Whole-genome sequencing of 13 Arctic plants and draft genomes of Oxyria digyna and Cochlearia groenlandica.

To understand the genomic characteristics of Arctic plants, we generated 28-44 Gb of short-read sequencing data from 13 Arctic plants collected from the High Arctic Svalbard. We successfully estimated the genome sizes of eight species by using the k-mer-based method (180-894 Mb). Among these plants, the mountain sorrel (Oxyria digyna) and Greenland scurvy grass (Cochlearia groenlandica) had relatively small genome sizes and chromosome numbers. We obtained 45 × and 121 × high-fidelity long-read sequencing data. We assembled their reads into high-quality draft genomes (genome size: 561 and 250 Mb; contig N50 length: 36.9 and 14.8 Mb, respectively), and correspondingly annotated 43,105 and 29,675 genes using ~46 and ~85 million RNA sequencing reads. We identified 765,012 and 88,959 single-nucleotide variants, and 18,082 and 7,698 structural variants (variant size ≥ 50 bp). This study provided high-quality genome assemblies of O. digyna and C. groenlandica, which are valuable resources for the population and molecular genetic studies of these plants.

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus).

The unique color and type characteristics of watermelon fruits are regulated by many molecular mechanisms. However, it still needs to be combined with more abundant genetic data to fine-tune the positioning. We assembled genomes of two Korean inbred watermelon lines (cv. 242-1 and 159-1) with unique color and fruit-type characteristics and identified 23,921 and 24,451 protein-coding genes in the two genomes, respectively. To obtain more precise results for further study, we resequenced one individual of each parental line and an F2 population composed of 87 individuals. This identified 1,539 single-nucleotide polymorphisms (SNPs) and 80 InDel markers that provided a high-density genetic linkage map with a total length of 3,036.9 cM. Quantitative trait locus mapping identified 15 QTLs for watermelon fruit quality-related traits, including ß-carotene and lycopene content in fruit flesh, fruit shape index, skin thickness, flesh color, and rind color. By investigating the mapping intervals, we identified 33 candidate genes containing variants in the coding sequence. Among them, Cla97C01G008760 was annotated as a phytoene synthase with a single-nucleotide variant (A → G) in the first exon at 9,539,129 bp of chromosome 1 that resulted in the conversion of a lysine to glutamic acid, indicating that this gene might regulate flesh color changes at the protein level. These findings not only prove the importance of a phytoene synthase gene in pigmentation but also explain an important reason for the color change of watermelon flesh.

The complete chloroplast genome of Ziziphus jujuba cv. Bokjo (Rhamnaceae).

We have sequenced the Ziziphus jujuba cv. Bokjo chloroplast genome by de novo assembly using next-generation sequencing. The complete circular chloroplast genome consisted of 161,714 bp and contained four parts: a large single-copy (LSC) region of 89,323 bp, a small single-copy (SSC) region of 19,361 bp, and two inverted repeat regions (IRa and IRb) of 26,515 bp each. The genome annotation predicted a total of 110 genes, including 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis demonstrated the close taxonomic relationship between Z. jujuba cv. Bokjo and two other members of the Ziziphus genus, Z. spina-christi and Z. mauritiana. We found 135 polymorphic loci, 63 single nucleotide polymorphism (SNP) and 72 insertion-deletion (InDel), from the comparison of Z. jujuba cultivar Bokjo and Z. jujuba reference (NC_030299). The polymorphic loci could be used for the differentiation of Z. jujuba genetic resources and for breeding in the future.