].…”

Mapping the Genetic Regions Responsible for Key Phenology-Related Traits in the European Hazelnut

“…Markers for map development and QTL analyses were initially identified using the “Jefferson” genome ( Torello Marinoni et al, 2018 ). Recently, the genome of the cultivar TGdL, containing a wider number of annotated genes, was publicly made available ( Pavese et al, 2021 ). Thus, candidate genes were retrieved by mapping the “Jefferson” scaffolds containing QTLs on the TGdL genome ( Pavese et al, 2021 ) using a BLAST search.…”

“…Recently, the genome of the cultivar TGdL, containing a wider number of annotated genes, was publicly made available ( Pavese et al, 2021 ). Thus, candidate genes were retrieved by mapping the “Jefferson” scaffolds containing QTLs on the TGdL genome ( Pavese et al, 2021 ) using a BLAST search. The structural/functional annotation of the genes in the QTL was carried out using the gff annotation file provided by Pavese et al (2021) (see text footnote 3).…”

“…Thus, candidate genes were retrieved by mapping the “Jefferson” scaffolds containing QTLs on the TGdL genome ( Pavese et al, 2021 ) using a BLAST search. The structural/functional annotation of the genes in the QTL was carried out using the gff annotation file provided by Pavese et al (2021) (see text footnote 3). Genes in the QTL intervals were discussed when showing a clear function/annotation related to flowering-like processes, as inferred from literature.…”

“…Some hazelnut genomic resources are also available in the public domain, including its transcriptome ( Rowley et al, 2012 ), a de novo assembled genome of the cultivar “Jefferson” and some resequencing data ( Rowley et al, 2018 ) 1 . Very recently, a fully assembled and annotated genome sequence of cultivar “Tombul” was published ( Lucas et al, 2021 ) 2 as well as that of the cultivar “Tonda Gentile delle Langhe” (TGdL) ( Pavese et al, 2021 ) 3 .…”