Data from: Chromosome scale genome assemblies and annotations for Poales species Carex cristatella, Carex scoparia, Juncus effusus and Juncus inflexus

<p>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: <em>Carex cristatella</em> and <em>Carex scoparia</em> from Cyperaceae and <em>Juncus effusus</em> and <em>Juncus inflexus</em> 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 <em>Carex</em> chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large <em>Juncus</em> 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 <em>Carex</em> genomes containing more DNA transposons than retrotransposons while the converse is true for the <em>Juncus</em> genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots.</p>