The Chinese chestnut genome: a reference for species restoration

Abstract

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally.

Construction of Pseudomolecules for the Chinese Chestnut (Castanea mollissima) Genome

“…Here, combining the advantages of both technologies coupled with high sequencing depth, we got the final genome assembly of 688.93 Mb, which was 104.87 Mb smaller than initial SMRT assembly. Compared with previous published genomes (Staton et al 2019;Xing et al 2019) (Table 3), the genomic continuity has been greatly improved, ex. contig N50 length were three times longer (2.83 Mb vs. 944 Kb); the contig number reduced more than three times (671 vs. 2,707).…”

“…As a perennial tree, the Chinese chestnut is highly heterozygous, meaning that genome assemblies for this species are typically highly fragmented, incomplete, and larger than they should be. Long read technologies can improve the resolution of highly repetitive regions (Waterston et al 2002;Eid et al 2009;Gnerre et al 2011;Ono et al 2013;Ghurye et al 2017;Jiao et al 2017;Staton et al 2019), and Hi-C techniques can capture interactions over much larger genomic distances and produce scaffolds spanning a complete chromosome arm (Lajoie et al 2015;Putnam et al 2016;Jia et al 2019;Liang et al 2019). Here, combining the advantages of both technologies coupled with high sequencing depth, we got the final genome assembly of 688.93 Mb, which was 104.87 Mb smaller than initial SMRT assembly.…”

“…The previous genome, especially the one supported by Staton et al (2015) has played a huge role in the early stage of Chinese chestnut researches and utilization, such as in disease resistance QTL (Quantitative Trait Loci) location (Kubisiak et al 2013). However, the existing genomic data of C. mollissima (Staton et al 2015(Staton et al , 2019Xing et al 2019) are still fragmented and with no complete chromosomal information, due to the high heterozygosity of the genome and technical limitations. In order to identify important structural and functional elements of genomes and use valuable genetic variation for breeding, accurate, complete and contiguous genome assemblies are essential (Love et al 2014).…”

Oak genomics is proving its worth

“…, 2018) and Q. lobata (Sork et al . , 2016) and other members of the Fagaceae, such as chestnut (Staton et al , 2019; Yu et al ., 2019) and beech (Mishra et al . , 2018), illustrates the dynamics of this research community gathered together as part of the highly active IUFRO working group dedicated to the conservation of the Fagaceae and Nothofagaceae families.…”

“…, 2018), illustrates the dynamics of this research community gathered together as part of the highly active IUFRO working group dedicated to the conservation of the Fagaceae and Nothofagaceae families. Most of the available genome sequences and genomic resources originate from temperate species (https://www.plabipd.de/plant_genomes_pa.ep), and the structure of the genome is highly conserved in Fagaceae (see Staton et al , 2019). We are therefore confident that findings will prove to be transferable across studies, species, and continents, especially for application to tropical species.…”