A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Abstract

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

A chromosome-scale genome assembly of Castanopsis hystrix provides new insights into the evolution and adaptation of Fagaceae species

“…The assembled genome was approximately 882.6 Mb, of which more than 98% of the sequences were anchored to 12 pseudo-chromosomes ranging from 51.5 to 103.2 Mb in size. The contig N50 of the C. hystrix genome assembly was 40.95 Mb, which is higher than those of recently published Fagaceae species, such as C. tibetana (3.32 Mb) (Sun et al, 2022), C. mollissima (2.83 Mb) (Wang et al, 2020), Castanea crenata (6.36 Mb) (Wang et al, 2022a), Quercus gilva (28.32 Mb) (Zhou et al, 2022c), Q. lobata (1.90 Mb) (Sork et al, 2022), Quercus variabilis (26.04 Mb) (Han et al, 2022), and F. sylvatica (0.14 Mb) (Mishra et al, 2022). Genome assembly integrity, as assessed by BUSCO, reached 99.5% for C. hystrix, surpassing that of previously assembled Fagaceae genomes (90.5%-98.6%; Table 1).…”

A first draft genome of Holm oak (Quercus ilexL.), the most representative species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem “dehesa”

“…For example, once a pair of allelic sequences exceeds a certain threshold of nucleotide diversity, assembler may assemble these regions as separate contigs, rather than the expected single haplotype-fused contig, resulting in a significantly larger genome size. The Quercus genus is known to contain species with high heterozygosity (Sork et al, 2016;Ramos et al, 2018;Han et al, 2022, Ai et al 2022, and the same was true for Q. ilex (1.93%) (Table 2). To solve assembly issues, contigs were separated into primary contigs and associated secondaries contigs using the Purge_haplotigs pipeline version 1.1.1 (key parameter: default) (https://bitbucket.org/mroachawri/purge:haplotigs/src/master) (Roach et al, 2018).…”

“…For example, once a pair of allelic sequences exceeds a certain threshold of nucleotide diversity, assembler may assemble these regions as separate contigs, rather than the expected single haplotype-fused contig, resulting in a significantly larger genome size. The Quercus genus is known to contain species with high heterozygosity (Sork et al, 2016; Ramos et al, 2018; Han et al, 2022, Ai et al 2022), and the same was true for Q. ilex (1.93%) (Table 2).…”

“…Repeat sequences in the Q. ilex genome assembly accounted for 53.3% (448,68 Mb) of the total genome length (Table 4). LTR Gypsy and Copia were the most abundant repeat types (14.37% and 11.58%, respectively) (Han et al, 2022). The proportion of repeat elements in Q. ilex genome was similar to other Quercus spp.…”

“…However, our research has so far been constrained by the lack of a Q. ilex reference genome, so the picture provided by these studies is still incomplete. The sequencing of the Q. ilex genome will add to the list of many recently published Quercus reference genomes (Plomión et al, 2016, 2018; Sork et al, 2016, 2022; Ramos et al, 2018; Han et al, 2022; Zhou et al, 2022, Ai et al, 2022), and will allow us to interpret Q. ilex - omics data in terms of its own gene products rather than relying on orthologs from other Quercus species. This should open new research avenues related to the genetic make-up of this species, the identification of novel genes, allelic variants, SNPs, epigenetic marks, and will allow for studies on broader topics such as phylogenetics, hybridization and introgression patterns, and breeding programs informed by GWAS and genome prediction (Plomión et al, 2018; Stocks et al, 2019; Sork et al, 2022).…”