The majority of sequenced genomes in the Monocots are from species belonging to the Poaceae, which includes many commercially important crops. Here, we expand the number of sequenced genomes from the Monocots to include the genomes of four related Cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these four Cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes.  We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2% to 9.5% of our sequenced genomes, showed dispersed distribution of large repeat clusters across all Carex chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large Juncus satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of the assemblies, with the Carex genomes containing more DNA transposons than retrotransposons while the converse is true for the Juncus genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.

Genome assemblies for Carex cristatella, Carex scoparia, Juncus effusus, and Juncus inflexus were generated using Nanopore long read data.  Assemblies were polished using Illumina short read DNA-seq data.  Scaffolding was performed with HiC Illumina sequencing.  Annotation was performed using the MAKER pipeline with Nanopore cDNA sequence and protein alignments used as evidence.  Functional descriptions were assigned based on homology to genes with functional annotation or by protein domain analysis using Pfam domain homology.