The genome of Eleocharis vivipara elucidates the genetics of C3–C4 photosynthetic plasticity and karyotype evolution in the Cyperaceae

作者：Hongbing Liu, Hang Zhao, Yanwen Zhang, Xiuli Li, Yi Zuo, Zhen Wu, Kaining Jin, Wenfei Xian, Wenzheng Wang, Weidong Ning, Zijian Liu, Xiaoxiao Zhao, Lei Wang, Rowan F. Sage, Tiegang Lu, Matt Stata, Shifeng Cheng · 发表于：Journal of Integrative Plant Biology · 年份：2024 · DOI：10.1111/jipb.13765 · 被引用次数：13 · 研究领域：Botany, Ecology, and Taxonomy Studies、Genetic diversity and population structure、Isotope Analysis in Ecology

ABSTRACT Eleocharis vivipara , an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C 3 photosynthesis underwater and C 4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high‐quality genome for E. vivipara , representing the first chromosome‐level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one‐to‐one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2 n = 4 x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole‐genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross‐section studies showed its terrestrial culms developed C 4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co‐expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C 4 pathway, and significant enrichmen...