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.

Water isotope studies in alpine wetlands have revealed the dynamic characteristics of the hydrological cycle and evapotranspiration processes in the Zoige region through hydrogen and oxygen isotope ratios. However, the hydrological continuity between marshes, rivers, and lakes in wetlands is relatively understudied. The study found that the Zoige Alpine Wetland local meteoric water line (LMWL) is δD = 8.33δ¹⁸O + 14.52 (R² = 0.92) by using linear regression analysis to confirm the Craig temperature effect equation backwards. Comparison with the global and Chinese LMWLs revealed that the slope of the Zoige LMWL is significantly higher than those of the global and Chinese LMWLs, indicating that the oceanic warm and humid airflow and the southwest monsoon significantly influence this region. The δ¹⁸O ranges of rivers, lakes, and marshes in the Zoige wetland were −12.86‰ to −2.02‰, −12.9‰ to −2.22‰, and −15.47‰ to −7.07‰, respectively. In terms of δD, marshes had the lowest δD values, with a mean value of −89.58‰, while rivers and lakes had close δD values of about −72‰. Rivers had the most dramatic variation in d-excess values, ranging from −34.16‰ to 3.68‰, while marshes and lakes had more concentrated d-excess values, with particularly negative values in marshes. Regression analysis yielded a trend line of δD = 5.41δ¹⁸O − 29.57 for evaporation from the water bodies, further demonstrating the importance of evaporation effects in this region. By using the Rayleigh fractionation model and estimating the climatic conditions, we found that the lake water had the highest evaporation intensity (41%). Those of the river and marsh water were 40% and 36%, respectively. The results of this study provide new scientific insights into the hydrological connectivity, evaporation processes, and water source characteristics in the Zoige wetland. Future studies can shed more light on how climate change affects wetland hydrological systems and how they change over time and space. This will help to manage water resources in the region and protect the environment.

Bolboschoenus planiculmis (F.Schmidt) T.V.Egorova is a typical wetland plant in the species-rich Cyperaceae family. This species contributes prominently to carbon dynamics and trophic integration in wetland ecosystems. Previous studies have reported that the chromosomes of B. planiculmis are holocentric; i.e. they have kinetic activity along their entire length and carry multiple centromeres. This feature was suggested to lead to a rapid genome evolution through chromosomal fissions and fusions and participate to the diversification and ecological success of the Bolboschoenus genus. However, the specific mechanism remains uncertain, partly due to the scarcity of genetic information on Bolboschoenus. We present here the first chromosome-level genome assembly for B. planiculmis. Through the integration of high-quality long-read and short-read data, together with chromatin conformation using Hi-C technology, the ultimate genome assembly was 238.01 Mb with a contig N50 value of 3.61 Mb. Repetitive elements constituted 37.04% of the genome, and 18,760 protein-coding genes were predicted. The low proportion of long terminal repeat retrotransposons (∼9.62%) was similar to that reported for other Cyperaceae species. The K_s (synonymous substitutions per synonymous site) distribution suggested no recent large-scale genome duplication in this genome. The haploid assembly contained a large number of 54 pseudochromosomes with a small mean size of 4.10 Mb, covering most of the karyotype. The results of centromere detection support that not all the chromosomes in B. planiculmis have multiple centromeres, indicating more efforts are needed to fully reveal the specific style of holocentricity in cyperids and its evolutionary significance.

Tussocks are unique vegetation structures in wetlands. Many tussock species mainly reproduce by clonal growth, resulting in genetically identical offspring distributed in various spatial patterns. These fine-scale patterns could influence mating patterns and thus the long-term evolution of wetland plants. Here, we contribute the first genetic and clonal structures of two key species in alpine wetlands on the Qinghai–Tibet Plateau, Kobresia tibetica and Blysmus sinocompressus, using > 5000 SNPs identified by 2b-RAD sequencing. The tussock-building species, K. tibetica, has a phalanx (clumping) growth form, but different genets could co-occur within the tussocks, indicating that it is not proper to treat a tussock as one genetic individual. Phalanx growth does not necessarily lead to increased inbreeding in K. tibetica. B. sinocompressus has a guerilla (spreading) growth form, with the largest detected clone size being 18.32 m, but genets at the local scale tend to be inbred offspring. Our results highlight that the combination of clone expansion and seedling recruitment facilitates the contemporary advantage of B. sinocompressus, but its evolutionary potential is limited by the input genetic load of the original genets. The tussocks of K. tibetica are more diverse and a valuable genetic legacy of former well-developed wet meadows, and they are worthy of conservation attention.

Schoenoplectus tabernaemontani (C. C. Gmelin) Palla is a typical macrophyte in diverse wetland ecosystems. This species holds great potential in decontamination applications and carbon sequestration. Previous studies have shown that this species may have experienced recent polyploidization. This would make S. tabernaemontani a unique model to study the processes and consequences of whole-genome duplications in the context of the well-documented holocentric chromosomes and dysploidy events in Cyperaceae. However, the inference was not completely solid because it lacked homology information that is essential to ascertain polyploidy. We present here the first chromosome-level genome assembly for S. tabernaemontani. By combining Oxford Nanopore Technologies (ONT) long reads and Illumina short reads, plus chromatin conformation via the Hi-C method, we assembled a genome spanning 507.96 Mb, with 99.43% of Hi-C data accurately mapped to the assembly. The assembly contig N50 value was 3.62 Mb. The overall BUSCO score was 94.40%. About 68.94% of the genome was comprised of repetitive elements. A total of 36,994 protein-coding genes were predicted and annotated. Long terminal repeat retrotransposons accounted for ∼26.99% of the genome, surpassing the content observed in most sequenced Cyperid genomes. Our well-supported haploid assembly comprised 21 pseudochromosomes, each harboring putative holocentric centromeres. Our findings corroborated a karyotype of 2n = 2X = 42. We also confirmed a recent whole-genome duplication occurring after the divergence between Schoenoplecteae and Bolboschoeneae. Our genome assembly expands the scope of sequenced genomes within the Cyperaceae family, encompassing the fifth genus. It also provides research resources on Cyperid evolution and wetland conservation.