Draft genomes assembly and annotation of Carex parvula and Carex kokanica reveals stress-specific genes

Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea

This study is the first to report the characterization of Carex pumila genomic information. Assembly of the genome generated a draft of C. pumila based on PacBio Sequel II and Illumina paired-end sequencing, which was assembled from 2941 contigs with an estimated genome size of 0.346 Gb. The estimate of repeats in the genome was 31.0%, and heterozygosity ranged from 0.426 to 0.441%. The integrity evaluation of the assembly revealed 1481 complete benchmarked universal single-copy orthologs (BUSCO) (91.76%), indicating the high quality of the draft assembly. A total of 23,402 protein-coding genes were successfully predicted and annotated in the protein database. UpsetR plots showed that 7481 orthogroups were shared by all species. The phylogenetic tree showed that C. pumila is a close but distant relative of Ananas comosus. C. pumila had greater contraction (3154) than expansion (392). Among the extended gene families, aquaporins have been found to be enriched. Primers for microsatellite markers determined 30 polymorphic markers out of 100. The average number of alleles amplified by these 30 polymorphic markers was 4 to 12, with an average polymorphism information content (PIC) value of 0.660. In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of C. pumila.

The chromosome-scale genome of Kobresia myosuroides sheds light on karyotype evolution and recent diversification of a dominant herb group on the Qinghai-Tibet Plateau

Kobresia species are common in meadows on the Qinghai-Tibet Plateau. They are important food resources for local livestock, and serve a critical foundation for ecosystem integration. Genetic resources of Kobresia species are scarce. Here, we generated a chromosome-level genome assembly for K. myosuroides (Cyperaceae), using PacBio long-reads, Illumina short-reads, and Hi-C technology. The final assembly had a total size of 399.9 Mb with a contig N50 value of 11.9 Mb. The Hi-C result supported a 29 pseudomolecules model which was in consistent with cytological results. A total of 185.5 Mb (44.89% of the genome) transposable elements were detected, and 26,748 protein-coding genes were predicted. Comparative analysis revealed that Kobresia plants have experienced recent diversification events during the late Miocene to Pliocene. Karyotypes analysis indicated that the fission and fusion of chromosomes have been a major driver of speciation, which complied with the lack of whole-genome duplication (WGD) in K. myosuroides genome. Generally, this high-quality reference genome provides insights into the evolution of alpine sedges, and may be helpful to endemic forage improvement and alpine ecosystem preservation.

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

The majority of sequenced genomes in the monocots are from species belonging to Poaceae, which include many commercially important crops. Here, we expand the number of sequenced genomes from the monocots to include the genomes of 4 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 4 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 3.2–9.5% of our sequenced genomes, showed dispersed distribution of large satellite 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 each of the 4 genome 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.