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Title: Investigating the cis- regulatory basis of C 3 and C 4 photosynthesis in grasses at single-cell resolution
While considerable knowledge exists about the enzymes pivotal for C4photosynthesis, much less is known about thecis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4enzymes for five different grass species. This study spans four C4species, covering three distinct photosynthetic subtypes:Zea maysandSorghum bicolor(NADP-dependent malic enzyme),Panicum miliaceum(NAD-dependent malic enzyme),Urochloa fusca(phosphoenolpyruvate carboxykinase), along with the C3outgroupOryza sativa. We studied thecis-regulatory landscape of enzymes essential across all C4species and those unique to C4subtypes, measuring cell-type-specific biases for C4enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C4evolution. Besides promoter proximal ACRs, we found that, on average, C4genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C4evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution ofcis-regulation at these C4loci. This study illuminates the dynamic and complex nature ofcis-regulatory elements evolution in C4photosynthesis, particularly highlighting the intricatecis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3crop performance under changing climatic conditions.  more » « less
Award ID(s):
1856627 2134912
PAR ID:
10580221
Author(s) / Creator(s):
; ; ; ; ; ; ;
Publisher / Repository:
National Academy of Sciences
Date Published:
Journal Name:
Proceedings of the National Academy of Sciences
Volume:
121
Issue:
40
ISSN:
0027-8424
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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