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Genome Sequence of Elaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae.

ABSTRACT: Elaeagnus mollis Diels (Elaeagnaceae) is a species of shrubs and/or dwarf trees that produces highly nutritious nuts with abundant oil and pharmaceutical properties. It is endemic to China but endangered. Therefore, to facilitate the protection of its genetic resources and the development of its commercially attractive traits we generated a high-quality genome of E. mollis. The contig version of the genome (630.96 Mb long) was assembled into 14 chromosomes using Hi-C data, with contig and scaffold N50 values of 18.40 and 38.86 Mb, respectively. Further analyses identified 397.49 Mb (63.0%) of repetitive sequences and 27,130 protein-coding genes, of which 26,725 (98.5%) were functionally annotated. Benchmarking Universal Single-Copy Ortholog assessment indicated that 98.0% of highly conserved plant genes are completely present in the genome. This is the first reference genome for any species of Elaeagnaceae and should greatly facilitate future efforts to conserve, utilize, and elucidate the evolution of this endangered endemic species.

SUBMITTER: Ren B

PROVIDER: S-EPMC8691057 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:The barred knifejaw (Oplegnathus fasciatus), a member of the Oplegnathidae family of the Centrarchiformes, is a commercially important rocky reef fish native to East Asia. Oplegnathus fasciatus has become an important fishery resource for offshore cage aquaculture and fish stocking of marine ranching in China, Japan, and Korea. Recently, sexual dimorphism in growth with neo-sex chromosome and widespread biotic diseases in O. fasciatus have been increasing concern in the industry. However, adequate genome resources for gaining insight into sex-determining mechanisms and establishing genetically resistant breeding systems for O. fasciatus are lacking. Here, we analyzed the entire genome of a female O. fasciatus fish using long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly. FINDINGS:We assembled the O. fasciatus genome with a total of 245.0 Gb of raw reads that were generated using both Pacific Bioscience (PacBio) Sequel and Illumina HiSeq 2000 platforms. The final draft genome assembly was approximately 778.7 Mb, which reached a high level of continuity with a contig N50 of 2.1 Mb. The genome size was consistent with the estimated genome size (777.5 Mb) based on k-mer analysis. We combined Hi-C data with a draft genome assembly to generate chromosome-length scaffolds. Twenty-four scaffolds corresponding to the 24 chromosomes were assembled to a final size of 768.8 Mb with a contig N50 of 2.1 Mb and a scaffold N50 of 33.5 Mb using 1,372 contigs. The identified repeat sequences accounted for 33.9% of the entire genome, and 24 003 protein-coding genes with an average of 10.1 exons per gene were annotated using de novo methods, with RNA sequencing data and homologies to other teleosts. According to phylogenetic analysis using protein-coding genes, O. fasciatus is closely related to Larimichthys crocea, with O. fasciatus diverging from their common ancestor approximately 70.5-88.5 million years ago. CONCLUSIONS:We generated a high-quality draft genome for O. fasciatus using long-read PacBio sequencing technology, which represents the first chromosome-level reference genome for Oplegnathidae species. Assembly of this genome assists research into fish sex-determining mechanisms and can serve as a resource for accelerating genome-assisted improvements in resistant breeding systems.

Dataset Information

Genome Sequence of Elaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae.

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